From tiagoantao at gmail.com Tue Nov 1 09:11:04 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 1 Nov 2011 13:11:04 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> Message-ID: Hi all, 2011/10/31 Peter Cock : > Let's work on the issues Tiago has identified (e.g. non-zero > return codes, option to disable network tests, etc) before > extending this to more build slaves, and to look at the gems. Peter summarized what needs to be done quite well. We currently have a bare bones server here: http://testing.open-bio.org/bioruby/ The issues are then: non-zero return code of ruby setup.rb test (on error) is necessary to detect errors automatically. disable network tests is convenient in order to avoid hammering online databases (especially if you have lots of builders). Later we can setup a weekly test for networked code. This might be more serious with biopython where we have lots of builders (see below). You will also have to provide slaves (ie machines that will actually run the actual tests). The buildmaster will only coordinate those slaves (and provide information on the outcomes). You will have to decide how many (and types of slaves that you have). I will describe the biopython situation so that you can use as a template. We support several operating systems with several architectures, so: Linux 32 bit Linux 64 bit Win XP Win 7 Win 7 64 bit OS X 10.6 This would mean at least 6 slaves (your desktop/laptop can be a slave, as long as you start buildbot slave either manually or automatically) In our case we support several Python versions 2.5, 2.6, 2.7, 3.1, 3.2, so this could mean up to 30 builders (5 operating systems/architectures, times 5 versions). I suppose with bioruby it will be much simpler... Have a look here: http://testing.open-bio.org/biopython/tgrid Finally, when things are running smoothly, you might want to take ownership of the buildbot server yourselves... Any issue/question do not hesitate to contact, Best regards, Tiago From p.j.a.cock at googlemail.com Tue Nov 1 10:19:32 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 1 Nov 2011 14:19:32 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> Message-ID: 2011/11/1 Tiago Ant?o : > Hi all, > > 2011/10/31 Peter Cock : >> Let's work on the issues Tiago has identified (e.g. non-zero >> return codes, option to disable network tests, etc) before >> extending this to more build slaves, and to look at the gems. > > Peter summarized what needs to be done quite well. We currently have a > bare bones server here: > http://testing.open-bio.org/bioruby/ > > The issues are then: > non-zero return code of > ruby setup.rb test > (on error) is necessary to detect errors automatically. > > disable network tests is convenient in order to avoid hammering online > databases (especially if you have lots of builders). Later we can > setup a weekly test for networked code. This might be more serious > with biopython where we have lots of builders (see below). > > You will also have to provide slaves (ie machines that will actually > run the actual tests). The buildmaster will only coordinate those > slaves (and provide information on the outcomes). You will have to > decide how many (and types of slaves that you have). I will describe > the biopython situation so that you can use as a template. > > We support several operating systems with several architectures, so: > Linux 32 bit > Linux 64 bit > Win XP > Win 7 > Win 7 64 bit > OS X 10.6 > > This would mean at least 6 slaves (your desktop/laptop can be a slave, > as long as you start buildbot slave either manually or automatically) Ideally the buildslave will be on and online all the time, so that it can be run on a nightly basis. Note we may want to choose this time carefully given I assume BioRuby will have some slaves in Europe, some in Japan, and maybe some in the USA/Canada? > In our case we support several Python versions 2.5, 2.6, 2.7, 3.1, > 3.2, so this could mean up to 30 builders (5 operating > systems/architectures, times 5 versions). I suppose with bioruby > it will be much simpler... Have a look here: > http://testing.open-bio.org/biopython/tgrid Note that one machine can cover several builds - we have one server doing tests for Python 2.5, 2.6, 2.7, 3.1, 3.2 and Jython (that makes 6 versions of Python, 7 if we start testing PyPy as well). For BioRuby I am expecting you to want to cover at least Ruby 1.8 and 1.9 as two separate targets. Do the minor versions matter enough to be tested separately? > Finally, when things are running smoothly, you might want to take > ownership of the buildbot server yourselves... > > Any issue/question do not hesitate to contact, Likewise I am happy to answer questions, and I hope to be able to offer some buildslaves for testing BioRuby (machines that already test Biopython). Regards, Peter From ngoto at gen-info.osaka-u.ac.jp Tue Nov 1 10:48:03 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 1 Nov 2011 23:48:03 +0900 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> Message-ID: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Hi Tiago and Peter, Thank you very much for setting up the buildbot server. > > 3. ruby setup.rb test is FAILING in two tests, but the script ends > > with exit code 0, thus not reporting an error. Would it be possible to > > end setup.rb test with a exit code noticing the error? Mode details > > here: > > http://testing.open-bio.org:8102/builders/Linux%2064%20-%20Ruby%201.8/builds/0/steps/compile/logs/stdio It seems this is a bug of setup.rb. However, the devlopment of setup.rb is now being stopped, and the bug would not be fixed. So, "ruby setup.rb test" to run test is going to be obsoleted. Please use alternative test running procedure. % ruby test/runner.rb or % testrb test/ or % rake test -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From tiagoantao at gmail.com Tue Nov 1 12:58:06 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 1 Nov 2011 16:58:06 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO wrote: > ?% ruby test/runner.rb I run with this and now it works fine: ie reports an error. The error is just that I do not have the XML parser installed. Please see: http://testing.open-bio.org/bioruby/waterfall Tiago From tiagoantao at gmail.com Tue Nov 1 16:21:31 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 1 Nov 2011 20:21:31 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: 2011/11/1 Tiago Ant?o : > On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO > wrote: >> ?% ruby test/runner.rb > > I run with this and now it works fine: ie reports an error. The error > is just that I do not have the XML parser installed. > Please see: > http://testing.open-bio.org/bioruby/waterfall Is anyone interested in receiving emails with errors? Should I send them to the list? At this initial stage I would recommend sending to a just few developers... There is now a potential real error: 1) Failure: test_convert(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:120]: Exception raised: Class: Message: <"Invalid argument - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:845:in `post' ./lib/bio/command.rb:702:in `http_post_form' ./lib/bio/io/togows.rb:414:in `post_data' ./lib/bio/io/togows.rb:305:in `convert' ./test/functional/bio/io/test_togows.rb:121:in `test_convert' ./test/functional/bio/io/test_togows.rb:120:in `test_convert' From cjfields at illinois.edu Tue Nov 1 16:33:56 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 1 Nov 2011 20:33:56 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <410D958E-8A64-4B3B-8CBB-5AF6FA079CA4@illinois.edu> On Nov 1, 2011, at 3:21 PM, Tiago Ant?o wrote: > 2011/11/1 Tiago Ant?o : >> On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO >> wrote: >>> % ruby test/runner.rb >> >> I run with this and now it works fine: ie reports an error. The error >> is just that I do not have the XML parser installed. >> Please see: >> http://testing.open-bio.org/bioruby/waterfall > > Is anyone interested in receiving emails with errors? Should I send > them to the list? At this initial stage I would recommend sending to a > just few developers... BioPerl has a 'guts' list this would get sent to, not sure about BioRuby... chris From p.j.a.cock at googlemail.com Tue Nov 1 17:09:03 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 1 Nov 2011 21:09:03 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: 2011/11/1 Tiago Ant?o : > 2011/11/1 Tiago Ant?o : >> On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO >> wrote: >>> ?% ruby test/runner.rb >> >> I run with this and now it works fine: ie reports an error. The error >> is just that I do not have the XML parser installed. >> Please see: >> http://testing.open-bio.org/bioruby/waterfall Is the XML dependency optional? In Biopython we skip tests where a optional dependency is missing (i.e. report this but don't count it as a failure). > > Is anyone interested in receiving emails with errors? Should I send > them to the list? At this initial stage I would recommend sending to a > just few developers... > > There is now a potential real error: > ?1) Failure: > test_convert(Bio::FuncTestTogoWSREST) > [./test/functional/bio/io/test_togows.rb:120]: > Exception raised: > Class: > Message: <"Invalid argument - connect(2)"> > ---Backtrace--- > /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' > /usr/lib/ruby/1.8/net/http.rb:560:in `open' > /usr/lib/ruby/1.8/net/http.rb:560:in `connect' > /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' > /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' > /usr/lib/ruby/1.8/net/http.rb:560:in `connect' > /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' > /usr/lib/ruby/1.8/net/http.rb:542:in `start' > /usr/lib/ruby/1.8/net/http.rb:1035:in `request' > /usr/lib/ruby/1.8/net/http.rb:845:in `post' > ./lib/bio/command.rb:702:in `http_post_form' > ./lib/bio/io/togows.rb:414:in `post_data' > ./lib/bio/io/togows.rb:305:in `convert' > ./test/functional/bio/io/test_togows.rb:121:in `test_convert' > ./test/functional/bio/io/test_togows.rb:120:in `test_convert' That's a TogoWS test using the network to connect the Togo Web Service (I have some similar tests and code ready for Biopython now). I can't tell you if the problem is in BioRuby, the network, or TogoWS though. Peter From p.j.a.cock at googlemail.com Wed Nov 2 17:01:40 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 2 Nov 2011 21:01:40 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO wrote: > Hi Tiago and Peter, > > Thank you very much for setting up the buildbot server. > No problem - Tiago has done almost all the work so far, so I'll join you in thanking Tiago (and Chris Dag. from the OBF on the server side). >> > 3. ruby setup.rb test is FAILING in two tests, but the script ends >> > with exit code 0, thus not reporting an error. Would it be possible to >> > end setup.rb test with a exit code noticing the error? Mode details >> > here: >> > http://testing.open-bio.org:8102/builders/Linux%2064%20-%20Ruby%201.8/builds/0/steps/compile/logs/stdio > > It seems this is a bug of setup.rb. However, the devlopment of > setup.rb is now being stopped, and the bug would not be fixed. > So, "ruby setup.rb test" to run test is going to be obsoleted. > Please use alternative test running procedure. > > ?% ruby test/runner.rb > or > ?% testrb test/ > or > ?% rake test > Tiago seems to have done that :) I have another suggestion, which is that the test suite print a tiny environment summary at the start (e.g. Ruby version and operating system information). We do this for Biopython and it has been useful sometimes (e.g. comparing test failures from slightly different platforms), but also helpful from end user error reports (when they copy and paste the test suite output for us). Have you decided which versions of Ruby should be tested? For example, do you just need two targets, 1.8.x and 1.9.x? Peter From tiagoantao at gmail.com Wed Nov 2 19:01:15 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Wed, 2 Nov 2011 23:01:15 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Wed, Nov 2, 2011 at 9:01 PM, Peter Cock wrote: > Have you decided which versions of Ruby should be tested? > For example, do you just need two targets, 1.8.x and 1.9.x? We also will need definitive slaves. I am currently using my personal machine, which is very unreliable. Another question: to who (persons and/or mailing lists) should I send warning messages? Between 0 and the number of builders (currently 1) per day. Tiago From pjotr.public14 at thebird.nl Thu Nov 3 02:18:23 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 07:18:23 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20111103061823.GA15531@thebird.nl> On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: > Have you decided which versions of Ruby should be tested? > For example, do you just need two targets, 1.8.x and 1.9.x? My feeling is that 1.9 is relevant for default testing. In the wild there may be versions running 1.8 - and if someone feels like it, they can set up the buildbot too. Right? It is more important to test plugins. Raoul and I will set that up, as soon as we grasp the infrastructure. Pj. From p.j.a.cock at googlemail.com Thu Nov 3 05:23:17 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 09:23:17 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103061823.GA15531@thebird.nl> References: <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: >> Have you decided which versions of Ruby should be tested? >> For example, do you just need two targets, 1.8.x and 1.9.x? > > My feeling is that 1.9 is relevant for default testing. In the wild > there may be versions running 1.8 - and if someone feels like it, > they can set up the buildbot too. Right? Yes, but we need to know the planned matrix to setup the server. So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? So that could be 8 targets. > It is more important to test plugins. Raoul and I will set that up, > as soon as we grasp the infrastructure. Right, we hear you. Essentially that will require knowing the commands to call. Right now we have (roughly - Tiago can correct me) the following to do an in-situ test (no installation): (1) Get BioRuby from github (usually the latest, but you can ask for a specific revision via the buildbot web interface) (2) Run: ruby test/runner.rb (or similar) If it possible to have Ruby 1.8 and 1.9 installed at the same time, is there a convention for calling them? I'd guess ruby1.8 and ruby1.9 if the same style as Python is used. Then we'd have two versions of the above: (1) Get BioRuby from github (2) Run: ruby1.8 test/runner.rb (or similar) or, (1) Get BioRuby from github (2) Run: ruby1.9 test/runner.rb (or similar) The server configuration tells it which "recipe" to call on which slaves, so if one machine only has Ruby 1.9, it will not be asked to test on Ruby 1.8. We may also need slight variants for Windows vs Linux vs Mac. So what we'll need is an extended recipe which also gets the appropriate gem versions for that revision, and tests them. This could be a shell script, but if given as a list of commands you can see the progress, output and success/failure of each on the buildbot web interface. Peter From pjotr.public14 at thebird.nl Thu Nov 3 06:37:12 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 11:37:12 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> Message-ID: <20111103103712.GB16931@thebird.nl> On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote: > On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: > > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: > >> Have you decided which versions of Ruby should be tested? > >> For example, do you just need two targets, 1.8.x and 1.9.x? > > > > My feeling is that 1.9 is relevant for default testing. In the wild > > there may be versions running 1.8 - and if someone feels like it, > > they can set up the buildbot too. Right? > > Yes, but we need to know the planned matrix to setup the server. > So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially > on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? > So that could be 8 targets. OK, sounds good. It makes sense, also for other languages, to have two versions of compiler or interpreter for testing. > > It is more important to test plugins. Raoul and I will set that up, > > as soon as we grasp the infrastructure. > > Right, we hear you. Essentially that will require knowing the > commands to call. Right now we have (roughly - Tiago can > correct me) the following to do an in-situ test (no installation): > (1) Get BioRuby from github (usually the latest, but you can > ask for a specific revision via the buildbot web interface) > (2) Run: ruby test/runner.rb (or similar) > > If it possible to have Ruby 1.8 and 1.9 installed at the same > time, is there a convention for calling them? I'd guess ruby1.8 > and ruby1.9 if the same style as Python is used. Then we'd > have two versions of the above: > > (1) Get BioRuby from github > (2) Run: ruby1.8 test/runner.rb (or similar) > > or, > > (1) Get BioRuby from github > (2) Run: ruby1.9 test/runner.rb (or similar) > > The server configuration tells it which "recipe" to call on > which slaves, so if one machine only has Ruby 1.9, it will > not be asked to test on Ruby 1.8. > > We may also need slight variants for Windows vs Linux > vs Mac. > > So what we'll need is an extended recipe which also gets the > appropriate gem versions for that revision, and tests them. > This could be a shell script, but if given as a list of commands > you can see the progress, output and success/failure of each > on the buildbot web interface. We don't have a protocol just yet. The important containers are bio-core, bio-core-ext and bio-biolinux. Each of these installs all important plugins. For testing you'd want a test of each *released* plugin on rubygems.org. The plugins to test are listed inside above containers - for example in https://github.com/helios/bioruby-core/blob/master/Rakefile and can also be queried on rubygems (REST interface). I do that to generate http://biogems.info/. The install of a released plugin is simple: gem install plugin installs the gem in cd ~/.gems/gems/plugin-0.7 and the tests should run with rake test Some dependencies may be needed at test time. These can (in principle) be run with cd ~/.gems/gems/plugin-0.7 bundle rake test Note1: all plugins should support 'rake test' - though now they don't. Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev Pj. From p.j.a.cock at googlemail.com Thu Nov 3 07:36:11 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 11:36:11 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103103712.GB16931@thebird.nl> References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 10:37 AM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote: >> On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: >> > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: >> >> Have you decided which versions of Ruby should be tested? >> >> For example, do you just need two targets, 1.8.x and 1.9.x? >> > >> > My feeling is that 1.9 is relevant for default testing. In the wild >> > there may be versions running 1.8 - and if someone feels like it, >> > they can set up the buildbot too. Right? >> >> Yes, but we need to know the planned matrix to setup the server. >> So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially >> on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? >> So that could be 8 targets. > > OK, sounds good. It makes sense, also for other languages, to have > two versions of compiler or interpreter for testing. OK (pending possible changes for plugins later, see below). >> > It is more important to test plugins. Raoul and I will set that up, >> > as soon as we grasp the infrastructure. >> >> Right, we hear you. Essentially that will require knowing the >> commands to call. Right now we have (roughly - Tiago can >> correct me) the following to do an in-situ test (no installation): > >> (1) Get BioRuby from github (usually the latest, but you can >> ask for a specific revision via the buildbot web interface) >> (2) Run: ruby test/runner.rb (or similar) >> >> If it possible to have Ruby 1.8 and 1.9 installed at the same >> time, is there a convention for calling them? I'd guess ruby1.8 >> and ruby1.9 if the same style as Python is used. Then we'd >> have two versions of the above: >> >> (1) Get BioRuby from github >> (2) Run: ruby1.8 test/runner.rb (or similar) >> >> or, >> >> (1) Get BioRuby from github >> (2) Run: ruby1.9 test/runner.rb (or similar) >> >> The server configuration tells it which "recipe" to call on >> which slaves, so if one machine only has Ruby 1.9, it will >> not be asked to test on Ruby 1.8. >> >> We may also need slight variants for Windows vs Linux >> vs Mac. Does such a convention exist in Ruby for explicitly calling Ruby 1.8 or 1.9? We can just require the aliases ruby1.8 and ruby1.9 as part of setting up a buildslave. >> So what we'll need is an extended recipe which also gets the >> appropriate gem versions for that revision, and tests them. >> This could be a shell script, but if given as a list of commands >> you can see the progress, output and success/failure of each >> on the buildbot web interface. > > We don't have a protocol just yet. The important containers are bio-core, > bio-core-ext and bio-biolinux. Each of these installs all important plugins. > > For testing you'd want a test of each *released* plugin on > rubygems.org. The plugins to test are listed inside above containers > - for example in > > ?https://github.com/helios/bioruby-core/blob/master/Rakefile > > and can also be queried on rubygems (REST interface). I do that to > generate http://biogems.info/. > > The install of a released plugin is simple: > > ?gem install plugin > > installs the gem in > > ?cd ~/.gems/gems/plugin-0.7 > > and the tests should run with > > ?rake test > > Some dependencies may be needed at test time. These can (in principle) > be run with > > ?cd ~/.gems/gems/plugin-0.7 > ?bundle > ?rake test > > Note1: all plugins should support 'rake test' - though now they don't. Is it possible to test the plugins *without* installing them? i.e. an in-situ test? Or, can we control where they are installed (i.e. a temp folder) and test them from there? The point is the buildslave may be running several tests at once, and while ideally it will be configured as a separate user account, we don't want it using anything outside the BuildSlave's folder (other than /tmp provided the usual precautions about name clashes are taken), > > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev > Maybe we'd want three targets (per OS) then?: BioRuby core only on Ruby 1.8.x BioRuby core only on Ruby 1.9.x BioRuby with plugins on Ruby 1.9.x Peter From pjotr.public14 at thebird.nl Thu Nov 3 09:17:21 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 14:17:21 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: <20111103131721.GA18555@thebird.nl> On Thu, Nov 03, 2011 at 11:36:11AM +0000, Peter Cock wrote: > Does such a convention exist in Ruby for explicitly calling > Ruby 1.8 or 1.9? We can just require the aliases ruby1.8 > and ruby1.9 as part of setting up a buildslave. There is no convention. But I think it is fine to have this convention for our purposes. Maybe we can use just ruby by default too? If it is not in the path, just ignore. > > Note1: all plugins should support 'rake test' - though now they don't. > > Is it possible to test the plugins *without* installing them? i.e. an > in-situ test? Or, can we control where they are installed (i.e. a temp > folder) and test them from there? The problem is that you need to fetch dependencies. This is automated in gem install. You could check out a git tree, but that is not linked to the actual stuff people install. I favour the latter. > The point is the buildslave may be running several tests at once, > and while ideally it will be configured as a separate user account, > we don't want it using anything outside the BuildSlave's folder > (other than /tmp provided the usual precautions about name > clashes are taken), 'gem install' will normally install in user space. What is the problem there? Also, you can tell it to use any folder. > > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev > > > > Maybe we'd want three targets (per OS) then?: > > BioRuby core only on Ruby 1.8.x > BioRuby core only on Ruby 1.9.x > BioRuby with plugins on Ruby 1.9.x Personally I don't see BioRuby as separate. It is simply another plugin (or gem). It is a nice one, since it is pure Ruby and has few dependencies. I would say: bio (the BioRuby gem) on ruby1.8 bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 and later If it is too difficult - we can create a structure ourselves. No worries. Pj. From p.j.a.cock at googlemail.com Thu Nov 3 10:19:49 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 14:19:49 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103131721.GA18555@thebird.nl> References: <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 1:17 PM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 11:36:11AM +0000, Peter Cock wrote: >> Does such a convention exist in Ruby for explicitly calling >> Ruby 1.8 or 1.9? We can just require the aliases ruby1.8 >> and ruby1.9 as part of setting up a buildslave. > > There is no convention. But I think it is fine to have this > convention for our purposes. Maybe we can use just ruby > by default too? If it is not in the path, just ignore. If any one buildslave only has Ruby 1.8 or Ruby 1.9, then sure - we can just call "ruby". The configuration of the buildbot on the server would know which machine was running Ruby 1.8 or 1.9 and record the results accordingly. However, it seems efficient to have some slaves testing under both Ruby 1.8 and 1.9 (assuming of course that is possible - can they co-exist?). >> > Note1: all plugins should support 'rake test' - though now they don't. >> >> Is it possible to test the plugins *without* installing them? i.e. an >> in-situ test? Or, can we control where they are installed (i.e. a temp >> folder) and test them from there? > > The problem is that you need to fetch dependencies. This is automated > in gem install. > > You could check out a git tree, but that is not linked to the actual > stuff people install. I favour the latter. > >> The point is the buildslave may be running several tests at once, >> and while ideally it will be configured as a separate user account, >> we don't want it using anything outside the BuildSlave's folder >> (other than /tmp provided the usual precautions about name >> clashes are taken), > > 'gem install' will normally install in user space. What is the problem > there? Also, you can tell it to use any folder. Ah - that sounds better. So we can tell it to install to: $HOME/$BUILDSLAVE/$CURRENTBUILD/gems or whatever. The point is that the buildbot creates a clean empty folder for each test. You start from a a clean git checkout, and put the downloaded and installed gems under this directory. >> > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev >> > >> >> Maybe we'd want three targets (per OS) then?: >> >> BioRuby core only on Ruby 1.8.x >> BioRuby core only on Ruby 1.9.x >> BioRuby with plugins on Ruby 1.9.x > > Personally I don't see BioRuby as separate. It is simply another > plugin (or gem). It is a nice one, since it is pure Ruby and has few > dependencies. I would say: > > bio (the BioRuby gem) on ruby1.8 > bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 and later > > If it is too difficult - we can create a structure ourselves. No > worries. I was thinking we can get the first two targets up and running quite quickly: * bio (the BioRuby gem) on ruby1.8 * bio (the BioRuby gem) on ruby1.9 And then work on the full set: * bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 with additional targets for ruby2.0 or whatever is next. But ultimately you guys get to decide of course. Peter From pjotr.public14 at thebird.nl Thu Nov 3 10:29:28 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 15:29:28 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> Message-ID: <20111103142928.GB20116@thebird.nl> On Thu, Nov 03, 2011 at 02:19:49PM +0000, Peter Cock wrote: > under both Ruby 1.8 and 1.9 (assuming of course that > is possible - can they co-exist?). That is no problem. Debian derived distros have it by default. You can also use rvm in user space. > Ah - that sounds better. So we can tell it to install to: > > $HOME/$BUILDSLAVE/$CURRENTBUILD/gems > > or whatever. The point is that the buildbot creates a clean empty > folder for each test. You start from a a clean git checkout, and > put the downloaded and installed gems under this directory. http://jbowes.wordpress.com/2008/05/13/installing-ruby-gems-in-your-home-directory/ > I was thinking we can get the first two targets up and running > quite quickly: > > * bio (the BioRuby gem) on ruby1.8 > * bio (the BioRuby gem) on ruby1.9 > > And then work on the full set: > > * bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 > > with additional targets for ruby2.0 or whatever is next. > But ultimately you guys get to decide of course. Sounds good to me. With the two targets configures, I am sure we can add the rest ourselves. I would also like to show the test results on http://biogems.info/ Pj. From p.j.a.cock at googlemail.com Thu Nov 3 11:15:12 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 15:15:12 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103142928.GB20116@thebird.nl> References: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> <20111103142928.GB20116@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 2:29 PM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 02:19:49PM +0000, Peter Cock wrote: >> under both Ruby 1.8 and 1.9 (assuming of course that >> is possible - can they co-exist?). > > That is no problem. Debian derived distros have it by default. You > can also use rvm in user space. How does Debian name the two Ruby binaries? >> I was thinking we can get the first two targets up and running >> quite quickly: >> >> * bio (the BioRuby gem) on ruby1.8 >> * bio (the BioRuby gem) on ruby1.9 >> >> And then work on the full set: >> >> * bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 >> >> with additional targets for ruby2.0 or whatever is next. >> But ultimately you guys get to decide of course. > > Sounds good to me. With the two targets configures, I am sure we > can add the rest ourselves. That sounds like a plan :-) > I would also like to show the test results on http://biogems.info/ > You can get an RSS feed from the buildbot, or something crude like an embedded frame. Would you want to narrow this down to test results on a per-plugin basis? That might be tricky. Peter From p.j.a.cock at googlemail.com Thu Nov 3 11:39:36 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 15:39:36 +0000 Subject: [BioRuby] Scheduled time for nightly buildbot? Message-ID: 2011/11/1 Peter Cock : > > Ideally the buildslave will be on and online all the time, so that it > can be run on a nightly basis. Note we may want to choose this > time carefully given I assume BioRuby will have some slaves in > Europe, some in Japan, and maybe some in the USA/Canada? > I suggest initially we run the nightly BioRuby tests at about 20:00 GMT/UTC, which is evening in Europe (after work) and 5:00 in Japan (before work). Does that suit everyone considering offering a machine to run as a buildslave? If not, we may have to have multiple tests scheduled on a rota system for machines in Europe, America and Asia (etc). That would be more complicated to administer though. Peter From pjotr.public14 at thebird.nl Thu Nov 3 12:02:55 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 17:02:55 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> <20111103142928.GB20116@thebird.nl> Message-ID: <20111103160255.GC20889@thebird.nl> On Thu, Nov 03, 2011 at 03:15:12PM +0000, Peter Cock wrote: > How does Debian name the two Ruby binaries? ruby1.8 and ruby1.9.1 From tiagoantao at gmail.com Thu Nov 3 12:29:16 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 16:29:16 +0000 Subject: [BioRuby] Scheduled time for nightly buildbot? In-Reply-To: References: Message-ID: 2011/11/3 Peter Cock : > If not, we may have to have multiple tests scheduled on a rota > system for machines in Europe, America and Asia (etc). That > would be more complicated to administer though. This might not be such a bad idea as bioruby will be making network connections (to spread the load) -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From p.j.a.cock at googlemail.com Thu Nov 3 12:40:05 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 16:40:05 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard Message-ID: Dear all, I'd like to setup my Mac as a BioRuby buildslave for nightly unit tests. This currently runs Mac OS X 10.6 Snow Leopard which comes with Ruby 1.8.7 (possibly as part of XCode?) $ git clone https://github.com/bioruby/bioruby.git ... $ cd bioruby $ ruby test/runner.rb $ ruby test/runner.rb Loaded suite . Started .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FF............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Finished in 215.591513 seconds. 1) Failure: test_libxml(Bio::TestPhyloXMLWriter_Check_LibXML) [./test/unit/bio/db/test_phyloxml_writer.rb:31]: Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed. is not true. 2) Failure: test_libxml(Bio::TestPhyloXML_Check_LibXML) [./test/unit/bio/db/test_phyloxml.rb:29]: Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed. is not true. 3640 tests, 21276 assertions, 2 failures, 0 errors I installed libxml-ruby with this command, $ gem install libxml-ruby WARNING: Installing to ~/.gem since /Library/Ruby/Gems/1.8 and /usr/bin aren't both writable. WARNING: You don't have /Users/pjcock/.gem/ruby/1.8/bin in your PATH, gem executables will not run. Building native extensions. This could take a while... Successfully installed libxml-ruby-2.2.2 1 gem installed Installing ri documentation for libxml-ruby-2.2.2... Installing RDoc documentation for libxml-ruby-2.2.2... Referring to the link from Pjotr, http://jbowes.wordpress.com/2008/05/13/installing-ruby-gems-in-your-home-directory/ $ export GEM_HOME=$HOME/gems $ export GEM_PATH=$HOME/gems:/usr/lib/ruby/gems/1.8/ $ export PATH=$PATH:$HOME/gems/bin $ gem install libxml-ruby Building native extensions. This could take a while... Successfully installed libxml-ruby-2.2.2 1 gem installed Installing ri documentation for libxml-ruby-2.2.2... Installing RDoc documentation for libxml-ruby-2.2.2... I tried the following test script: $ more dummy.rb require 'rubygems' require 'libxml' include LibXML puts "Using libxml version #{XML::LIBXML_VERSION}" $ ruby dummy.rb Using libxml version 2.7.3 So Ruby does seem to find the library... yet the test suite still fails the same way (in the same terminal window with the above environment variables present). I'm a little lost now - any suggestions please? Thanks, Peter From p.j.a.cock at googlemail.com Thu Nov 3 13:24:47 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 17:24:47 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: <20111103165529.GA21817@thebird.nl> References: <20111103165529.GA21817@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 4:55 PM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 04:40:05PM +0000, Peter Cock wrote: >> $ export GEM_HOME=$HOME/gems >> $ export GEM_PATH=$HOME/gems:/usr/lib/ruby/gems/1.8/ >> $ export PATH=$PATH:$HOME/gems/bin > > Are these available during the BioRuby test run? ruby1.8 is notorious > for not finding gems - make sure you see libxml in the path. ... Double checking, there were some inconsistencies between the paths on disk, and the environment variables copied from the webpage, e.g. $HOME/gems vs $HOME/.gems I tried again with: $ export GEM_HOME=$HOME/.gem $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ $ ruby test/runner.rb ... Same error. Can I / should I just install libxml-ruby at system level? How? Thanks, Peter From tiagoantao at gmail.com Thu Nov 3 13:37:24 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 17:37:24 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103103712.GB16931@thebird.nl> References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: I am slighthly confused with the gem stuff. Lets see if I got this correct 1. we test ruby1.8 git 2. we test ruby1.9.1 git 3. we test ruby1.9.1 gems So 3 types of tests correct? for 1.9.1. we do BOTH git and gems (which are separate things)? For gems we use gem install. I noticed that the install dir can be changed on gem install, this might be useful. What gems to test? I noticed the reference to the list and a REST interface to get the list. Can you be more detailed? Thanks On Thu, Nov 3, 2011 at 10:37 AM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote: >> On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: >> > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: >> >> Have you decided which versions of Ruby should be tested? >> >> For example, do you just need two targets, 1.8.x and 1.9.x? >> > >> > My feeling is that 1.9 is relevant for default testing. In the wild >> > there may be versions running 1.8 - and if someone feels like it, >> > they can set up the buildbot too. Right? >> >> Yes, but we need to know the planned matrix to setup the server. >> So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially >> on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? >> So that could be 8 targets. > > OK, sounds good. It makes sense, also for other languages, to have > two versions of compiler or interpreter for testing. > >> > It is more important to test plugins. Raoul and I will set that up, >> > as soon as we grasp the infrastructure. >> >> Right, we hear you. Essentially that will require knowing the >> commands to call. Right now we have (roughly - Tiago can >> correct me) the following to do an in-situ test (no installation): > >> (1) Get BioRuby from github (usually the latest, but you can >> ask for a specific revision via the buildbot web interface) >> (2) Run: ruby test/runner.rb (or similar) >> >> If it possible to have Ruby 1.8 and 1.9 installed at the same >> time, is there a convention for calling them? I'd guess ruby1.8 >> and ruby1.9 if the same style as Python is used. Then we'd >> have two versions of the above: >> >> (1) Get BioRuby from github >> (2) Run: ruby1.8 test/runner.rb (or similar) >> >> or, >> >> (1) Get BioRuby from github >> (2) Run: ruby1.9 test/runner.rb (or similar) >> >> The server configuration tells it which "recipe" to call on >> which slaves, so if one machine only has Ruby 1.9, it will >> not be asked to test on Ruby 1.8. >> >> We may also need slight variants for Windows vs Linux >> vs Mac. >> >> So what we'll need is an extended recipe which also gets the >> appropriate gem versions for that revision, and tests them. >> This could be a shell script, but if given as a list of commands >> you can see the progress, output and success/failure of each >> on the buildbot web interface. > > We don't have a protocol just yet. The important containers are bio-core, > bio-core-ext and bio-biolinux. Each of these installs all important plugins. > > For testing you'd want a test of each *released* plugin on > rubygems.org. The plugins to test are listed inside above containers > - for example in > > ?https://github.com/helios/bioruby-core/blob/master/Rakefile > > and can also be queried on rubygems (REST interface). I do that to > generate http://biogems.info/. > > The install of a released plugin is simple: > > ?gem install plugin > > installs the gem in > > ?cd ~/.gems/gems/plugin-0.7 > > and the tests should run with > > ?rake test > > Some dependencies may be needed at test time. These can (in principle) > be run with > > ?cd ~/.gems/gems/plugin-0.7 > ?bundle > ?rake test > > Note1: all plugins should support 'rake test' - though now they don't. > > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev > > Pj. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From p.j.a.cock at googlemail.com Thu Nov 3 13:40:28 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 17:40:28 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: 2011/11/3 Tiago Ant?o : > I am slighthly confused with the gem stuff. Lets see if I got this correct > > 1. we test ruby1.8 git > 2. we test ruby1.9.1 git > 3. we test ruby1.9.1 gems > > So 3 types of tests correct? for 1.9.1. we do BOTH git and gems > (which are separate things)? Essentially. As I understand it, the gem/plugins are BioRuby extras, which use or add to BioRuby - see also http://www.biogems.info/ But let's get the basics working first (testing the core of BioRuby under Ruby 1.8 and 1.9 on a range of OS platforms). Peter From tiagoantao at gmail.com Thu Nov 3 13:43:56 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 17:43:56 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: 2011/11/3 Peter Cock : > But let's get the basics working first (testing the core of BioRuby > under Ruby 1.8 and 1.9 on a range of OS platforms). For testing purposes I will send a few error messages to the bioruby list to warm up. Should be at most a couple. Tiago From ngoto at gen-info.osaka-u.ac.jp Thu Nov 3 14:22:57 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 04 Nov 2011 03:22:57 +0900 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111103103712.GB16931@thebird.nl> Message-ID: <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> > 2. we test ruby1.9.1 git > 3. we test ruby1.9.1 gems Please use Ruby 1.9.3, latest stable release. Ruby 1.9.1 is declared as almost dead, and no security fix will be provided after Jan 31, 2012 JST. http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-core/40523 -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Thu Nov 3 14:30:21 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 19:30:21 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111103103712.GB16931@thebird.nl> <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111103183021.GE22715@thebird.nl> With Debian, ruby1.9.1 actually represents the latest and greatest :). The numbering scheme is kinda weird. On Fri, Nov 04, 2011 at 03:22:57AM +0900, Naohisa Goto wrote: > > 2. we test ruby1.9.1 git > > 3. we test ruby1.9.1 gems > > Please use Ruby 1.9.3, latest stable release. > Ruby 1.9.1 is declared as almost dead, and no security fix will be > provided after Jan 31, 2012 JST. > http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-core/40523 > > -- > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > From ngoto at gen-info.osaka-u.ac.jp Thu Nov 3 14:34:02 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 04 Nov 2011 03:34:02 +0900 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: References: <20111103165529.GA21817@thebird.nl> Message-ID: <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > $ export GEM_HOME=$HOME/.gem > $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems > $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ > $ ruby test/runner.rb In Ruby 1.8, Rubygems is an optional software and it is not loaded by default. Please try $ ruby -rubygems test/runner.rb or set RUBYOPT environment variable $ export RUBYOPT=-rubygems After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed by using Rubygems are ready by default without -rubygems. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From p.j.a.cock at googlemail.com Thu Nov 3 15:00:38 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 19:00:38 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111103165529.GA21817@thebird.nl> <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Thu, Nov 3, 2011 at 6:34 PM, Naohisa Goto wrote: > Hi Peter, > >> $ export GEM_HOME=$HOME/.gem >> $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems >> $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ >> $ ruby test/runner.rb > > In Ruby 1.8, Rubygems is an optional software and it is not loaded by > default. Please try > ?$ ruby -rubygems test/runner.rb > or set RUBYOPT environment variable > ?$ export RUBYOPT=-rubygems > > After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed > by using Rubygems are ready by default without -rubygems. That worked - thank you - we should use this for the buildslaves on Ruby 1.8 then, $ ruby -rubygems test/runner.rb Loaded suite . Started ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Finished in 259.549581 seconds. 3704 tests, 21456 assertions, 0 failures, 0 errors Peter From pjotr.public14 at thebird.nl Thu Nov 3 15:16:46 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 20:16:46 +0100 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: References: <20111103165529.GA21817@thebird.nl> <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111103191646.GA23293@thebird.nl> Way to go! On Thu, Nov 03, 2011 at 07:00:38PM +0000, Peter Cock wrote: > On Thu, Nov 3, 2011 at 6:34 PM, Naohisa Goto > wrote: > > Hi Peter, > > > >> $ export GEM_HOME=$HOME/.gem > >> $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems > >> $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ > >> $ ruby test/runner.rb > > > > In Ruby 1.8, Rubygems is an optional software and it is not loaded by > > default. Please try > > ?$ ruby -rubygems test/runner.rb > > or set RUBYOPT environment variable > > ?$ export RUBYOPT=-rubygems > > > > After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed > > by using Rubygems are ready by default without -rubygems. > > That worked - thank you - we should use this for the buildslaves on > Ruby 1.8 then, > > $ ruby -rubygems test/runner.rb > Loaded suite . > Started > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > Finished in 259.549581 seconds. > > 3704 tests, 21456 assertions, 0 failures, 0 errors > > > Peter > From bonnal at ingm.org Thu Nov 3 15:15:38 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 03 Nov 2011 20:15:38 +0100 Subject: [BioRuby] =?iso-8859-1?q?Missing_libxml-ruby_and_unit_tests_on_Ma?= =?iso-8859-1?q?c_OS_X_Snow=09Leopard?= In-Reply-To: Message-ID: <20111103191538.8492f8d9@mail.ingm.it> Hi guys, this is a great work! I would strongly suggest to use rvm to install multiple instances of ruby. As I see in a old email, I would say that plugins must be 1.9 compliant I don't care about 1.8. About JRuby please take care that it's default interpreter is v1.8 you have to set up by hand to use v1.9 http://beginrescueend.com/interpreters/jruby/ I must check this project and see if it works https://rubygems.org/gems/rubygems-test I'll try to be more active in coming days. I think I could provide a virtual machine as mirror, in the near future. _____ From: Peter Cock [mailto:p.j.a.cock at googlemail.com] To: Naohisa Goto [mailto:ngoto at gen-info.osaka-u.ac.jp] Cc: BioRuby ML [mailto:bioruby at lists.open-bio.org] Sent: Thu, 03 Nov 2011 20:00:38 +0100 Subject: Re: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard On Thu, Nov 3, 2011 at 6:34 PM, Naohisa Goto wrote: > Hi Peter, > >> $ export GEM_HOME=$HOME/.gem >> $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems >> $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ >> $ ruby test/runner.rb > > In Ruby 1.8, Rubygems is an optional software and it is not loaded by > default. Please try > $ ruby -rubygems test/runner.rb > or set RUBYOPT environment variable > $ export RUBYOPT=-rubygems > > After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed > by using Rubygems are ready by default without -rubygems. That worked - thank you - we should use this for the buildslaves on Ruby 1.8 then, $ ruby -rubygems test/runner.rb Loaded suite . Started ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Finished in 259.549581 seconds. 3704 tests, 21456 assertions, 0 failures, 0 errors Peter _______________________________________________ BioRuby Project - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Thu Nov 3 15:26:32 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 19:26:32 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: <20111103191538.8492f8d9@mail.ingm.it> References: <20111103191538.8492f8d9@mail.ingm.it> Message-ID: On Thu, Nov 3, 2011 at 7:15 PM, Raoul Bonnal wrote: > Hi guys, this is a great work! > I would strongly suggest to use rvm to install multiple instances of ruby. Initially I will use whatever Ruby comes with my systems or their default package. That seems simplest - and a realistic test case. For a multi-ruby test slave I'm sure you guys know best. > As I see in a old email, I would say that plugins must be 1.9 compliant I > don't care about 1.8. Pjotr agreed, but initially we're not going to test any of the biogem plugins. > About JRuby please take care that it's default interpreter is v1.8 you have > to set up by hand to use v1.9 http://beginrescueend.com/interpreters/jruby/ > > I must check this project and see if it works > https://rubygems.org/gems/rubygems-test > > I'll try to be more active in coming days. > I think I could provide a virtual machine as mirror, in the near future. So should we add JRuby v1.8 and JRuby v1.9 to the test matrix? Peter From tiagoantao at gmail.com Thu Nov 3 18:09:03 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 22:09:03 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103183021.GE22715@thebird.nl> References: <20111103103712.GB16931@thebird.nl> <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> <20111103183021.GE22715@thebird.nl> Message-ID: Hi, I had a silly bug with mail sending. But a barebones server is now working. it includes ruby 1.8 and 1.9.1 (Debian/Ubuntu). http://testing.open-bio.org/bioruby Honestly I had to read all the ongoing emails superficially, because I was chasing this silly bug. In my view now we have to: 1. setup slaves 2. give some of you the password for the admin web interface 3. get you an area on the testing machine so that you get familiarized with buildbot. We, of course, will support you during the first times 4. Think about gems. Tiago On Thu, Nov 3, 2011 at 6:30 PM, Pjotr Prins wrote: > With Debian, ruby1.9.1 actually represents the latest and greatest > :). The numbering scheme is kinda weird. > > On Fri, Nov 04, 2011 at 03:22:57AM +0900, Naohisa Goto wrote: >> > 2. we test ruby1.9.1 git >> > 3. we test ruby1.9.1 gems >> >> Please use Ruby 1.9.3, latest stable release. >> Ruby 1.9.1 is declared as almost dead, and no security fix will be >> provided after Jan 31, 2012 JST. >> http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-core/40523 >> >> -- >> Naohisa Goto >> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org >> > -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From ngoto at gen-info.osaka-u.ac.jp Fri Nov 4 02:51:17 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Fri, 4 Nov 2011 15:51:17 +0900 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20111104065117.D94F01CBC479@idnmail.gen-info.osaka-u.ac.jp> Hi, On Wed, 2 Nov 2011 21:01:40 +0000 Peter Cock wrote: > I have another suggestion, which is that the test suite print > a tiny environment summary at the start (e.g. Ruby version > and operating system information). Since Ruby 1.9.3 (or after svn trunk r33205), the default test runner in Ruby prints this message at the end of all tests, e.g. 3640 tests, 21267 assertions, 2 failures, 4 errors, 0 skips ruby -v: ruby 2.0.0dev (2011-11-01) [x86_64-linux] I think this is enough. For older Ruby versions, please put a line "ruby -v" in the shell script. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Fri Nov 4 03:14:30 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 4 Nov 2011 08:14:30 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111103103712.GB16931@thebird.nl> <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> <20111103183021.GE22715@thebird.nl> Message-ID: <20111104071430.GA25058@thebird.nl> On Thu, Nov 03, 2011 at 10:09:03PM +0000, Tiago Ant?o wrote: > I had a silly bug with mail sending. But a barebones server is now > working. it includes ruby 1.8 and 1.9.1 (Debian/Ubuntu). > http://testing.open-bio.org/bioruby > > Honestly I had to read all the ongoing emails superficially, because I > was chasing this silly bug. > > In my view now we have to: > 1. setup slaves > 2. give some of you the password for the admin web interface > 3. get you an area on the testing machine so that you get familiarized > with buildbot. We, of course, will support you during the first times > 4. Think about gems. Excellent stuff. I can add slaves for Debian stable and testing on 64 and 32 bit (interesting to see BioRuby-64 fails on SOAP/WSDL). I propose Naohisa, Raoul and myself to get access to buildbot, so we can maintain and develop the build/integration tests for BioRuby and plugins. This is a big step forward for the Bio* projects, in my opinion. Pj. From p.j.a.cock at googlemail.com Fri Nov 4 11:38:45 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 15:38:45 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 Message-ID: Dear all, I plan to setup one of our servers as a BioRuby buildslave, but it is running CentOS 5.4 which comes with Ruby 1.8.5, and that is too old to use for BioRuby. So, I am installing Ruby 1.9 under the home directory instead, and using that. However, there is a problem with libyaml that I need help with. Note that I have a lot of development tools and libraries already installed (e.g. git), so I'm not mentioning them here - during the configure step nothing seemed to be missing, lucky for me. I did apparently need to install libyaml, $ sudo yum install libyaml $ sudo yum install libyaml-devel This gave 0.1.3-1.el5.rf -------------------------------------------- Step one, download latest stable Ruby 1.9.x and uncompress it, $ cd ~/Downloads $ wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p0.tar.gz $ tar -zxvf ruby-1.9.3-p0.tar.gz $ cd ruby-1.9.3-p0 -------------------------------------------- Step two, compile Ruby, test it, install it Note I tried passing -prefix and --prefix to configure, but it didn't accept it - use prefix with no minus at all, $ ./configure prefix=$HOME $ make $ make test $ make install -------------------------------------------- Step Three, check it Note I have already configured $HOME/bin to be on my $PATH $ which ruby ~/bin/ruby $ ruby -v ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux] $ which gem ~/bin/gem $ gem --version /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': It seems your ruby installation is missing psych (for YAML output). To eliminate this warning, please install libyaml and reinstall your ruby. 1.8.11 Why isn't Ruby finding libyaml? It is installed at system level via yum. Thanks, Peter -------------------------------------------- I went ahead and tried BioRuby, which told me to install libxml-ruby which I did, so I think it is just the libyaml problem to solve.... $ gem install libxml-ruby /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': It seems your ruby installation is missing psych (for YAML output). To eliminate this warning, please install libyaml and reinstall your ruby. Building native extensions. This could take a while... Successfully installed libxml-ruby-2.2.2 1 gem installed Installing ri documentation for libxml-ruby-2.2.2... Installing RDoc documentation for libxml-ruby-2.2.2... From francesco.strozzi at gmail.com Fri Nov 4 11:44:32 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 4 Nov 2011 16:44:32 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: Hi Peter, first of all huge thanks for the work you guys are doing with the automated test! I strongly suggested you to use RVM http://beginrescueend.com/ to compile and install many different versions of Ruby in the home directory or even system wide. Also RVM takes care of Ruby compiling from source and if you have the required libraries it should link them automatically during the installation process. Cheers, Francesco On Fri, Nov 4, 2011 at 16:38, Peter Cock wrote: > Dear all, > > I plan to setup one of our servers as a BioRuby buildslave, but it is > running CentOS 5.4 which comes with Ruby 1.8.5, and that is too old > to use for BioRuby. So, I am installing Ruby 1.9 under the home > directory instead, and using that. However, there is a problem with > libyaml that I need help with. > > Note that I have a lot of development tools and libraries already > installed (e.g. git), so I'm not mentioning them here - during the > configure step nothing seemed to be missing, lucky for me. > > I did apparently need to install libyaml, > > $ sudo yum install libyaml > $ sudo yum install libyaml-devel > > This gave 0.1.3-1.el5.rf > > -------------------------------------------- > > Step one, download latest stable Ruby 1.9.x and uncompress it, > > $ cd ~/Downloads > $ wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p0.tar.gz > $ tar -zxvf ruby-1.9.3-p0.tar.gz > $ cd ruby-1.9.3-p0 > > -------------------------------------------- > > Step two, compile Ruby, test it, install it > > Note I tried passing -prefix and --prefix to configure, but it didn't > accept it - use prefix with no minus at all, > > $ ./configure prefix=$HOME > $ make > $ make test > $ make install > > -------------------------------------------- > > Step Three, check it > > Note I have already configured $HOME/bin to be on my $PATH > > $ which ruby > ~/bin/ruby > $ ruby -v > ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux] > > $ which gem > ~/bin/gem > $ gem --version > /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': > It seems your ruby installation is missing psych (for YAML output). > To eliminate this warning, please install libyaml and reinstall your ruby. > 1.8.11 > > Why isn't Ruby finding libyaml? It is installed at system level via yum. > > Thanks, > > Peter > > -------------------------------------------- > > I went ahead and tried BioRuby, which told me to install libxml-ruby > which I did, so I think it is just the libyaml problem to solve.... > > $ gem install libxml-ruby > /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': > It seems your ruby installation is missing psych (for YAML output). > To eliminate this warning, please install libyaml and reinstall your ruby. > Building native extensions. This could take a while... > Successfully installed libxml-ruby-2.2.2 > 1 gem installed > Installing ri documentation for libxml-ruby-2.2.2... > Installing RDoc documentation for libxml-ruby-2.2.2... > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From p.j.a.cock at googlemail.com Fri Nov 4 11:54:23 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 15:54:23 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 3:44 PM, Francesco Strozzi wrote: > Hi Peter, > first of all huge thanks for the work you guys are doing with the automated > test! > I strongly suggested you to use RVM?http://beginrescueend.com/ to compile > and install many different versions of Ruby in the home directory or even > system wide. Also RVM takes care of Ruby compiling from source and if you > have the required libraries it should link them automatically during the > installation process. > Cheers, > Francesco Hi Francesco, There is surely value in having a mixture of setups for the buildslaves? So certainly some should use RVM, but it seems wise to have others using a more old fashioned installation? Just my perspective from the outside. For this particular machine, I wasn't planning multiple installations of ruby, just Ruby 1.9.x only. I'll leave setting up and looking after a multi-target BioRuby buildslave to you guys ;) The Ruby website seemed to suggest going with the source code installation for me: "Installing from the source code is a great solution for when you are comfortable enough with your platform and perhaps need specific settings for your environment. It?s also a good solution in the event that there are no other premade packages for your platform." Well there are Ruby 1.8 packages for CentOS 5.4 but that's too old. Any ideas on the libyaml problem? Peter From francesco.strozzi at gmail.com Fri Nov 4 12:07:00 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 4 Nov 2011 17:07:00 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: Try to install libyaml from source, here it seems they have faced the same problem: http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-libyaml-on-centos/ Cheers, Francesco On Fri, Nov 4, 2011 at 16:54, Peter Cock wrote: > On Fri, Nov 4, 2011 at 3:44 PM, Francesco Strozzi > wrote: > > Hi Peter, > > first of all huge thanks for the work you guys are doing with the > automated > > test! > > I strongly suggested you to use RVM http://beginrescueend.com/ to > compile > > and install many different versions of Ruby in the home directory or even > > system wide. Also RVM takes care of Ruby compiling from source and if you > > have the required libraries it should link them automatically during the > > installation process. > > Cheers, > > Francesco > > Hi Francesco, > > There is surely value in having a mixture of setups for the buildslaves? > So certainly some should use RVM, but it seems wise to have others > using a more old fashioned installation? Just my perspective from the > outside. > > For this particular machine, I wasn't planning multiple installations of > ruby, just Ruby 1.9.x only. I'll leave setting up and looking after a > multi-target BioRuby buildslave to you guys ;) > > The Ruby website seemed to suggest going with the source code > installation for me: > > "Installing from the source code is a great solution for when you are > comfortable enough with your platform and perhaps need specific > settings for your environment. It?s also a good solution in the event > that there are no other premade packages for your platform." > > Well there are Ruby 1.8 packages for CentOS 5.4 but that's too old. > > Any ideas on the libyaml problem? > > Peter > -- Francesco From p.j.a.cock at googlemail.com Fri Nov 4 12:34:41 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 16:34:41 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 4:07 PM, Francesco Strozzi wrote: > Try to install libyaml from source, here it seems they have faced the same > problem: > http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-libyaml-on-centos/ > Cheers, > Francesco That didn't seem to work, $ sudo yum erase libyaml-devel $ sudo yum erase libyaml then: $ cd ~/Downloads $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz $ tar -xzvf yaml-0.1.4.tar.gz $ cd yaml-0.1.4 $ ./configure --prefix=$HOME $ make $ make check $ make install Then back to reinstall Ruby as before. Maybe there is a problem in the configure script, or I need to tell it to look for libyaml under $HOME. Peter From francesco.strozzi at gmail.com Fri Nov 4 12:41:00 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 4 Nov 2011 17:41:00 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: Yes maybe try to use --with-opt-dir=path/to/libyaml in configure. Hope it helps in resolving this issue.... Francesco On Fri, Nov 4, 2011 at 17:34, Peter Cock wrote: > On Fri, Nov 4, 2011 at 4:07 PM, Francesco Strozzi > wrote: > > Try to install libyaml from source, here it seems they have faced the > same > > problem: > > > http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-libyaml-on-centos/ > > Cheers, > > Francesco > > That didn't seem to work, > > $ sudo yum erase libyaml-devel > $ sudo yum erase libyaml > > then: > > $ cd ~/Downloads > $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz > $ tar -xzvf yaml-0.1.4.tar.gz > $ cd yaml-0.1.4 > $ ./configure --prefix=$HOME > $ make > $ make check > $ make install > > Then back to reinstall Ruby as before. > > Maybe there is a problem in the configure script, or I need > to tell it to look for libyaml under $HOME. > > Peter > -- Francesco From bonnal at ingm.org Fri Nov 4 12:44:01 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 04 Nov 2011 17:44:01 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: Message-ID: Hi Peter, CentOS 5.4 seems to be very old the lates is 5.7 and I would say it has very old packages. 1 Day ago I installed sqlite3 and the default version in 5.7 was too old as well, it's odd but I don't think CentOS is the right distro for these stuffs. This is what I did to update sqlite " I had an old sqlite package installed on my CentOS box and sqlite3-ruby wouldnt install without atleast sqlite 3.6.16 So for installing from source wget http://www.sqlite.org/sqlite-autoconf-3070500.tar.gz tar xvzf sqlite-autoconf-3070500.tar.gz cd sqlite-autoconf-3070500 ./configure make sudo make install *Modifica del percorso di ricerca delle librerie: - create file /etc/ld.conf.d/aaa.conf - add row: /usr/local/lib - ldconf (per ricaricare i percorsi di ricerca delle librerie) Now you also need to install the sqlite-devel packages, that is a yum install so sudo yum install sqlite-devel To install the gem sudo gem install sqlite3-ruby Probably the best thing to do is to help Peter in setting up a VM with a pre installed Ruby environment, what about using CloudBioLinux as base distro for testing ? On 04/11/11 17.34, "Peter Cock" wrote: > On Fri, Nov 4, 2011 at 4:07 PM, Francesco Strozzi > wrote: >> Try to install libyaml from source, here it seems they have faced the same >> problem: >> http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-liby >> aml-on-centos/ >> Cheers, >> Francesco > > That didn't seem to work, > > $ sudo yum erase libyaml-devel > $ sudo yum erase libyaml > > then: > > $ cd ~/Downloads > $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz > $ tar -xzvf yaml-0.1.4.tar.gz > $ cd yaml-0.1.4 > $ ./configure --prefix=$HOME > $ make > $ make check > $ make install > > Then back to reinstall Ruby as before. > > Maybe there is a problem in the configure script, or I need > to tell it to look for libyaml under $HOME. > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Fri Nov 4 12:48:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 16:48:18 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 4:44 PM, Raoul Bonnal wrote: > Hi Peter, CentOS 5.4 seems to be very old the lates is 5.7 and I would say > it has very old packages. I agree that CenOS 5.4 is very old, but we're stuck with it I'm afraid :( > Probably the best thing to do is to help Peter in setting up a VM with a pre > installed Ruby environment, what about using CloudBioLinux as base distro > for testing ? As I've said before, having (at least one) CloudBioLinux installation as a buildslave is a wonderful idea. But one of my aims in having a pool of buildslaves is to cover as many likely end user configurations as possible. So I think is it sensible to include BioRuby and Ruby installed from source on an otherwise solid/old Linux distribution. Peter From p.j.a.cock at googlemail.com Fri Nov 4 13:14:01 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 17:14:01 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 4:41 PM, Francesco Strozzi wrote: > Yes maybe try to use --with-opt-dir=path/to/libyaml in configure. Hope it > helps in resolving this issue.... > Francesco $ ./configure prefix=$HOME --with-opt-dir=$HOME/lib ... $ make ... configuring objspace configuring openssl Failed to configure openssl. It will not be installed. configuring pathname configuring psych yaml.h is missing. Please install libyaml. Failed to configure psych. It will not be installed. configuring pty ... Clues! But quite what is going wrong any why configure failed to complain is a puzzle. I came up with a plan B, installing ruby-1.9.2-p290.tar.gz instead. This worked, and I could run the BioRuby test suite: $ ruby test/runner.rb Loaded suite test/runner Started .....................................................................................EEEE............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Finished in 86.123565 seconds. 1) Error: test_log(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 2) Error: test_set_log(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 3) Error: test_set_wsdl(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 4) Error: test_wsdl(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 3704 tests, 21447 assertions, 0 failures, 4 errors, 0 skips Test run options: --seed 21073 Anyone care to comment on this NameError? Peter From ngoto at gen-info.osaka-u.ac.jp Sat Nov 5 08:10:57 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sat, 05 Nov 2011 21:10:57 +0900 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > Note I tried passing -prefix and --prefix to configure, but it didn't > accept it - use prefix with no minus at all, This seems to be very strange. I'm afraid if the machine might have serious trouble. > $ cd ~/Downloads > $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz > $ tar -xzvf yaml-0.1.4.tar.gz > $ cd yaml-0.1.4 > $ ./configure --prefix=$HOME > $ make > $ make check > $ make install The above process seems completely right. In addition, install libffi is recommended. $ cd ~/Downloads $ wget ftp://sourceware.org/pub/libffi/libffi-3.0.10.tar.gz $ tar zxvf libffi-3.0.10.tar.gz $ cd libffi-3.0.10 $ ./configure --prefix=$HOME $ make $ make check $ make install "yum install openssl-devel" is also strongly recommended. And then, configureing Ruby. For using libraries installed other than system-wide directory, additional options to specify paths of C header files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. $ tar zxvf ruby-1.9.3-p0.tar.gz $ cd ruby-1.9.3-p0 $ ./configure --prefix=$HOME \ CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" $ make $ make check $ make install If you think the gcc in CentOS 5.4 is buggy, adding optflags="-O2" to supress optimize level is suggested. During make check, few error would be happened, due to incomplete IPv6 network settings, kernel and glibc bug, older libraries bug, etc. FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully installed ruby-1.9.3-p0 in my home directory without root privilege. RedHat 4.6 uses gcc 3.4.6 that may have bug about symbol visibility options, and the following error happened during make process. Generating RDoc documentation ./ruby: symbol lookup error: /XXXXX/src/ruby-1.9.3-p0/.ext/ x86_64-linux/enc/encdb.so: undefined symbol: rb_encdb_declare For the workaround of the (very old gcc's) bug, editing Makefile is needed. after configure before make. $ cp Makefile Makefile.bak $ sed -e "s/-fvisibility=hidden/-fvisibility=default/" Makefile.bak > Makefile $ make clean $ make Note that the workaround is needed only when you see the symbol lookup error. On, CentOS 5.4, it seems the workaround is not needed (and it may have bad effect for systems without the problem). -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp From ngoto at gen-info.osaka-u.ac.jp Sat Nov 5 13:16:49 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sun, 06 Nov 2011 02:16:49 +0900 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: <20111106021649.20EF.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > 1) Error: > test_log(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > 2) Error: > test_set_log(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > 3) Error: > test_set_wsdl(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > 4) Error: > test_wsdl(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > > 3704 tests, 21447 assertions, 0 failures, 4 errors, 0 skips > > Test run options: --seed 21073 > > Anyone care to comment on this NameError? These 4 errors are caused by the drop of SOAP4R from the standard bundled library since Ruby 1.9. It is written in KNOWN_ISSUES.rdoc. "gem install soap4r-ruby1.9" should solve the problem. This is described in the latest (unreleased) README.rdoc. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp From pjotr.public14 at thebird.nl Sat Nov 5 13:34:34 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 5 Nov 2011 18:34:34 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: <20111106021649.20EF.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111106021649.20EF.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111105173434.GB2541@thebird.nl> It is a dependency. Should it not be in the BioRuby gemspec? On Sun, Nov 06, 2011 at 02:16:49AM +0900, Naohisa Goto wrote: > Hi Peter, > > > 1) Error: > > test_log(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > 2) Error: > > test_set_log(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > 3) Error: > > test_set_wsdl(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > 4) Error: > > test_wsdl(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > > > 3704 tests, 21447 assertions, 0 failures, 4 errors, 0 skips > > > > Test run options: --seed 21073 > > > > Anyone care to comment on this NameError? > > These 4 errors are caused by the drop of SOAP4R from the standard > bundled library since Ruby 1.9. It is written in KNOWN_ISSUES.rdoc. > > "gem install soap4r-ruby1.9" should solve the problem. > This is described in the latest (unreleased) README.rdoc. > > -- > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Mon Nov 7 04:59:17 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 09:59:17 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Sat, Nov 5, 2011 at 12:10 PM, Naohisa Goto wrote: >> Note I tried passing -prefix and --prefix to configure, but it didn't >> accept it - use prefix with no minus at all, > > This seems to be very strange. I'm afraid if the machine might have > serious trouble. Odd - it worked today. Maybe it wasn't a minus sign last week, but a different dash if I copied and pasted it from a webpage? Not sure. > In addition, install libffi is recommended. > ?$ cd ~/Downloads > ?$ wget ftp://sourceware.org/pub/libffi/libffi-3.0.10.tar.gz > ?$ tar zxvf libffi-3.0.10.tar.gz > ?$ cd libffi-3.0.10 > ?$ ./configure --prefix=$HOME > ?$ make > ?$ make check > ?$ make install Done > "yum install openssl-devel" is also strongly recommended. > Done, I'm surprised that wasn't installed on this server already. > And then, configureing Ruby. For using libraries installed other than > system-wide directory, additional options to specify paths of C header > files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. > > ?$ tar zxvf ruby-1.9.3-p0.tar.gz > ?$ cd ruby-1.9.3-p0 > ?$ ./configure --prefix=$HOME \ > ? CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ > ? LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" > ?$ make > ?$ make check > ?$ make install > > If you think the gcc in CentOS 5.4 is buggy, adding optflags="-O2" > to supress optimize level is suggested. > > During make check, few error would be happened, due to incomplete IPv6 > network settings, kernel and glibc bug, older libraries bug, etc. > > FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully > installed ruby-1.9.3-p0 in my home directory without root privilege. That was very encouraging, as it is almost exactly what I'm trying to do :) I think it was the flags that I was missing. I also did "gem install soap4r-ruby1.9" as you suggested, and now BioRuby's test pass using ruby-1.9.3-p0: $ ruby test/runner.rb /home/buildslave/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: .......................................................................................ignored attr: {}arrayType ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Finished tests in 130.295656s, 28.4277 tests/s, 164.6333 assertions/s. 3704 tests, 21451 assertions, 0 failures, 0 errors, 0 skips Do you need to look at this iconv deprecation warning, and the "ignored attr: {}arrayType" message? > RedHat 4.6 uses gcc 3.4.6 that may have bug about symbol visibility > options, and the following error happened during make process. > > ?Generating RDoc documentation > ?./ruby: symbol lookup error: /XXXXX/src/ruby-1.9.3-p0/.ext/ > ?x86_64-linux/enc/encdb.so: undefined symbol: rb_encdb_declare > > For the workaround of ?the (very old gcc's) bug, editing Makefile is > needed. after configure before make. > > ?$ cp Makefile Makefile.bak > ?$ sed -e "s/-fvisibility=hidden/-fvisibility=default/" Makefile.bak > Makefile > ?$ make clean > ?$ make > > Note that the workaround is needed only when you see the symbol > lookup error. On, CentOS 5.4, it seems the workaround is not needed > (and it may have bad effect for systems without the problem). I didn't see that error, so didn't apply this change to the Makefile. Thank you very much Goto-san :) Peter From p.j.a.cock at googlemail.com Mon Nov 7 05:49:38 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 10:49:38 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Mon, Nov 7, 2011 at 9:59 AM, Peter Cock wrote: > On Sat, Nov 5, 2011 at 12:10 PM, Naohisa Goto >> And then, configureing Ruby. For using libraries installed other than >> system-wide directory, additional options to specify paths of C header >> files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. >> >> ?$ tar zxvf ruby-1.9.3-p0.tar.gz >> ?$ cd ruby-1.9.3-p0 >> ?$ ./configure --prefix=$HOME \ >> ? CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ >> ? LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" >> ?$ make >> ?$ make check >> ?$ make install >> >> ... >> >> FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully >> installed ruby-1.9.3-p0 in my home directory without root privilege. > > That was very encouraging, as it is almost exactly what I'm trying to do :) > I think it was the flags that I was missing. > > I also did "gem install soap4r-ruby1.9" as you suggested, and now > BioRuby's test pass using ruby-1.9.3-p0: This 64 bit Linux machine and a 32bit Linux box are now setup and running as buildslaves for BioRuby, bringing us to three slaves so far: http://testing.open-bio.org/bioruby/buildslaves Next up: My Windows machine... Peter From p.j.a.cock at googlemail.com Mon Nov 7 06:26:53 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:26:53 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows Message-ID: Hi all, Again I thought it would be useful to write down what I did to get BioRuby running on my Windows XP 32 bit machine (which will be a buildslave). Note I have some things already installed, like git. 1. Download http://rubyforge.org/frs/download.php/75465/rubyinstaller-1.9.3-p0.exe 2. Run it, using default options except I ticked "Add Ruby executables to your PATH" Otherwise the path installed to will be C:\Ruby193 or similar, and thus version dependent, which I anticipate will complicate things for the buildbot setup. I then tried the BioRuby tests which confirmed it was missing the next two gems (although there were some other errors, e.g. in the sanger_chromatogram example). 3. gem install libxml-ruby 4. gem install soap4r-ruby1.9 5. git clone git://github.com/bioruby/bioruby.git 6. cd bioruby 7. ruby test/runner.rb Error message popped up three times, typed in by hand: ruby.exe - Unable to Locate Component This application has failed to start because libxml2-2.dll was not found. Re-installing the application my fix this problem. [OK] Perhaps the gem install wasn't quite right? Or it doesn't actually link to the DLL properly? I could find the DLL here, C:\Ruby193\lib\ruby\gems\1.9.1\gems\libxml-ruby-2.2.2-x86-mingw32\lib\libs\libxml2-2.dll The following StackOverflow question looked relevant, although on a much older version of Ruby: http://stackoverflow.com/questions/4323234/ I tried the work around mentioned and copied the 3 DLL files in that folder to C:\Ruby193\bin - that solved the missing DLL error message, but seems like a hack. After that there were 4 failures and 7 errors, which I will cover in the next email. Peter -------------------------------------------------- C:\repositories\bioruby>gem install libxml-ruby Fetching: libxml-ruby-2.2.2-x86-mingw32.gem (100%) Successfully installed libxml-ruby-2.2.2-x86-mingw32 1 gem installed Installing ri documentation for libxml-ruby-2.2.2-x86-mingw32... Installing RDoc documentation for libxml-ruby-2.2.2-x86-mingw32... C:\repositories\bioruby>gem install soap4r-ruby1.9 Fetching: soap4r-ruby1.9-2.0.3.gem (100%) Successfully installed soap4r-ruby1.9-2.0.3 1 gem installed Installing ri documentation for soap4r-ruby1.9-2.0.3... Installing RDoc documentation for soap4r-ruby1.9-2.0.3... From pjotr.public14 at thebird.nl Mon Nov 7 06:31:28 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 7 Nov 2011 12:31:28 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111107113128.GA12989@thebird.nl> Very cool. Would it be possible to show the builder names including the distro? So instead of the too generic Linux 32 - Ruby 1.9 show Linux CentOS 4.6 32bits - Ruby 1.9 so the output is immediately self descriptive? Pj. On Mon, Nov 07, 2011 at 10:49:38AM +0000, Peter Cock wrote: > On Mon, Nov 7, 2011 at 9:59 AM, Peter Cock wrote: > > On Sat, Nov 5, 2011 at 12:10 PM, Naohisa Goto > >> And then, configureing Ruby. For using libraries installed other than > >> system-wide directory, additional options to specify paths of C header > >> files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. > >> > >> ?$ tar zxvf ruby-1.9.3-p0.tar.gz > >> ?$ cd ruby-1.9.3-p0 > >> ?$ ./configure --prefix=$HOME \ > >> ? CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ > >> ? LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" > >> ?$ make > >> ?$ make check > >> ?$ make install > >> > >> ... > >> > >> FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully > >> installed ruby-1.9.3-p0 in my home directory without root privilege. > > > > That was very encouraging, as it is almost exactly what I'm trying to do :) > > I think it was the flags that I was missing. > > > > I also did "gem install soap4r-ruby1.9" as you suggested, and now > > BioRuby's test pass using ruby-1.9.3-p0: > > This 64 bit Linux machine and a 32bit Linux box are now setup and > running as buildslaves for BioRuby, bringing us to three slaves so far: > > http://testing.open-bio.org/bioruby/buildslaves > > Next up: My Windows machine... > > Peter > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Mon Nov 7 06:38:28 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:38:28 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock wrote: > Hi all, > > Again I thought it would be useful to write down what I did to get > BioRuby running on my Windows XP 32 bit machine (which will > be a buildslave). > ... > After that there were 4 failures and 7 errors, which I will cover in the > next email. Full details at end of email, here is my attempt to summarise and guess what is wrong: Errors (1), (2) and (3) are permission failures in testing calling commands. My guess is this is something about the batch file being used, C:\repositories\bioruby>test/data/command/echoarg2.bat Hello test: missing argument after `Hello' C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World test: Hello: binary operator expected Errors (4) and (5) may be transient network problems with efetch? Errors (6), (7) and (8) are all from Bio::TestAbif about NoMethodError: undefined method `match' for nil:NilClass Errors (9) and (10) look like a path name escape test being too strict and/or unaware of cross platform path separators. Error (11) looks like it could be an error removing a file - note you can't do this on Windows if there is an open handle to the file If any of these are specific to my Windows setup, with some guidance we can try to work out what is different. Peter --------------------------------------------------------- C:\repositories\bioruby>ruby test/runner.rb C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: ...................E.EE................................................F......F. .......ignored attr: {}arrayType ................................................................................ ..............EEE............................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ...........................................................................F.... ....F........................................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ....................................................................E........... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................. Finished tests in 145.575330s, 25.4439 tests/s, 147.2434 assertions/s. 1) Error: test_call_command(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call _command' 2) Error: test_call_command_open3(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/test/functional/bio/test_command.rb:71:in `test_call _command_open3' test/runner.rb:27:in `
' 3) Error: test_call_command_popen(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/test/functional/bio/test_command.rb:48:in `test_call _command_popen' 4) Failure: test_efetch_multiple_xml(Bio::FuncTestPubmed) [C:/repositories/bioruby/test/func tional/bio/io/test_pubmed.rb:108]: Failed assertion, no message given. 5) Failure: test_efetch_multiple(Bio::FuncTestPubmedClassMethod) [C:/repositories/bioruby/te st/functional/bio/io/test_pubmed.rb:91]: <3> expected but was <47>. 6) Error: test_complement(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 7) Error: test_seq(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 8) Error: test_to_biosequence(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 9) Failure: test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_ command.rb:59]: <"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 10) Failure: test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/ test_command.rb:76]: <"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 11) Error: test_simple_xml(Bio::TestPhyloXMLWriter): Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-1116-m0djng/example_ tree1.xml C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure' C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback' C:/repositories/bioruby/lib/bio/command.rb:607:in `call' C:/repositories/bioruby/lib/bio/command.rb:607:in `close!' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test _passed' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea rdown' test/runner.rb:27:in `
' 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips From p.j.a.cock at googlemail.com Mon Nov 7 06:43:54 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:43:54 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: <20111107113128.GA12989@thebird.nl> References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> <20111107113128.GA12989@thebird.nl> Message-ID: On Mon, Nov 7, 2011 at 11:31 AM, Pjotr Prins wrote: > Very cool. Would it be possible to show the builder names including > the distro? So instead of the too generic > > ?Linux 32 - Ruby 1.9 > > show > > ?Linux CentOS 4.6 32bits - Ruby 1.9 > > so the output is immediately self descriptive? > > Pj. That short name is configurable, but it would be used for multiple buildslaves supporting that target. The question is do you want to lump together all your 32 bit Linux machines testing Ruby 1.9 under one group (as it is now, although currently with just one buildslave for this grouping), or have a more fine grained listing? i.e. More build targets which will show up as more rows or columns here: http://testing.open-bio.org/bioruby/grid http://testing.open-bio.org/bioruby/tgrid http://testing.open-bio.org/bioruby/waterfall This is what we were trying to ask earlier about the build targets, and initially we agreed to go for Ruby 1.8 and 1.9 on a range of operating systems - Windows 32, Win 64, Linux 32, Linux 64, Mac OS Snow Leopard (64 bit), etc Hopefully this is starting to become clearer now. Peter From p.j.a.cock at googlemail.com Mon Nov 7 06:48:06 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:48:06 +0000 Subject: [BioRuby] Buildbot target platforms Message-ID: Retitling thread On Mon, Nov 7, 2011 at 11:43 AM, Peter Cock wrote: > On Mon, Nov 7, 2011 at 11:31 AM, Pjotr Prins wrote: >> Very cool. Would it be possible to show the builder names including >> the distro? So instead of the too generic >> >> ?Linux 32 - Ruby 1.9 >> >> show >> >> ?Linux CentOS 4.6 32bits - Ruby 1.9 >> >> so the output is immediately self descriptive? >> >> Pj. > > That short name is configurable, but it would be used for multiple > buildslaves supporting that target. > > The question is do you want to lump together all your 32 bit > Linux machines testing Ruby 1.9 under one group (as it is > now, although currently with just one buildslave for this > grouping), or have a more fine grained listing? > > i.e. More build targets which will show up as more rows or > columns here: > > http://testing.open-bio.org/bioruby/grid > http://testing.open-bio.org/bioruby/tgrid > http://testing.open-bio.org/bioruby/waterfall > > This is what we were trying to ask earlier about the build > targets, and initially we agreed to go for Ruby 1.8 and 1.9 > on a range of operating systems - Windows 32, Win 64, > Linux 32, Linux 64, Mac OS Snow Leopard (64 bit), etc > Hopefully this is starting to become clearer now. These are the Biopython targets, 23 of them right now: testing.open-bio.org/biopython/grid testing.open-bio.org/biopython/tgrid For us since we test several variants of Python, having the OS broken down into anything finer would be too much. Note that I am beginning to think that on Ruby the revision number seems to be much more important than in Python. i.e. Maybe we should have separate testing for Ruby 1.9.1, 1.9.2, 1.9.3 etc rather than just bundling them together under Ruby 1.9? Peter From p.j.a.cock at googlemail.com Mon Nov 7 07:35:07 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 12:35:07 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: On Mon, Nov 7, 2011 at 11:38 AM, Peter Cock wrote: > On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock wrote: >> Hi all, >> >> Again I thought it would be useful to write down what I did to get >> BioRuby running on my Windows XP 32 bit machine (which will >> be a buildslave). >> ... >> After that there were 4 failures and 7 errors, which I will cover in the >> next email. > > Full details at end of email, here is my attempt to summarise and guess > what is wrong: > > Errors (1), (2) and (3) are permission failures in testing calling commands. > My guess is this is something about the batch file being used, > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello > test: missing argument after `Hello' > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World > test: Hello: binary operator expected > Wrong slashes - that would have been cygwin's echo rather than Window's, C:\repositories\bioruby>test\data\command\echoarg2.bat Hello ECHO is on. C:\repositories\bioruby>test\data\command\echoarg2.bat Hello World World So there isn't a problem with the batch file itself. Peter From p.j.a.cock at googlemail.com Mon Nov 7 08:48:48 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 13:48:48 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: On Mon, Nov 7, 2011 at 11:38 AM, Peter Cock wrote: > > C:\repositories\bioruby>ruby test/runner.rb > C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will > ?be deprecated in the future, use String#encode instead. > Run options: > > # Running tests: > > ...................E.EE................................................F......F. > .......ignored attr: {}arrayType > ................................................................................ > etc > 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips Interestingly I gave Ruby the path name with Windows style slashes, and the pattern is a little different, 3 failures, 8 errors. However, some of these seem to be network related or stochastic, so a direct comparison is not fair. On closer inspection it looks like the same problems. We've got a couple of stochastic tests in Biopython and even after relaxing the test criteria they still can fail every so often, which is annoying. Peter -- C:\repositories\bioruby>ruby test\runner.rb C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: ...................E.EE...................................................E..... .......ignored attr: {}arrayType ................................................................................ ..............EEE............................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ...........................................................................F.... ....F........................................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ....................................................................E........... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ..........................................................................F..... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................. Finished tests in 214.230262s, 17.2898 tests/s, 99.9765 assertions/s. 1) Error: test_call_command(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call _command' 2) Error: test_call_command_open3(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/test/functional/bio/test_command.rb:71:in `test_call _command_open3' test/runner.rb:27:in `
' 3) Error: test_call_command_popen(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/test/functional/bio/test_command.rb:48:in `test_call _command_popen' 4) Error: test_esearch(Bio::FuncTestPubmed): Errno::ETIMEDOUT: A connection attempt failed because the connected party did no t properly respond after a period of time, or established connection failed beca use connected host has failed to respond. - connect(2) C:/repositories/bioruby/lib/bio/command.rb:649:in `start_http' C:/repositories/bioruby/lib/bio/command.rb:735:in `post_form' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:131:in `ncbi_post_form' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:268:in `block in esearch' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:265:in `step' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:265:in `esearch' C:/repositories/bioruby/lib/bio/io/pubmed.rb:96:in `esearch' C:/repositories/bioruby/test/functional/bio/io/test_pubmed.rb:26:in `test_es earch' test/runner.rb:27:in `
' 5) Error: test_complement(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 6) Error: test_seq(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 7) Error: test_to_biosequence(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 8) Failure: test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_ command.rb:59]: <"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 9) Failure: test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/ test_command.rb:76]: <"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 10) Error: test_simple_xml(Bio::TestPhyloXMLWriter): Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-3360-1ksuohs/example _tree1.xml C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure' C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback' C:/repositories/bioruby/lib/bio/command.rb:607:in `call' C:/repositories/bioruby/lib/bio/command.rb:607:in `close!' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test _passed' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea rdown' test/runner.rb:27:in `
' 11) Failure: test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandom ize) [C:/repositories/bioruby/test/unit/bio/sequence/test_common.rb:286]: test of chi2 < 21.666 failed (25.8). Expected 21.666 to be > 25.8. 3704 tests, 21418 assertions, 3 failures, 8 errors, 0 skips From rob.syme at gmail.com Mon Nov 14 01:07:47 2011 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 14 Nov 2011 14:07:47 +0800 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection Message-ID: Hi all, Full details are up at: http://gist.github.com/1363302 This might just be the result of a schema change in BioSQL, but my SQL knowledge doesn't extend quite far enough. Has anyone come across this before? When connecting to an empty postgres BioSQL db, I get an ActiveRecord::StatementInvalid error: PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" HINT: You need an unconditional ON INSERT DO INSTEAD rule with a RETURNING clause. : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) RETURNING "ontology_id" ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" HINT: You need an unconditional ON INSERT DO INSTEAD rule with a RETURNING clause. : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) RETURNING "ontology_id" from /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/connection_adapters/postgresql_adapter.rb:1009:in `prepare' from /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/biosql.rb:31:in `establish_connection' The offending SQL was: SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') LIMIT 1 # This works fine INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) RETURNING "ontology_id" [["definition", nil], ["name", "Annotation Tags"]] # This fails Relevant gems installed: activerecord (3.1.1) composite_primary_keys (4.1.1) pg (0.11.0) bio (1.4.2.5000) Using: psql (PostgreSQL) 9.1.1 BioSQL schema version 1.0.1 and ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] -r From bonnal at ingm.org Mon Nov 14 05:43:51 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 14 Nov 2011 11:43:51 +0100 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: Message-ID: Hi Rob, may be a problem of my biosql implementation, I suppose. I didn't update the library and I didn't check compatibility with new active record stuff and composite primary keys. Now, I can not take care of this, if there is someone wants to take care of I'll be happy to support him/her. On 14/11/11 07.07, "Rob Syme" wrote: > Hi all, > Full details are up at: http://gist.github.com/1363302 > > This might just be the result of a schema change in BioSQL, but my SQL > knowledge doesn't extend quite far enough. Has anyone come across this > before? > > When connecting to an empty postgres BioSQL db, I get an > ActiveRecord::StatementInvalid error: > > PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > RETURNING clause. > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > RETURNING "ontology_id" > ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT > RETURNING on relation "ontology" > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > RETURNING clause. > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > RETURNING "ontology_id" > from > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/ > connection_adapters/postgresql_adapter.rb:1009:in > `prepare' > > from > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios > ql.rb:31:in > `establish_connection' > > > The offending SQL was: > > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') > LIMIT 1 # This works fine > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > RETURNING "ontology_id" [["definition", nil], ["name", "Annotation > Tags"]] # This fails > > Relevant gems installed: > activerecord (3.1.1) > composite_primary_keys (4.1.1) > pg (0.11.0) > bio (1.4.2.5000) > > Using: > psql (PostgreSQL) 9.1.1 > BioSQL schema version 1.0.1 and > ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] > > -r > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From rob.syme at gmail.com Mon Nov 14 08:03:13 2011 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 14 Nov 2011 21:03:13 +0800 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: References: Message-ID: Cool. Just checking that I wasn't struggling with something that was already known. I'll have a poke around tomorrow. -r On 14 Nov 2011 18:43, "Raoul Bonnal" wrote: > Hi Rob, > may be a problem of my biosql implementation, I suppose. > I didn't update the library and I didn't check compatibility with new > active > record stuff and composite primary keys. > Now, I can not take care of this, if there is someone wants to take care of > I'll be happy to support him/her. > > > On 14/11/11 07.07, "Rob Syme" wrote: > > > Hi all, > > Full details are up at: http://gist.github.com/1363302 > > > > This might just be the result of a schema change in BioSQL, but my SQL > > knowledge doesn't extend quite far enough. Has anyone come across this > > before? > > > > When connecting to an empty postgres BioSQL db, I get an > > ActiveRecord::StatementInvalid error: > > > > PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT > > RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > from > > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/ > > connection_adapters/postgresql_adapter.rb:1009:in > > `prepare' > > > > from > > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios > > ql.rb:31:in > > `establish_connection' > > > > > > The offending SQL was: > > > > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') > > LIMIT 1 # This works fine > > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" [["definition", nil], ["name", "Annotation > > Tags"]] # This fails > > > > Relevant gems installed: > > activerecord (3.1.1) > > composite_primary_keys (4.1.1) > > pg (0.11.0) > > bio (1.4.2.5000) > > > > Using: > > psql (PostgreSQL) 9.1.1 > > BioSQL schema version 1.0.1 and > > ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] > > > > -r > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > From ngoto at gen-info.osaka-u.ac.jp Mon Nov 14 08:14:22 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 14 Nov 2011 22:14:22 +0900 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: References: Message-ID: <20111114131423.6D6F61CBC513@idnmail.gen-info.osaka-u.ac.jp> Hi Raoul, Which version of ActiveRecord is suitable with the current BioRuby's biosql implementation? With RubyGems and (optionally) with Bundler, we can specify specific version number to be used. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 14 Nov 2011 11:43:51 +0100 Raoul Bonnal wrote: > Hi Rob, > may be a problem of my biosql implementation, I suppose. > I didn't update the library and I didn't check compatibility with new active > record stuff and composite primary keys. > Now, I can not take care of this, if there is someone wants to take care of > I'll be happy to support him/her. > > > On 14/11/11 07.07, "Rob Syme" wrote: > > > Hi all, > > Full details are up at: http://gist.github.com/1363302 > > > > This might just be the result of a schema change in BioSQL, but my SQL > > knowledge doesn't extend quite far enough. Has anyone come across this > > before? > > > > When connecting to an empty postgres BioSQL db, I get an > > ActiveRecord::StatementInvalid error: > > > > PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT > > RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > from > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/ > > connection_adapters/postgresql_adapter.rb:1009:in > > `prepare' > > > > from > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios > > ql.rb:31:in > > `establish_connection' > > > > > > The offending SQL was: > > > > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') > > LIMIT 1 # This works fine > > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" [["definition", nil], ["name", "Annotation > > Tags"]] # This fails > > > > Relevant gems installed: > > activerecord (3.1.1) > > composite_primary_keys (4.1.1) > > pg (0.11.0) > > bio (1.4.2.5000) > > > > Using: > > psql (PostgreSQL) 9.1.1 > > BioSQL schema version 1.0.1 and > > ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] > > > > -r > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnal at ingm.org Mon Nov 14 08:34:25 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 14 Nov 2011 14:34:25 +0100 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: <20111114131423.6D6F61CBC513@idnmail.gen-info.osaka-u.ac.jp> Message-ID: It should work with versions prior to Rails 3.x. But if you are not in a rush after paper submission I'll look into it, let'say 2 weeks ? There was another BioSQL issue around, i didn't answer because I was busy. @Rob: could you give me the script to replicate the error ? We could extract BioSQL from BioRuby and create a plugin, is something I'm considering. On 14/11/11 14.14, "Naohisa GOTO" wrote: > Hi Raoul, > > Which version of ActiveRecord is suitable with the current > BioRuby's biosql implementation? > > With RubyGems and (optionally) with Bundler, we can specify > specific version number to be used. > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Mon, 14 Nov 2011 11:43:51 +0100 > Raoul Bonnal wrote: > >> Hi Rob, >> may be a problem of my biosql implementation, I suppose. >> I didn't update the library and I didn't check compatibility with new active >> record stuff and composite primary keys. >> Now, I can not take care of this, if there is someone wants to take care of >> I'll be happy to support him/her. >> >> >> On 14/11/11 07.07, "Rob Syme" wrote: >> >>> Hi all, >>> Full details are up at: http://gist.github.com/1363302 >>> >>> This might just be the result of a schema change in BioSQL, but my SQL >>> knowledge doesn't extend quite far enough. Has anyone come across this >>> before? >>> >>> When connecting to an empty postgres BioSQL db, I get an >>> ActiveRecord::StatementInvalid error: >>> >>> PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" >>> HINT: You need an unconditional ON INSERT DO INSTEAD rule with a >>> RETURNING clause. >>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>> RETURNING "ontology_id" >>> ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT >>> RETURNING on relation "ontology" >>> HINT: You need an unconditional ON INSERT DO INSTEAD rule with a >>> RETURNING clause. >>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>> RETURNING "ontology_id" >>> from >>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_recor >>> d/ >>> connection_adapters/postgresql_adapter.rb:1009:in >>> `prepare' >>> >>> from >>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bi >>> os >>> ql.rb:31:in >>> `establish_connection' >>> >>> >>> The offending SQL was: >>> >>> SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') >>> LIMIT 1 # This works fine >>> INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>> RETURNING "ontology_id" [["definition", nil], ["name", "Annotation >>> Tags"]] # This fails >>> >>> Relevant gems installed: >>> activerecord (3.1.1) >>> composite_primary_keys (4.1.1) >>> pg (0.11.0) >>> bio (1.4.2.5000) >>> >>> Using: >>> psql (PostgreSQL) 9.1.1 >>> BioSQL schema version 1.0.1 and >>> ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] >>> >>> -r >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > From bonnal at ingm.org Mon Nov 14 10:08:08 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 14 Nov 2011 16:08:08 +0100 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: Message-ID: Hi Rob, Thanks, I'll try to replicate the issue later this week. Having this dependencies perhaps is better to extract biosql from bioruby. On 14/11/11 15.37, "Rob Syme" wrote: > The script is very simple, just try and connect to the db. Replication > is easiest when your postgres install includes a database $USER with > permissions such that you can create databases with `createdb` without > sudo. Instructions up at https://help.ubuntu.com/community/PostgreSQL > under "Alternative Setup". If you have a more secure postgres setup, > just supply the username password in the final line: > > # Setup the postgres db > git clone https://github.com/biosql/biosql.git > createdb biosql > psql biosql < biosql/sql/biosqldb-pg.sql > > # Grab all the gems > gem install activerecord bio composite_primary_keys pg > activerecord-postgres-adapter > > # Try and establish the db connection > # The connection hash is minimal, username defaults to the $USER, and > hostname defaults to localhost. > ruby -r bio -e "Bio::SQL.establish_connection({'development'=>{ > 'database'=>'biosql','adapter'=>'postgresql' }},'development')" > > > > > On Mon, Nov 14, 2011 at 9:34 PM, Raoul Bonnal wrote: >> It should work with versions prior to Rails 3.x. >> But if you are not in a rush after paper submission I'll look into it, >> let'say 2 weeks ?? There was another BioSQL issue around, i didn't answer >> because I was busy. >> >> @Rob: could you give me the script to replicate the error ? >> >> We could extract BioSQL from BioRuby and create a plugin, is something I'm >> considering. >> >> On 14/11/11 14.14, "Naohisa GOTO" wrote: >> >>> Hi Raoul, >>> >>> Which version of ActiveRecord is suitable with the current >>> BioRuby's biosql implementation? >>> >>> With RubyGems and (optionally) with Bundler, we can specify >>> specific version number to be used. >>> >>> Naohisa Goto >>> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org >>> >>> On Mon, 14 Nov 2011 11:43:51 +0100 >>> Raoul Bonnal wrote: >>> >>>> Hi Rob, >>>> may be a problem of my biosql implementation, I suppose. >>>> I didn't update the library and I didn't check compatibility with new >>>> active >>>> record stuff and composite primary keys. >>>> Now, I can not take care of this, if there is someone wants to take care of >>>> I'll be happy to support him/her. >>>> >>>> >>>> On 14/11/11 07.07, "Rob Syme" wrote: >>>> >>>>> Hi all, >>>>> Full details are up at: http://gist.github.com/1363302 >>>>> >>>>> This might just be the result of a schema change in BioSQL, but my SQL >>>>> knowledge doesn't extend quite far enough. Has anyone come across this >>>>> before? >>>>> >>>>> When connecting to an empty postgres BioSQL db, I get an >>>>> ActiveRecord::StatementInvalid error: >>>>> >>>>> PGError: ERROR: ?cannot perform INSERT RETURNING on relation "ontology" >>>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>>> RETURNING clause. >>>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>>> RETURNING "ontology_id" >>>>> ActiveRecord::StatementInvalid: PGError: ERROR: ?cannot perform INSERT >>>>> RETURNING on relation "ontology" >>>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>>> RETURNING clause. >>>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>>> RETURNING "ontology_id" >>>>> from >>>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_rec >>>>> or >>>>> d/ >>>>> connection_adapters/postgresql_adapter.rb:1009:in >>>>> `prepare' >>>>> >>>>> from >>>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/ >>>>> bi >>>>> os >>>>> ql.rb:31:in >>>>> `establish_connection' >>>>> >>>>> >>>>> The offending SQL was: >>>>> >>>>> SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') >>>>> LIMIT 1 # This works fine >>>>> INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>>> RETURNING "ontology_id" ?[["definition", nil], ["name", "Annotation >>>>> Tags"]] # This fails >>>>> >>>>> Relevant gems installed: >>>>> ? activerecord (3.1.1) >>>>> ? composite_primary_keys (4.1.1) >>>>> ? pg (0.11.0) >>>>> ? bio (1.4.2.5000) >>>>> >>>>> Using: >>>>> ? psql (PostgreSQL) 9.1.1 >>>>> ? BioSQL schema version 1.0.1 and >>>>> ? ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] >>>>> >>>>> -r >>>>> _______________________________________________ >>>>> BioRuby Project - http://www.bioruby.org/ >>>>> BioRuby mailing list >>>>> BioRuby at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> From rob.syme at gmail.com Mon Nov 14 09:37:55 2011 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 14 Nov 2011 22:37:55 +0800 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: References: <20111114131423.6D6F61CBC513@idnmail.gen-info.osaka-u.ac.jp> Message-ID: The script is very simple, just try and connect to the db. Replication is easiest when your postgres install includes a database $USER with permissions such that you can create databases with `createdb` without sudo. Instructions up at https://help.ubuntu.com/community/PostgreSQL under "Alternative Setup". If you have a more secure postgres setup, just supply the username password in the final line: # Setup the postgres db git clone https://github.com/biosql/biosql.git createdb biosql psql biosql < biosql/sql/biosqldb-pg.sql # Grab all the gems gem install activerecord bio composite_primary_keys pg activerecord-postgres-adapter # Try and establish the db connection # The connection hash is minimal, username defaults to the $USER, and hostname defaults to localhost. ruby -r bio -e "Bio::SQL.establish_connection({'development'=>{ 'database'=>'biosql','adapter'=>'postgresql' }},'development')" On Mon, Nov 14, 2011 at 9:34 PM, Raoul Bonnal wrote: > It should work with versions prior to Rails 3.x. > But if you are not in a rush after paper submission I'll look into it, > let'say 2 weeks ?? There was another BioSQL issue around, i didn't answer > because I was busy. > > @Rob: could you give me the script to replicate the error ? > > We could extract BioSQL from BioRuby and create a plugin, is something I'm > considering. > > On 14/11/11 14.14, "Naohisa GOTO" wrote: > >> Hi Raoul, >> >> Which version of ActiveRecord is suitable with the current >> BioRuby's biosql implementation? >> >> With RubyGems and (optionally) with Bundler, we can specify >> specific version number to be used. >> >> Naohisa Goto >> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org >> >> On Mon, 14 Nov 2011 11:43:51 +0100 >> Raoul Bonnal wrote: >> >>> Hi Rob, >>> may be a problem of my biosql implementation, I suppose. >>> I didn't update the library and I didn't check compatibility with new active >>> record stuff and composite primary keys. >>> Now, I can not take care of this, if there is someone wants to take care of >>> I'll be happy to support him/her. >>> >>> >>> On 14/11/11 07.07, "Rob Syme" wrote: >>> >>>> Hi all, >>>> Full details are up at: http://gist.github.com/1363302 >>>> >>>> This might just be the result of a schema change in BioSQL, but my SQL >>>> knowledge doesn't extend quite far enough. Has anyone come across this >>>> before? >>>> >>>> When connecting to an empty postgres BioSQL db, I get an >>>> ActiveRecord::StatementInvalid error: >>>> >>>> PGError: ERROR: ?cannot perform INSERT RETURNING on relation "ontology" >>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>> RETURNING clause. >>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>> RETURNING "ontology_id" >>>> ActiveRecord::StatementInvalid: PGError: ERROR: ?cannot perform INSERT >>>> RETURNING on relation "ontology" >>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>> RETURNING clause. >>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>> RETURNING "ontology_id" >>>> from >>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_recor >>>> d/ >>>> connection_adapters/postgresql_adapter.rb:1009:in >>>> `prepare' >>>> >>>> from >>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bi >>>> os >>>> ql.rb:31:in >>>> `establish_connection' >>>> >>>> >>>> The offending SQL was: >>>> >>>> SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') >>>> LIMIT 1 # This works fine >>>> INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>> RETURNING "ontology_id" ?[["definition", nil], ["name", "Annotation >>>> Tags"]] # This fails >>>> >>>> Relevant gems installed: >>>> ? activerecord (3.1.1) >>>> ? composite_primary_keys (4.1.1) >>>> ? pg (0.11.0) >>>> ? bio (1.4.2.5000) >>>> >>>> Using: >>>> ? psql (PostgreSQL) 9.1.1 >>>> ? BioSQL schema version 1.0.1 and >>>> ? ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] >>>> >>>> -r >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ngoto at gen-info.osaka-u.ac.jp Mon Nov 21 03:09:13 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Mon, 21 Nov 2011 17:09:13 +0900 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, Sorry very late. On my Windows 7 (32-bit, Business or Enterprise) machines, with Ruby 1.9.3-p0 downloaded from rubyinstaller.org, the 1), 2), and 3) "Errno::EACCES: Permission denied" cannot be reproduced. Instead, failure occur due to the change of command-line escaping in Ruby 1.9, which would be the same as 9) and 10). The "Errno::EACCESS" might occurr when using other shell than cmd.exe e.g. Cygwin's Bash, execution prohibition by security software, or by access controll on NTFS. For 9) and 10): In Windows, command-line escaping is treated by each software, and no "general" escaping way exists. This means the test is bad for Windows. With Ruby 1.8.x, current BioRuby uses its internal command-line string builder, but with Ruby 1.9.x, it uses Ruby's. 6), 7), and 8) may be due to text mode that is default file reading mode when Ruby on windows and that may break things when reading binary files. 11) may be the problem of removing a file before closing, as you said. Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > 1) Error: > test_call_command(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call > _command' > On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock wrote: > > Hi all, > > > > Again I thought it would be useful to write down what I did to get > > BioRuby running on my Windows XP 32 bit machine (which will > > be a buildslave). > > ... > > After that there were 4 failures and 7 errors, which I will cover in the > > next email. > > Full details at end of email, here is my attempt to summarise and guess > what is wrong: > > Errors (1), (2) and (3) are permission failures in testing calling commands. > My guess is this is something about the batch file being used, > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello > test: missing argument after `Hello' > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World > test: Hello: binary operator expected > > > Errors (4) and (5) may be transient network problems with efetch? > > > Errors (6), (7) and (8) are all from Bio::TestAbif about > NoMethodError: undefined method `match' for nil:NilClass > > > Errors (9) and (10) look like a path name escape test being too > strict and/or unaware of cross platform path separators. > > > Error (11) looks like it could be an error removing a file - note you > can't do this on Windows if there is an open handle to the file > > > If any of these are specific to my Windows setup, with some guidance we > can try to work out what is different. > > Peter > > --------------------------------------------------------- > > C:\repositories\bioruby>ruby test/runner.rb > C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will > be deprecated in the future, use String#encode instead. > Run options: > > # Running tests: > > ...................E.EE................................................F......F. > .......ignored attr: {}arrayType > ................................................................................ > ..............EEE............................................................... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ...........................................................................F.... > ....F........................................................................... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ....................................................................E........... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................. > > Finished tests in 145.575330s, 25.4439 tests/s, 147.2434 assertions/s. > > 1) Error: > test_call_command(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call > _command' > > 2) Error: > test_call_command_open3(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/test/functional/bio/test_command.rb:71:in `test_call > _command_open3' > test/runner.rb:27:in `
' > > 3) Error: > test_call_command_popen(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/test/functional/bio/test_command.rb:48:in `test_call > _command_popen' > > 4) Failure: > test_efetch_multiple_xml(Bio::FuncTestPubmed) [C:/repositories/bioruby/test/func > tional/bio/io/test_pubmed.rb:108]: > Failed assertion, no message given. > > 5) Failure: > test_efetch_multiple(Bio::FuncTestPubmedClassMethod) [C:/repositories/bioruby/te > st/functional/bio/io/test_pubmed.rb:91]: > <3> expected but was > <47>. > > 6) Error: > test_complement(Bio::TestAbif): > NoMethodError: undefined method `match' for nil:NilClass > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e > ntry_data' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block > in get_directory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' > > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di > rectory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia > lize' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `new' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `setup' > > 7) Error: > test_seq(Bio::TestAbif): > NoMethodError: undefined method `match' for nil:NilClass > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e > ntry_data' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block > in get_directory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' > > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di > rectory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia > lize' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `new' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `setup' > > 8) Error: > test_to_biosequence(Bio::TestAbif): > NoMethodError: undefined method `match' for nil:NilClass > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e > ntry_data' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block > in get_directory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' > > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di > rectory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia > lize' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `new' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `setup' > > 9) Failure: > test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_ > command.rb:59]: > <"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was > <"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">. > > 10) Failure: > test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/ > test_command.rb:76]: > <"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was > <"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">. > > 11) Error: > test_simple_xml(Bio::TestPhyloXMLWriter): > Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-1116-m0djng/example_ > tree1.xml > C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure' > C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback' > C:/repositories/bioruby/lib/bio/command.rb:607:in `call' > C:/repositories/bioruby/lib/bio/command.rb:607:in `close!' > C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test > _passed' > C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea > rdown' > test/runner.rb:27:in `
' > > 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From p.j.a.cock at googlemail.com Mon Nov 21 04:42:45 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 21 Nov 2011 09:42:45 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Mon, Nov 21, 2011 at 8:09 AM, Naohisa Goto wrote: > Hi Peter, > > Sorry very late. > > On my Windows 7 (32-bit, Business or Enterprise) machines, > with Ruby 1.9.3-p0 downloaded from rubyinstaller.org, the 1), 2), and 3) > "Errno::EACCES: Permission denied" cannot be reproduced. > Instead, failure occur due to the change of command-line escaping in > Ruby 1.9, which would be the same as 9) and 10). > > The "Errno::EACCESS" might occurr when using other shell than cmd.exe > e.g. Cygwin's Bash, execution prohibition by security software, or by > access controll on NTFS. > > For 9) and 10): In Windows, command-line escaping is treated by each > software, and no "general" escaping way exists. This means the test is > bad for Windows. With Ruby 1.8.x, current BioRuby uses its internal > command-line string builder, but with Ruby 1.9.x, it uses Ruby's. > > 6), 7), and 8) may be due to text mode that is default file reading mode > when Ruby on windows and that ?may break things when reading binary > files. > > 11) may be the problem of removing a file before closing, as you said. > > Thanks, > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org Hi Goto-san, Hmm. Can you mark some of these as known failures under Windows, or skip those tests under Windows? Otherwise right now having a nightly build on Windows will always fail, and always send an error email. So It won't be helpful. Regards, Peter From ngoto at gen-info.osaka-u.ac.jp Wed Nov 23 01:34:21 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Wed, 23 Nov 2011 15:34:21 +0900 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> Hi, I've fixed all of the test failures/errors which are reproduced on my Windows machines. Now 0 failures 0 errors, with latest git version, on Windows 7 Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32). Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at biourby.org > On Mon, Nov 21, 2011 at 8:09 AM, Naohisa Goto > wrote: > > Hi Peter, > > > > Sorry very late. > > > > On my Windows 7 (32-bit, Business or Enterprise) machines, > > with Ruby 1.9.3-p0 downloaded from rubyinstaller.org, the 1), 2), and 3) > > "Errno::EACCES: Permission denied" cannot be reproduced. > > Instead, failure occur due to the change of command-line escaping in > > Ruby 1.9, which would be the same as 9) and 10). > > > > The "Errno::EACCESS" might occurr when using other shell than cmd.exe > > e.g. Cygwin's Bash, execution prohibition by security software, or by > > access controll on NTFS. > > > > For 9) and 10): In Windows, command-line escaping is treated by each > > software, and no "general" escaping way exists. This means the test is > > bad for Windows. With Ruby 1.8.x, current BioRuby uses its internal > > command-line string builder, but with Ruby 1.9.x, it uses Ruby's. > > > > 6), 7), and 8) may be due to text mode that is default file reading mode > > when Ruby on windows and that ?may break things when reading binary > > files. > > > > 11) may be the problem of removing a file before closing, as you said. > > > > Thanks, > > > > Naohisa Goto > > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > Hi Goto-san, > > Hmm. Can you mark some of these as known failures under > Windows, or skip those tests under Windows? > > Otherwise right now having a nightly build on Windows will always > fail, and always send an error email. So It won't be helpful. > > Regards, > > Peter Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From p.j.a.cock at googlemail.com Thu Nov 24 04:41:09 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 24 Nov 2011 09:41:09 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: 2011/11/23 Naohisa Goto : > Hi, > > I've fixed all of the test failures/errors which are reproduced on my > Windows machines. > > Now 0 failures 0 errors, with latest git version, on Windows 7 > Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32). Great. I ran the tests again on my machine, using commit d2d66f833d0b20647e8d761d2a240b99b206eaa8 and things have improved a lot - I'm only seeing some kind of permissions problem calling batch files now: Note my machine is Windows XP (32 bit), whereas you have Windows 7 Enterprise 32 bit. This may be important. I have the same version of Ruby (I think): C:\repositories\bioruby>ruby -v ruby 1.9.3p0 (2011-10-30) [i386-mingw32] C:\repositories\bioruby>ruby Test\runner.rb C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: ...........E.EEE.EEE.EE......................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ...................................................... Finished tests in 25.234052s, 144.8043 tests/s, 832.0503 assertions/s. 1) Error: test_call_command(Bio::FuncTestCommandCallMisc1): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call _command' 2) Error: test_call_command_open3(Bio::FuncTestCommandCallMisc1): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call _command_open3' Test/runner.rb:36:in `
' 3) Error: test_call_command_popen(Bio::FuncTestCommandCallMisc1): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call _command_popen' 4) Error: test_call_command(Bio::FuncTestCommandCallSimple): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call _command' 5) Error: test_call_command_open3(Bio::FuncTestCommandCallSimple): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call _command_open3' Test/runner.rb:36:in `
' 6) Error: test_call_command_popen(Bio::FuncTestCommandCallSimple): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call _command_popen' 7) Error: test_call_command(Bio::FuncTestCommandCallWithSpace): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call _command' 8) Error: test_call_command_open3(Bio::FuncTestCommandCallWithSpace): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call _command_open3' Test/runner.rb:36:in `
' 9) Error: test_call_command_popen(Bio::FuncTestCommandCallWithSpace): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call _command_popen' 3654 tests, 20996 assertions, 0 failures, 9 errors, 0 skips C:\repositories\bioruby> Thanks, Peter From ngoto at gen-info.osaka-u.ac.jp Thu Nov 24 23:50:35 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 25 Nov 2011 13:50:35 +0900 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111125135033.3B84.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, I think the failure may be due to the setting of permission for the file or the folder. Please look at the permisson for the file C:\repositories\bioruby\Test\data\command\echoarg2.bat By using explorer, right click the file and see "Property" -- "Security" and see details. Please confirm if the ACL "Traverse Folder/Execute File" is allowed and is not denyed. http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/acl_special_permissions.mspx?mfr=true The file permission can also be viewed by using cacls command on Windows. Please show the output of the command. C:\> cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat If the special ACL "FILE_EXECUTE" is shown as "DENY", its execution is denyed and thus the tests failed. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > 2011/11/23 Naohisa Goto : > > Hi, > > > > I've fixed all of the test failures/errors which are reproduced on my > > Windows machines. > > > > Now 0 failures 0 errors, with latest git version, on Windows 7 > > Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32). > > Great. I ran the tests again on my machine, using commit > d2d66f833d0b20647e8d761d2a240b99b206eaa8 and things > have improved a lot - I'm only seeing some kind of permissions > problem calling batch files now: > > Note my machine is Windows XP (32 bit), whereas you have > Windows 7 Enterprise 32 bit. This may be important. > > I have the same version of Ruby (I think): > > C:\repositories\bioruby>ruby -v > ruby 1.9.3p0 (2011-10-30) [i386-mingw32] > > C:\repositories\bioruby>ruby Test\runner.rb > C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will > be deprecated in the future, use String#encode instead. > Run options: > > # Running tests: > > ...........E.EEE.EEE.EE......................................................... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ...................................................... > > Finished tests in 25.234052s, 144.8043 tests/s, 832.0503 assertions/s. > > 1) Error: > test_call_command(Bio::FuncTestCommandCallMisc1): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call > _command' > > 2) Error: > test_call_command_open3(Bio::FuncTestCommandCallMisc1): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call > _command_open3' > Test/runner.rb:36:in `
' > > 3) Error: > test_call_command_popen(Bio::FuncTestCommandCallMisc1): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call > _command_popen' > > 4) Error: > test_call_command(Bio::FuncTestCommandCallSimple): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call > _command' > > 5) Error: > test_call_command_open3(Bio::FuncTestCommandCallSimple): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call > _command_open3' > Test/runner.rb:36:in `
' > > 6) Error: > test_call_command_popen(Bio::FuncTestCommandCallSimple): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call > _command_popen' > > 7) Error: > test_call_command(Bio::FuncTestCommandCallWithSpace): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call > _command' > > 8) Error: > test_call_command_open3(Bio::FuncTestCommandCallWithSpace): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call > _command_open3' > Test/runner.rb:36:in `
' > > 9) Error: > test_call_command_popen(Bio::FuncTestCommandCallWithSpace): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call > _command_popen' > > 3654 tests, 20996 assertions, 0 failures, 9 errors, 0 skips > > C:\repositories\bioruby> > > Thanks, > > Peter From p.j.a.cock at googlemail.com Fri Nov 25 06:25:35 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 25 Nov 2011 11:25:35 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: <20111125135033.3B84.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> <20111125135033.3B84.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Fri, Nov 25, 2011 at 4:50 AM, Naohisa Goto wrote: > Hi Peter, > > I think the failure may be due to the setting of permission for the file > or the folder. Yes, you are right :) > Please look at the permisson for the file > C:\repositories\bioruby\Test\data\command\echoarg2.bat > > By using explorer, right click the file and see "Property" -- "Security" > and see details. Please confirm if the ACL "Traverse Folder/Execute File" > is allowed and is not denyed. > http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/acl_special_permissions.mspx?mfr=true I see the following table, with two columns of tick boxes: Permissions for XXX: Allow? Deny? Full Control: Neither ticked Modify: Neither ticked Read and Execute: Neither ticked Read: Allow ticked Write: Allow ticked for me, not everyone or administrators Special Permissions: Greyed out Via the advanced settings button, it seems allow permissions are not inherited. > The file permission can also be viewed by using cacls command > on Windows. ?Please show the output of the command. > C:\> cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat > > If the special ACL "FILE_EXECUTE" is shown as "DENY", its execution is > denyed and thus the tests failed. > I've had to edit the line wrapping because otherwise it was unreadable, but there is no mention of FILE_EXECUTE at all. C:\repositories\bioruby>cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat C:\repositories\bioruby\Test\data\command\echoarg2.bat XXX:(special access:) STANDARD_RIGHTS_ALL DELETE READ_CONTROL WRITE_DAC WRITE_OWNER SYNCHRONIZE STANDARD_RIGHTS_REQUIRED FILE_GENERIC_READ FILE_GENERIC_WRITE FILE_READ_DATA FILE_WRITE_DATA FILE_APPEND_DATA FILE_READ_EA FILE_WRITE_EA FILE_READ_ATTRIBUTES FILE_WRITE_ATTRIBUTES BUILTIN\Administrators:(special access:) READ_CONTROL SYNCHRONIZE FILE_GENERIC_READ FILE_READ_DATA FILE_READ_EA FILE_READ_ATTRIBUTES Everyone:(special access:) READ_CONTROL SYNCHRONIZE FILE_GENERIC_READ FILE_READ_DATA FILE_READ_EA FILE_READ_ATTRIBUTES C:\repositories\bioruby> Via the cygwin's ls command the execute permission is not set for echoarg2.bat or echoarg2.sh The following seems to fix it, and the tests then pass on my machine: https://github.com/peterjc/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d https://github.com/bioruby/bioruby/pull/42 If you can commit that (or something similar), we can set this machine up as a buildslave :) Regards, Peter From p.j.a.cock at googlemail.com Fri Nov 25 09:32:50 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 25 Nov 2011 14:32:50 +0000 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) Message-ID: Hello all, There seems to have been a new test failure or regression in Linux 64 Ruby 1.9, Revision 48bd150a6180d59879872bd85dd95c7ddf1a19c0 passed, http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/22/steps/test/logs/stdio commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0 Author: Naohisa Goto Date: Tue Nov 22 17:32:23 2011 +0900 Test bug fix: fixed incomplete Windows platform detection. https://github.com/bioruby/bioruby/commit/48bd150a6180d59879872bd85dd95c7ddf1a19c0 Revision 688779e71a27e861fb01e07f816384561b8cfe45 failed, http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/23/steps/test/logs/stdio commit 688779e71a27e861fb01e07f816384561b8cfe45 Author: Naohisa Goto Date: Thu Nov 24 11:49:30 2011 +0900 Rakefile: new tasks: test-all to run all tests, etc. https://github.com/bioruby/bioruby/commit/688779e71a27e861fb01e07f816384561b8cfe45 1) Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) [/home/buildslave/BuildBot_BioRuby/lin1964/build/test/functional/bio/sequence/test_output_embl.rb:47]: Exception raised: <#>. I hope that helps and that someone can reproduce the failure locally. If need be I can try to bisect the failure here. Peter From tiagoantao at gmail.com Tue Nov 1 13:11:04 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 1 Nov 2011 13:11:04 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> Message-ID: Hi all, 2011/10/31 Peter Cock : > Let's work on the issues Tiago has identified (e.g. non-zero > return codes, option to disable network tests, etc) before > extending this to more build slaves, and to look at the gems. Peter summarized what needs to be done quite well. We currently have a bare bones server here: http://testing.open-bio.org/bioruby/ The issues are then: non-zero return code of ruby setup.rb test (on error) is necessary to detect errors automatically. disable network tests is convenient in order to avoid hammering online databases (especially if you have lots of builders). Later we can setup a weekly test for networked code. This might be more serious with biopython where we have lots of builders (see below). You will also have to provide slaves (ie machines that will actually run the actual tests). The buildmaster will only coordinate those slaves (and provide information on the outcomes). You will have to decide how many (and types of slaves that you have). I will describe the biopython situation so that you can use as a template. We support several operating systems with several architectures, so: Linux 32 bit Linux 64 bit Win XP Win 7 Win 7 64 bit OS X 10.6 This would mean at least 6 slaves (your desktop/laptop can be a slave, as long as you start buildbot slave either manually or automatically) In our case we support several Python versions 2.5, 2.6, 2.7, 3.1, 3.2, so this could mean up to 30 builders (5 operating systems/architectures, times 5 versions). I suppose with bioruby it will be much simpler... Have a look here: http://testing.open-bio.org/biopython/tgrid Finally, when things are running smoothly, you might want to take ownership of the buildbot server yourselves... Any issue/question do not hesitate to contact, Best regards, Tiago From p.j.a.cock at googlemail.com Tue Nov 1 14:19:32 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 1 Nov 2011 14:19:32 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> Message-ID: 2011/11/1 Tiago Ant?o : > Hi all, > > 2011/10/31 Peter Cock : >> Let's work on the issues Tiago has identified (e.g. non-zero >> return codes, option to disable network tests, etc) before >> extending this to more build slaves, and to look at the gems. > > Peter summarized what needs to be done quite well. We currently have a > bare bones server here: > http://testing.open-bio.org/bioruby/ > > The issues are then: > non-zero return code of > ruby setup.rb test > (on error) is necessary to detect errors automatically. > > disable network tests is convenient in order to avoid hammering online > databases (especially if you have lots of builders). Later we can > setup a weekly test for networked code. This might be more serious > with biopython where we have lots of builders (see below). > > You will also have to provide slaves (ie machines that will actually > run the actual tests). The buildmaster will only coordinate those > slaves (and provide information on the outcomes). You will have to > decide how many (and types of slaves that you have). I will describe > the biopython situation so that you can use as a template. > > We support several operating systems with several architectures, so: > Linux 32 bit > Linux 64 bit > Win XP > Win 7 > Win 7 64 bit > OS X 10.6 > > This would mean at least 6 slaves (your desktop/laptop can be a slave, > as long as you start buildbot slave either manually or automatically) Ideally the buildslave will be on and online all the time, so that it can be run on a nightly basis. Note we may want to choose this time carefully given I assume BioRuby will have some slaves in Europe, some in Japan, and maybe some in the USA/Canada? > In our case we support several Python versions 2.5, 2.6, 2.7, 3.1, > 3.2, so this could mean up to 30 builders (5 operating > systems/architectures, times 5 versions). I suppose with bioruby > it will be much simpler... Have a look here: > http://testing.open-bio.org/biopython/tgrid Note that one machine can cover several builds - we have one server doing tests for Python 2.5, 2.6, 2.7, 3.1, 3.2 and Jython (that makes 6 versions of Python, 7 if we start testing PyPy as well). For BioRuby I am expecting you to want to cover at least Ruby 1.8 and 1.9 as two separate targets. Do the minor versions matter enough to be tested separately? > Finally, when things are running smoothly, you might want to take > ownership of the buildbot server yourselves... > > Any issue/question do not hesitate to contact, Likewise I am happy to answer questions, and I hope to be able to offer some buildslaves for testing BioRuby (machines that already test Biopython). Regards, Peter From ngoto at gen-info.osaka-u.ac.jp Tue Nov 1 14:48:03 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 1 Nov 2011 23:48:03 +0900 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> Message-ID: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Hi Tiago and Peter, Thank you very much for setting up the buildbot server. > > 3. ruby setup.rb test is FAILING in two tests, but the script ends > > with exit code 0, thus not reporting an error. Would it be possible to > > end setup.rb test with a exit code noticing the error? Mode details > > here: > > http://testing.open-bio.org:8102/builders/Linux%2064%20-%20Ruby%201.8/builds/0/steps/compile/logs/stdio It seems this is a bug of setup.rb. However, the devlopment of setup.rb is now being stopped, and the bug would not be fixed. So, "ruby setup.rb test" to run test is going to be obsoleted. Please use alternative test running procedure. % ruby test/runner.rb or % testrb test/ or % rake test -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From tiagoantao at gmail.com Tue Nov 1 16:58:06 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 1 Nov 2011 16:58:06 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO wrote: > ?% ruby test/runner.rb I run with this and now it works fine: ie reports an error. The error is just that I do not have the XML parser installed. Please see: http://testing.open-bio.org/bioruby/waterfall Tiago From tiagoantao at gmail.com Tue Nov 1 20:21:31 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Tue, 1 Nov 2011 20:21:31 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: 2011/11/1 Tiago Ant?o : > On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO > wrote: >> ?% ruby test/runner.rb > > I run with this and now it works fine: ie reports an error. The error > is just that I do not have the XML parser installed. > Please see: > http://testing.open-bio.org/bioruby/waterfall Is anyone interested in receiving emails with errors? Should I send them to the list? At this initial stage I would recommend sending to a just few developers... There is now a potential real error: 1) Failure: test_convert(Bio::FuncTestTogoWSREST) [./test/functional/bio/io/test_togows.rb:120]: Exception raised: Class: Message: <"Invalid argument - connect(2)"> ---Backtrace--- /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' /usr/lib/ruby/1.8/net/http.rb:560:in `open' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' /usr/lib/ruby/1.8/net/http.rb:560:in `connect' /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' /usr/lib/ruby/1.8/net/http.rb:542:in `start' /usr/lib/ruby/1.8/net/http.rb:1035:in `request' /usr/lib/ruby/1.8/net/http.rb:845:in `post' ./lib/bio/command.rb:702:in `http_post_form' ./lib/bio/io/togows.rb:414:in `post_data' ./lib/bio/io/togows.rb:305:in `convert' ./test/functional/bio/io/test_togows.rb:121:in `test_convert' ./test/functional/bio/io/test_togows.rb:120:in `test_convert' From cjfields at illinois.edu Tue Nov 1 20:33:56 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 1 Nov 2011 20:33:56 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <410D958E-8A64-4B3B-8CBB-5AF6FA079CA4@illinois.edu> On Nov 1, 2011, at 3:21 PM, Tiago Ant?o wrote: > 2011/11/1 Tiago Ant?o : >> On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO >> wrote: >>> % ruby test/runner.rb >> >> I run with this and now it works fine: ie reports an error. The error >> is just that I do not have the XML parser installed. >> Please see: >> http://testing.open-bio.org/bioruby/waterfall > > Is anyone interested in receiving emails with errors? Should I send > them to the list? At this initial stage I would recommend sending to a > just few developers... BioPerl has a 'guts' list this would get sent to, not sure about BioRuby... chris From p.j.a.cock at googlemail.com Tue Nov 1 21:09:03 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 1 Nov 2011 21:09:03 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: 2011/11/1 Tiago Ant?o : > 2011/11/1 Tiago Ant?o : >> On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO >> wrote: >>> ?% ruby test/runner.rb >> >> I run with this and now it works fine: ie reports an error. The error >> is just that I do not have the XML parser installed. >> Please see: >> http://testing.open-bio.org/bioruby/waterfall Is the XML dependency optional? In Biopython we skip tests where a optional dependency is missing (i.e. report this but don't count it as a failure). > > Is anyone interested in receiving emails with errors? Should I send > them to the list? At this initial stage I would recommend sending to a > just few developers... > > There is now a potential real error: > ?1) Failure: > test_convert(Bio::FuncTestTogoWSREST) > [./test/functional/bio/io/test_togows.rb:120]: > Exception raised: > Class: > Message: <"Invalid argument - connect(2)"> > ---Backtrace--- > /usr/lib/ruby/1.8/net/http.rb:560:in `initialize' > /usr/lib/ruby/1.8/net/http.rb:560:in `open' > /usr/lib/ruby/1.8/net/http.rb:560:in `connect' > /usr/lib/ruby/1.8/timeout.rb:53:in `timeout' > /usr/lib/ruby/1.8/timeout.rb:101:in `timeout' > /usr/lib/ruby/1.8/net/http.rb:560:in `connect' > /usr/lib/ruby/1.8/net/http.rb:553:in `do_start' > /usr/lib/ruby/1.8/net/http.rb:542:in `start' > /usr/lib/ruby/1.8/net/http.rb:1035:in `request' > /usr/lib/ruby/1.8/net/http.rb:845:in `post' > ./lib/bio/command.rb:702:in `http_post_form' > ./lib/bio/io/togows.rb:414:in `post_data' > ./lib/bio/io/togows.rb:305:in `convert' > ./test/functional/bio/io/test_togows.rb:121:in `test_convert' > ./test/functional/bio/io/test_togows.rb:120:in `test_convert' That's a TogoWS test using the network to connect the Togo Web Service (I have some similar tests and code ready for Biopython now). I can't tell you if the problem is in BioRuby, the network, or TogoWS though. Peter From p.j.a.cock at googlemail.com Wed Nov 2 21:01:40 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 2 Nov 2011 21:01:40 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Tue, Nov 1, 2011 at 2:48 PM, Naohisa GOTO wrote: > Hi Tiago and Peter, > > Thank you very much for setting up the buildbot server. > No problem - Tiago has done almost all the work so far, so I'll join you in thanking Tiago (and Chris Dag. from the OBF on the server side). >> > 3. ruby setup.rb test is FAILING in two tests, but the script ends >> > with exit code 0, thus not reporting an error. Would it be possible to >> > end setup.rb test with a exit code noticing the error? Mode details >> > here: >> > http://testing.open-bio.org:8102/builders/Linux%2064%20-%20Ruby%201.8/builds/0/steps/compile/logs/stdio > > It seems this is a bug of setup.rb. However, the devlopment of > setup.rb is now being stopped, and the bug would not be fixed. > So, "ruby setup.rb test" to run test is going to be obsoleted. > Please use alternative test running procedure. > > ?% ruby test/runner.rb > or > ?% testrb test/ > or > ?% rake test > Tiago seems to have done that :) I have another suggestion, which is that the test suite print a tiny environment summary at the start (e.g. Ruby version and operating system information). We do this for Biopython and it has been useful sometimes (e.g. comparing test failures from slightly different platforms), but also helpful from end user error reports (when they copy and paste the test suite output for us). Have you decided which versions of Ruby should be tested? For example, do you just need two targets, 1.8.x and 1.9.x? Peter From tiagoantao at gmail.com Wed Nov 2 23:01:15 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Wed, 2 Nov 2011 23:01:15 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Wed, Nov 2, 2011 at 9:01 PM, Peter Cock wrote: > Have you decided which versions of Ruby should be tested? > For example, do you just need two targets, 1.8.x and 1.9.x? We also will need definitive slaves. I am currently using my personal machine, which is very unreliable. Another question: to who (persons and/or mailing lists) should I send warning messages? Between 0 and the number of builders (currently 1) per day. Tiago From pjotr.public14 at thebird.nl Thu Nov 3 06:18:23 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 07:18:23 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20111103061823.GA15531@thebird.nl> On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: > Have you decided which versions of Ruby should be tested? > For example, do you just need two targets, 1.8.x and 1.9.x? My feeling is that 1.9 is relevant for default testing. In the wild there may be versions running 1.8 - and if someone feels like it, they can set up the buildbot too. Right? It is more important to test plugins. Raoul and I will set that up, as soon as we grasp the infrastructure. Pj. From p.j.a.cock at googlemail.com Thu Nov 3 09:23:17 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 09:23:17 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103061823.GA15531@thebird.nl> References: <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: >> Have you decided which versions of Ruby should be tested? >> For example, do you just need two targets, 1.8.x and 1.9.x? > > My feeling is that 1.9 is relevant for default testing. In the wild > there may be versions running 1.8 - and if someone feels like it, > they can set up the buildbot too. Right? Yes, but we need to know the planned matrix to setup the server. So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? So that could be 8 targets. > It is more important to test plugins. Raoul and I will set that up, > as soon as we grasp the infrastructure. Right, we hear you. Essentially that will require knowing the commands to call. Right now we have (roughly - Tiago can correct me) the following to do an in-situ test (no installation): (1) Get BioRuby from github (usually the latest, but you can ask for a specific revision via the buildbot web interface) (2) Run: ruby test/runner.rb (or similar) If it possible to have Ruby 1.8 and 1.9 installed at the same time, is there a convention for calling them? I'd guess ruby1.8 and ruby1.9 if the same style as Python is used. Then we'd have two versions of the above: (1) Get BioRuby from github (2) Run: ruby1.8 test/runner.rb (or similar) or, (1) Get BioRuby from github (2) Run: ruby1.9 test/runner.rb (or similar) The server configuration tells it which "recipe" to call on which slaves, so if one machine only has Ruby 1.9, it will not be asked to test on Ruby 1.8. We may also need slight variants for Windows vs Linux vs Mac. So what we'll need is an extended recipe which also gets the appropriate gem versions for that revision, and tests them. This could be a shell script, but if given as a list of commands you can see the progress, output and success/failure of each on the buildbot web interface. Peter From pjotr.public14 at thebird.nl Thu Nov 3 10:37:12 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 11:37:12 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> Message-ID: <20111103103712.GB16931@thebird.nl> On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote: > On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: > > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: > >> Have you decided which versions of Ruby should be tested? > >> For example, do you just need two targets, 1.8.x and 1.9.x? > > > > My feeling is that 1.9 is relevant for default testing. In the wild > > there may be versions running 1.8 - and if someone feels like it, > > they can set up the buildbot too. Right? > > Yes, but we need to know the planned matrix to setup the server. > So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially > on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? > So that could be 8 targets. OK, sounds good. It makes sense, also for other languages, to have two versions of compiler or interpreter for testing. > > It is more important to test plugins. Raoul and I will set that up, > > as soon as we grasp the infrastructure. > > Right, we hear you. Essentially that will require knowing the > commands to call. Right now we have (roughly - Tiago can > correct me) the following to do an in-situ test (no installation): > (1) Get BioRuby from github (usually the latest, but you can > ask for a specific revision via the buildbot web interface) > (2) Run: ruby test/runner.rb (or similar) > > If it possible to have Ruby 1.8 and 1.9 installed at the same > time, is there a convention for calling them? I'd guess ruby1.8 > and ruby1.9 if the same style as Python is used. Then we'd > have two versions of the above: > > (1) Get BioRuby from github > (2) Run: ruby1.8 test/runner.rb (or similar) > > or, > > (1) Get BioRuby from github > (2) Run: ruby1.9 test/runner.rb (or similar) > > The server configuration tells it which "recipe" to call on > which slaves, so if one machine only has Ruby 1.9, it will > not be asked to test on Ruby 1.8. > > We may also need slight variants for Windows vs Linux > vs Mac. > > So what we'll need is an extended recipe which also gets the > appropriate gem versions for that revision, and tests them. > This could be a shell script, but if given as a list of commands > you can see the progress, output and success/failure of each > on the buildbot web interface. We don't have a protocol just yet. The important containers are bio-core, bio-core-ext and bio-biolinux. Each of these installs all important plugins. For testing you'd want a test of each *released* plugin on rubygems.org. The plugins to test are listed inside above containers - for example in https://github.com/helios/bioruby-core/blob/master/Rakefile and can also be queried on rubygems (REST interface). I do that to generate http://biogems.info/. The install of a released plugin is simple: gem install plugin installs the gem in cd ~/.gems/gems/plugin-0.7 and the tests should run with rake test Some dependencies may be needed at test time. These can (in principle) be run with cd ~/.gems/gems/plugin-0.7 bundle rake test Note1: all plugins should support 'rake test' - though now they don't. Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev Pj. From p.j.a.cock at googlemail.com Thu Nov 3 11:36:11 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 11:36:11 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103103712.GB16931@thebird.nl> References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 10:37 AM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote: >> On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: >> > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: >> >> Have you decided which versions of Ruby should be tested? >> >> For example, do you just need two targets, 1.8.x and 1.9.x? >> > >> > My feeling is that 1.9 is relevant for default testing. In the wild >> > there may be versions running 1.8 - and if someone feels like it, >> > they can set up the buildbot too. Right? >> >> Yes, but we need to know the planned matrix to setup the server. >> So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially >> on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? >> So that could be 8 targets. > > OK, sounds good. It makes sense, also for other languages, to have > two versions of compiler or interpreter for testing. OK (pending possible changes for plugins later, see below). >> > It is more important to test plugins. Raoul and I will set that up, >> > as soon as we grasp the infrastructure. >> >> Right, we hear you. Essentially that will require knowing the >> commands to call. Right now we have (roughly - Tiago can >> correct me) the following to do an in-situ test (no installation): > >> (1) Get BioRuby from github (usually the latest, but you can >> ask for a specific revision via the buildbot web interface) >> (2) Run: ruby test/runner.rb (or similar) >> >> If it possible to have Ruby 1.8 and 1.9 installed at the same >> time, is there a convention for calling them? I'd guess ruby1.8 >> and ruby1.9 if the same style as Python is used. Then we'd >> have two versions of the above: >> >> (1) Get BioRuby from github >> (2) Run: ruby1.8 test/runner.rb (or similar) >> >> or, >> >> (1) Get BioRuby from github >> (2) Run: ruby1.9 test/runner.rb (or similar) >> >> The server configuration tells it which "recipe" to call on >> which slaves, so if one machine only has Ruby 1.9, it will >> not be asked to test on Ruby 1.8. >> >> We may also need slight variants for Windows vs Linux >> vs Mac. Does such a convention exist in Ruby for explicitly calling Ruby 1.8 or 1.9? We can just require the aliases ruby1.8 and ruby1.9 as part of setting up a buildslave. >> So what we'll need is an extended recipe which also gets the >> appropriate gem versions for that revision, and tests them. >> This could be a shell script, but if given as a list of commands >> you can see the progress, output and success/failure of each >> on the buildbot web interface. > > We don't have a protocol just yet. The important containers are bio-core, > bio-core-ext and bio-biolinux. Each of these installs all important plugins. > > For testing you'd want a test of each *released* plugin on > rubygems.org. The plugins to test are listed inside above containers > - for example in > > ?https://github.com/helios/bioruby-core/blob/master/Rakefile > > and can also be queried on rubygems (REST interface). I do that to > generate http://biogems.info/. > > The install of a released plugin is simple: > > ?gem install plugin > > installs the gem in > > ?cd ~/.gems/gems/plugin-0.7 > > and the tests should run with > > ?rake test > > Some dependencies may be needed at test time. These can (in principle) > be run with > > ?cd ~/.gems/gems/plugin-0.7 > ?bundle > ?rake test > > Note1: all plugins should support 'rake test' - though now they don't. Is it possible to test the plugins *without* installing them? i.e. an in-situ test? Or, can we control where they are installed (i.e. a temp folder) and test them from there? The point is the buildslave may be running several tests at once, and while ideally it will be configured as a separate user account, we don't want it using anything outside the BuildSlave's folder (other than /tmp provided the usual precautions about name clashes are taken), > > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev > Maybe we'd want three targets (per OS) then?: BioRuby core only on Ruby 1.8.x BioRuby core only on Ruby 1.9.x BioRuby with plugins on Ruby 1.9.x Peter From pjotr.public14 at thebird.nl Thu Nov 3 13:17:21 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 14:17:21 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: <20111103131721.GA18555@thebird.nl> On Thu, Nov 03, 2011 at 11:36:11AM +0000, Peter Cock wrote: > Does such a convention exist in Ruby for explicitly calling > Ruby 1.8 or 1.9? We can just require the aliases ruby1.8 > and ruby1.9 as part of setting up a buildslave. There is no convention. But I think it is fine to have this convention for our purposes. Maybe we can use just ruby by default too? If it is not in the path, just ignore. > > Note1: all plugins should support 'rake test' - though now they don't. > > Is it possible to test the plugins *without* installing them? i.e. an > in-situ test? Or, can we control where they are installed (i.e. a temp > folder) and test them from there? The problem is that you need to fetch dependencies. This is automated in gem install. You could check out a git tree, but that is not linked to the actual stuff people install. I favour the latter. > The point is the buildslave may be running several tests at once, > and while ideally it will be configured as a separate user account, > we don't want it using anything outside the BuildSlave's folder > (other than /tmp provided the usual precautions about name > clashes are taken), 'gem install' will normally install in user space. What is the problem there? Also, you can tell it to use any folder. > > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev > > > > Maybe we'd want three targets (per OS) then?: > > BioRuby core only on Ruby 1.8.x > BioRuby core only on Ruby 1.9.x > BioRuby with plugins on Ruby 1.9.x Personally I don't see BioRuby as separate. It is simply another plugin (or gem). It is a nice one, since it is pure Ruby and has few dependencies. I would say: bio (the BioRuby gem) on ruby1.8 bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 and later If it is too difficult - we can create a structure ourselves. No worries. Pj. From p.j.a.cock at googlemail.com Thu Nov 3 14:19:49 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 14:19:49 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103131721.GA18555@thebird.nl> References: <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 1:17 PM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 11:36:11AM +0000, Peter Cock wrote: >> Does such a convention exist in Ruby for explicitly calling >> Ruby 1.8 or 1.9? We can just require the aliases ruby1.8 >> and ruby1.9 as part of setting up a buildslave. > > There is no convention. But I think it is fine to have this > convention for our purposes. Maybe we can use just ruby > by default too? If it is not in the path, just ignore. If any one buildslave only has Ruby 1.8 or Ruby 1.9, then sure - we can just call "ruby". The configuration of the buildbot on the server would know which machine was running Ruby 1.8 or 1.9 and record the results accordingly. However, it seems efficient to have some slaves testing under both Ruby 1.8 and 1.9 (assuming of course that is possible - can they co-exist?). >> > Note1: all plugins should support 'rake test' - though now they don't. >> >> Is it possible to test the plugins *without* installing them? i.e. an >> in-situ test? Or, can we control where they are installed (i.e. a temp >> folder) and test them from there? > > The problem is that you need to fetch dependencies. This is automated > in gem install. > > You could check out a git tree, but that is not linked to the actual > stuff people install. I favour the latter. > >> The point is the buildslave may be running several tests at once, >> and while ideally it will be configured as a separate user account, >> we don't want it using anything outside the BuildSlave's folder >> (other than /tmp provided the usual precautions about name >> clashes are taken), > > 'gem install' will normally install in user space. What is the problem > there? Also, you can tell it to use any folder. Ah - that sounds better. So we can tell it to install to: $HOME/$BUILDSLAVE/$CURRENTBUILD/gems or whatever. The point is that the buildbot creates a clean empty folder for each test. You start from a a clean git checkout, and put the downloaded and installed gems under this directory. >> > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev >> > >> >> Maybe we'd want three targets (per OS) then?: >> >> BioRuby core only on Ruby 1.8.x >> BioRuby core only on Ruby 1.9.x >> BioRuby with plugins on Ruby 1.9.x > > Personally I don't see BioRuby as separate. It is simply another > plugin (or gem). It is a nice one, since it is pure Ruby and has few > dependencies. I would say: > > bio (the BioRuby gem) on ruby1.8 > bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 and later > > If it is too difficult - we can create a structure ourselves. No > worries. I was thinking we can get the first two targets up and running quite quickly: * bio (the BioRuby gem) on ruby1.8 * bio (the BioRuby gem) on ruby1.9 And then work on the full set: * bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 with additional targets for ruby2.0 or whatever is next. But ultimately you guys get to decide of course. Peter From pjotr.public14 at thebird.nl Thu Nov 3 14:29:28 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 15:29:28 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> Message-ID: <20111103142928.GB20116@thebird.nl> On Thu, Nov 03, 2011 at 02:19:49PM +0000, Peter Cock wrote: > under both Ruby 1.8 and 1.9 (assuming of course that > is possible - can they co-exist?). That is no problem. Debian derived distros have it by default. You can also use rvm in user space. > Ah - that sounds better. So we can tell it to install to: > > $HOME/$BUILDSLAVE/$CURRENTBUILD/gems > > or whatever. The point is that the buildbot creates a clean empty > folder for each test. You start from a a clean git checkout, and > put the downloaded and installed gems under this directory. http://jbowes.wordpress.com/2008/05/13/installing-ruby-gems-in-your-home-directory/ > I was thinking we can get the first two targets up and running > quite quickly: > > * bio (the BioRuby gem) on ruby1.8 > * bio (the BioRuby gem) on ruby1.9 > > And then work on the full set: > > * bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 > > with additional targets for ruby2.0 or whatever is next. > But ultimately you guys get to decide of course. Sounds good to me. With the two targets configures, I am sure we can add the rest ourselves. I would also like to show the test results on http://biogems.info/ Pj. From p.j.a.cock at googlemail.com Thu Nov 3 15:15:12 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 15:15:12 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103142928.GB20116@thebird.nl> References: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> <20111103142928.GB20116@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 2:29 PM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 02:19:49PM +0000, Peter Cock wrote: >> under both Ruby 1.8 and 1.9 (assuming of course that >> is possible - can they co-exist?). > > That is no problem. Debian derived distros have it by default. You > can also use rvm in user space. How does Debian name the two Ruby binaries? >> I was thinking we can get the first two targets up and running >> quite quickly: >> >> * bio (the BioRuby gem) on ruby1.8 >> * bio (the BioRuby gem) on ruby1.9 >> >> And then work on the full set: >> >> * bio, and all plugins contained in bio-core, bio-core-ext on ruby1.9 >> >> with additional targets for ruby2.0 or whatever is next. >> But ultimately you guys get to decide of course. > > Sounds good to me. With the two targets configures, I am sure we > can add the rest ourselves. That sounds like a plan :-) > I would also like to show the test results on http://biogems.info/ > You can get an RSS feed from the buildbot, or something crude like an embedded frame. Would you want to narrow this down to test results on a per-plugin basis? That might be tricky. Peter From p.j.a.cock at googlemail.com Thu Nov 3 15:39:36 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 15:39:36 +0000 Subject: [BioRuby] Scheduled time for nightly buildbot? Message-ID: 2011/11/1 Peter Cock : > > Ideally the buildslave will be on and online all the time, so that it > can be run on a nightly basis. Note we may want to choose this > time carefully given I assume BioRuby will have some slaves in > Europe, some in Japan, and maybe some in the USA/Canada? > I suggest initially we run the nightly BioRuby tests at about 20:00 GMT/UTC, which is evening in Europe (after work) and 5:00 in Japan (before work). Does that suit everyone considering offering a machine to run as a buildslave? If not, we may have to have multiple tests scheduled on a rota system for machines in Europe, America and Asia (etc). That would be more complicated to administer though. Peter From pjotr.public14 at thebird.nl Thu Nov 3 16:02:55 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 17:02:55 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> <20111103131721.GA18555@thebird.nl> <20111103142928.GB20116@thebird.nl> Message-ID: <20111103160255.GC20889@thebird.nl> On Thu, Nov 03, 2011 at 03:15:12PM +0000, Peter Cock wrote: > How does Debian name the two Ruby binaries? ruby1.8 and ruby1.9.1 From tiagoantao at gmail.com Thu Nov 3 16:29:16 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 16:29:16 +0000 Subject: [BioRuby] Scheduled time for nightly buildbot? In-Reply-To: References: Message-ID: 2011/11/3 Peter Cock : > If not, we may have to have multiple tests scheduled on a rota > system for machines in Europe, America and Asia (etc). That > would be more complicated to administer though. This might not be such a bad idea as bioruby will be making network connections (to spread the load) -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From p.j.a.cock at googlemail.com Thu Nov 3 16:40:05 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 16:40:05 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard Message-ID: Dear all, I'd like to setup my Mac as a BioRuby buildslave for nightly unit tests. This currently runs Mac OS X 10.6 Snow Leopard which comes with Ruby 1.8.7 (possibly as part of XCode?) $ git clone https://github.com/bioruby/bioruby.git ... $ cd bioruby $ ruby test/runner.rb $ ruby test/runner.rb Loaded suite . Started .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FF............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Finished in 215.591513 seconds. 1) Failure: test_libxml(Bio::TestPhyloXMLWriter_Check_LibXML) [./test/unit/bio/db/test_phyloxml_writer.rb:31]: Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed. is not true. 2) Failure: test_libxml(Bio::TestPhyloXML_Check_LibXML) [./test/unit/bio/db/test_phyloxml.rb:29]: Error: libxml-ruby library is not present. Please install libxml-ruby library. It is needed for Bio::PhyloXML module. Unit test for PhyloXML will not be performed. is not true. 3640 tests, 21276 assertions, 2 failures, 0 errors I installed libxml-ruby with this command, $ gem install libxml-ruby WARNING: Installing to ~/.gem since /Library/Ruby/Gems/1.8 and /usr/bin aren't both writable. WARNING: You don't have /Users/pjcock/.gem/ruby/1.8/bin in your PATH, gem executables will not run. Building native extensions. This could take a while... Successfully installed libxml-ruby-2.2.2 1 gem installed Installing ri documentation for libxml-ruby-2.2.2... Installing RDoc documentation for libxml-ruby-2.2.2... Referring to the link from Pjotr, http://jbowes.wordpress.com/2008/05/13/installing-ruby-gems-in-your-home-directory/ $ export GEM_HOME=$HOME/gems $ export GEM_PATH=$HOME/gems:/usr/lib/ruby/gems/1.8/ $ export PATH=$PATH:$HOME/gems/bin $ gem install libxml-ruby Building native extensions. This could take a while... Successfully installed libxml-ruby-2.2.2 1 gem installed Installing ri documentation for libxml-ruby-2.2.2... Installing RDoc documentation for libxml-ruby-2.2.2... I tried the following test script: $ more dummy.rb require 'rubygems' require 'libxml' include LibXML puts "Using libxml version #{XML::LIBXML_VERSION}" $ ruby dummy.rb Using libxml version 2.7.3 So Ruby does seem to find the library... yet the test suite still fails the same way (in the same terminal window with the above environment variables present). I'm a little lost now - any suggestions please? Thanks, Peter From p.j.a.cock at googlemail.com Thu Nov 3 17:24:47 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 17:24:47 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: <20111103165529.GA21817@thebird.nl> References: <20111103165529.GA21817@thebird.nl> Message-ID: On Thu, Nov 3, 2011 at 4:55 PM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 04:40:05PM +0000, Peter Cock wrote: >> $ export GEM_HOME=$HOME/gems >> $ export GEM_PATH=$HOME/gems:/usr/lib/ruby/gems/1.8/ >> $ export PATH=$PATH:$HOME/gems/bin > > Are these available during the BioRuby test run? ruby1.8 is notorious > for not finding gems - make sure you see libxml in the path. ... Double checking, there were some inconsistencies between the paths on disk, and the environment variables copied from the webpage, e.g. $HOME/gems vs $HOME/.gems I tried again with: $ export GEM_HOME=$HOME/.gem $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ $ ruby test/runner.rb ... Same error. Can I / should I just install libxml-ruby at system level? How? Thanks, Peter From tiagoantao at gmail.com Thu Nov 3 17:37:24 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 17:37:24 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103103712.GB16931@thebird.nl> References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: I am slighthly confused with the gem stuff. Lets see if I got this correct 1. we test ruby1.8 git 2. we test ruby1.9.1 git 3. we test ruby1.9.1 gems So 3 types of tests correct? for 1.9.1. we do BOTH git and gems (which are separate things)? For gems we use gem install. I noticed that the install dir can be changed on gem install, this might be useful. What gems to test? I noticed the reference to the list and a REST interface to get the list. Can you be more detailed? Thanks On Thu, Nov 3, 2011 at 10:37 AM, Pjotr Prins wrote: > On Thu, Nov 03, 2011 at 09:23:17AM +0000, Peter Cock wrote: >> On Thu, Nov 3, 2011 at 6:18 AM, Pjotr Prins wrote: >> > On Wed, Nov 02, 2011 at 09:01:40PM +0000, Peter Cock wrote: >> >> Have you decided which versions of Ruby should be tested? >> >> For example, do you just need two targets, 1.8.x and 1.9.x? >> > >> > My feeling is that 1.9 is relevant for default testing. In the wild >> > there may be versions running 1.8 - and if someone feels like it, >> > they can set up the buildbot too. Right? >> >> Yes, but we need to know the planned matrix to setup the server. >> So both Ruby 1.8.x and Ruby 1.9.x as two targets then, potentially >> on the usual Windows 32 bit, Linux 32bit, Linux 64bit and Mac OS X? >> So that could be 8 targets. > > OK, sounds good. It makes sense, also for other languages, to have > two versions of compiler or interpreter for testing. > >> > It is more important to test plugins. Raoul and I will set that up, >> > as soon as we grasp the infrastructure. >> >> Right, we hear you. Essentially that will require knowing the >> commands to call. Right now we have (roughly - Tiago can >> correct me) the following to do an in-situ test (no installation): > >> (1) Get BioRuby from github (usually the latest, but you can >> ask for a specific revision via the buildbot web interface) >> (2) Run: ruby test/runner.rb (or similar) >> >> If it possible to have Ruby 1.8 and 1.9 installed at the same >> time, is there a convention for calling them? I'd guess ruby1.8 >> and ruby1.9 if the same style as Python is used. Then we'd >> have two versions of the above: >> >> (1) Get BioRuby from github >> (2) Run: ruby1.8 test/runner.rb (or similar) >> >> or, >> >> (1) Get BioRuby from github >> (2) Run: ruby1.9 test/runner.rb (or similar) >> >> The server configuration tells it which "recipe" to call on >> which slaves, so if one machine only has Ruby 1.9, it will >> not be asked to test on Ruby 1.8. >> >> We may also need slight variants for Windows vs Linux >> vs Mac. >> >> So what we'll need is an extended recipe which also gets the >> appropriate gem versions for that revision, and tests them. >> This could be a shell script, but if given as a list of commands >> you can see the progress, output and success/failure of each >> on the buildbot web interface. > > We don't have a protocol just yet. The important containers are bio-core, > bio-core-ext and bio-biolinux. Each of these installs all important plugins. > > For testing you'd want a test of each *released* plugin on > rubygems.org. The plugins to test are listed inside above containers > - for example in > > ?https://github.com/helios/bioruby-core/blob/master/Rakefile > > and can also be queried on rubygems (REST interface). I do that to > generate http://biogems.info/. > > The install of a released plugin is simple: > > ?gem install plugin > > installs the gem in > > ?cd ~/.gems/gems/plugin-0.7 > > and the tests should run with > > ?rake test > > Some dependencies may be needed at test time. These can (in principle) > be run with > > ?cd ~/.gems/gems/plugin-0.7 > ?bundle > ?rake test > > Note1: all plugins should support 'rake test' - though now they don't. > > Note2: plugins require ruby 1.9.x - on Debian install ruby-1.9.1-dev > > Pj. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From p.j.a.cock at googlemail.com Thu Nov 3 17:40:28 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 17:40:28 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: 2011/11/3 Tiago Ant?o : > I am slighthly confused with the gem stuff. Lets see if I got this correct > > 1. we test ruby1.8 git > 2. we test ruby1.9.1 git > 3. we test ruby1.9.1 gems > > So 3 types of tests correct? for 1.9.1. we do BOTH git and gems > (which are separate things)? Essentially. As I understand it, the gem/plugins are BioRuby extras, which use or add to BioRuby - see also http://www.biogems.info/ But let's get the basics working first (testing the core of BioRuby under Ruby 1.8 and 1.9 on a range of OS platforms). Peter From tiagoantao at gmail.com Thu Nov 3 17:43:56 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 17:43:56 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> <20111103061823.GA15531@thebird.nl> <20111103103712.GB16931@thebird.nl> Message-ID: 2011/11/3 Peter Cock : > But let's get the basics working first (testing the core of BioRuby > under Ruby 1.8 and 1.9 on a range of OS platforms). For testing purposes I will send a few error messages to the bioruby list to warm up. Should be at most a couple. Tiago From ngoto at gen-info.osaka-u.ac.jp Thu Nov 3 18:22:57 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 04 Nov 2011 03:22:57 +0900 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111103103712.GB16931@thebird.nl> Message-ID: <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> > 2. we test ruby1.9.1 git > 3. we test ruby1.9.1 gems Please use Ruby 1.9.3, latest stable release. Ruby 1.9.1 is declared as almost dead, and no security fix will be provided after Jan 31, 2012 JST. http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-core/40523 -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Thu Nov 3 18:30:21 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 19:30:21 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111103103712.GB16931@thebird.nl> <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111103183021.GE22715@thebird.nl> With Debian, ruby1.9.1 actually represents the latest and greatest :). The numbering scheme is kinda weird. On Fri, Nov 04, 2011 at 03:22:57AM +0900, Naohisa Goto wrote: > > 2. we test ruby1.9.1 git > > 3. we test ruby1.9.1 gems > > Please use Ruby 1.9.3, latest stable release. > Ruby 1.9.1 is declared as almost dead, and no security fix will be > provided after Jan 31, 2012 JST. > http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-core/40523 > > -- > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > From ngoto at gen-info.osaka-u.ac.jp Thu Nov 3 18:34:02 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 04 Nov 2011 03:34:02 +0900 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: References: <20111103165529.GA21817@thebird.nl> Message-ID: <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > $ export GEM_HOME=$HOME/.gem > $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems > $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ > $ ruby test/runner.rb In Ruby 1.8, Rubygems is an optional software and it is not loaded by default. Please try $ ruby -rubygems test/runner.rb or set RUBYOPT environment variable $ export RUBYOPT=-rubygems After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed by using Rubygems are ready by default without -rubygems. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From p.j.a.cock at googlemail.com Thu Nov 3 19:00:38 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 19:00:38 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111103165529.GA21817@thebird.nl> <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Thu, Nov 3, 2011 at 6:34 PM, Naohisa Goto wrote: > Hi Peter, > >> $ export GEM_HOME=$HOME/.gem >> $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems >> $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ >> $ ruby test/runner.rb > > In Ruby 1.8, Rubygems is an optional software and it is not loaded by > default. Please try > ?$ ruby -rubygems test/runner.rb > or set RUBYOPT environment variable > ?$ export RUBYOPT=-rubygems > > After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed > by using Rubygems are ready by default without -rubygems. That worked - thank you - we should use this for the buildslaves on Ruby 1.8 then, $ ruby -rubygems test/runner.rb Loaded suite . Started ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Finished in 259.549581 seconds. 3704 tests, 21456 assertions, 0 failures, 0 errors Peter From pjotr.public14 at thebird.nl Thu Nov 3 19:16:46 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 3 Nov 2011 20:16:46 +0100 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: References: <20111103165529.GA21817@thebird.nl> <20111104033402.20E4.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111103191646.GA23293@thebird.nl> Way to go! On Thu, Nov 03, 2011 at 07:00:38PM +0000, Peter Cock wrote: > On Thu, Nov 3, 2011 at 6:34 PM, Naohisa Goto > wrote: > > Hi Peter, > > > >> $ export GEM_HOME=$HOME/.gem > >> $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems > >> $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ > >> $ ruby test/runner.rb > > > > In Ruby 1.8, Rubygems is an optional software and it is not loaded by > > default. Please try > > ?$ ruby -rubygems test/runner.rb > > or set RUBYOPT environment variable > > ?$ export RUBYOPT=-rubygems > > > > After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed > > by using Rubygems are ready by default without -rubygems. > > That worked - thank you - we should use this for the buildslaves on > Ruby 1.8 then, > > $ ruby -rubygems test/runner.rb > Loaded suite . > Started > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... > Finished in 259.549581 seconds. > > 3704 tests, 21456 assertions, 0 failures, 0 errors > > > Peter > From bonnal at ingm.org Thu Nov 3 19:15:38 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 03 Nov 2011 20:15:38 +0100 Subject: [BioRuby] =?iso-8859-1?q?Missing_libxml-ruby_and_unit_tests_on_Ma?= =?iso-8859-1?q?c_OS_X_Snow=09Leopard?= In-Reply-To: Message-ID: <20111103191538.8492f8d9@mail.ingm.it> Hi guys, this is a great work! I would strongly suggest to use rvm to install multiple instances of ruby. As I see in a old email, I would say that plugins must be 1.9 compliant I don't care about 1.8. About JRuby please take care that it's default interpreter is v1.8 you have to set up by hand to use v1.9 http://beginrescueend.com/interpreters/jruby/ I must check this project and see if it works https://rubygems.org/gems/rubygems-test I'll try to be more active in coming days. I think I could provide a virtual machine as mirror, in the near future. _____ From: Peter Cock [mailto:p.j.a.cock at googlemail.com] To: Naohisa Goto [mailto:ngoto at gen-info.osaka-u.ac.jp] Cc: BioRuby ML [mailto:bioruby at lists.open-bio.org] Sent: Thu, 03 Nov 2011 20:00:38 +0100 Subject: Re: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard On Thu, Nov 3, 2011 at 6:34 PM, Naohisa Goto wrote: > Hi Peter, > >> $ export GEM_HOME=$HOME/.gem >> $ export $HOME/.gem:$HOME/.gem/ruby/1.8/gems >> $ export PATH=$PATH:$HOME/.gem/ruby/1.8/gems/:$HOME/.gem/ruby/1.8/gems/libxml-ruby-2.2.2/ext/libxml/ >> $ ruby test/runner.rb > > In Ruby 1.8, Rubygems is an optional software and it is not loaded by > default. Please try > $ ruby -rubygems test/runner.rb > or set RUBYOPT environment variable > $ export RUBYOPT=-rubygems > > After Ruby 1.9, Rubygems is bundled within Ruby and libraries installed > by using Rubygems are ready by default without -rubygems. That worked - thank you - we should use this for the buildslaves on Ruby 1.8 then, $ ruby -rubygems test/runner.rb Loaded suite . Started ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Finished in 259.549581 seconds. 3704 tests, 21456 assertions, 0 failures, 0 errors Peter _______________________________________________ BioRuby Project - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Thu Nov 3 19:26:32 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 3 Nov 2011 19:26:32 +0000 Subject: [BioRuby] Missing libxml-ruby and unit tests on Mac OS X Snow Leopard In-Reply-To: <20111103191538.8492f8d9@mail.ingm.it> References: <20111103191538.8492f8d9@mail.ingm.it> Message-ID: On Thu, Nov 3, 2011 at 7:15 PM, Raoul Bonnal wrote: > Hi guys, this is a great work! > I would strongly suggest to use rvm to install multiple instances of ruby. Initially I will use whatever Ruby comes with my systems or their default package. That seems simplest - and a realistic test case. For a multi-ruby test slave I'm sure you guys know best. > As I see in a old email, I would say that plugins must be 1.9 compliant I > don't care about 1.8. Pjotr agreed, but initially we're not going to test any of the biogem plugins. > About JRuby please take care that it's default interpreter is v1.8 you have > to set up by hand to use v1.9 http://beginrescueend.com/interpreters/jruby/ > > I must check this project and see if it works > https://rubygems.org/gems/rubygems-test > > I'll try to be more active in coming days. > I think I could provide a virtual machine as mirror, in the near future. So should we add JRuby v1.8 and JRuby v1.9 to the test matrix? Peter From tiagoantao at gmail.com Thu Nov 3 22:09:03 2011 From: tiagoantao at gmail.com (=?ISO-8859-1?Q?Tiago_Ant=E3o?=) Date: Thu, 3 Nov 2011 22:09:03 +0000 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: <20111103183021.GE22715@thebird.nl> References: <20111103103712.GB16931@thebird.nl> <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> <20111103183021.GE22715@thebird.nl> Message-ID: Hi, I had a silly bug with mail sending. But a barebones server is now working. it includes ruby 1.8 and 1.9.1 (Debian/Ubuntu). http://testing.open-bio.org/bioruby Honestly I had to read all the ongoing emails superficially, because I was chasing this silly bug. In my view now we have to: 1. setup slaves 2. give some of you the password for the admin web interface 3. get you an area on the testing machine so that you get familiarized with buildbot. We, of course, will support you during the first times 4. Think about gems. Tiago On Thu, Nov 3, 2011 at 6:30 PM, Pjotr Prins wrote: > With Debian, ruby1.9.1 actually represents the latest and greatest > :). The numbering scheme is kinda weird. > > On Fri, Nov 04, 2011 at 03:22:57AM +0900, Naohisa Goto wrote: >> > 2. we test ruby1.9.1 git >> > 3. we test ruby1.9.1 gems >> >> Please use Ruby 1.9.3, latest stable release. >> Ruby 1.9.1 is declared as almost dead, and no security fix will be >> provided after Jan 31, 2012 JST. >> http://blade.nagaokaut.ac.jp/cgi-bin/scat.rb/ruby/ruby-core/40523 >> >> -- >> Naohisa Goto >> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org >> > -- "If you want to get laid, go to college.? If you want an education, go to the library." - Frank Zappa From ngoto at gen-info.osaka-u.ac.jp Fri Nov 4 06:51:17 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Fri, 4 Nov 2011 15:51:17 +0900 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <4EAEA028.1090906@bioteam.net> <4EAEA4D6.7090805@sonsorol.org> <4EAEA6FA.3070100@bioteam.net> <4EAEA99C.8020906@sonsorol.org> <7D5B084D-7592-422B-90CA-38BA310F2D92@illinois.edu> <20111101144804.446EC1CBC3FE@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20111104065117.D94F01CBC479@idnmail.gen-info.osaka-u.ac.jp> Hi, On Wed, 2 Nov 2011 21:01:40 +0000 Peter Cock wrote: > I have another suggestion, which is that the test suite print > a tiny environment summary at the start (e.g. Ruby version > and operating system information). Since Ruby 1.9.3 (or after svn trunk r33205), the default test runner in Ruby prints this message at the end of all tests, e.g. 3640 tests, 21267 assertions, 2 failures, 4 errors, 0 skips ruby -v: ruby 2.0.0dev (2011-11-01) [x86_64-linux] I think this is enough. For older Ruby versions, please put a line "ruby -v" in the shell script. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Fri Nov 4 07:14:30 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 4 Nov 2011 08:14:30 +0100 Subject: [BioRuby] [Open-bio Board] Buildbot on testing.open-bio.org In-Reply-To: References: <20111103103712.GB16931@thebird.nl> <20111104032256.20E1.EEF6E030@gen-info.osaka-u.ac.jp> <20111103183021.GE22715@thebird.nl> Message-ID: <20111104071430.GA25058@thebird.nl> On Thu, Nov 03, 2011 at 10:09:03PM +0000, Tiago Ant?o wrote: > I had a silly bug with mail sending. But a barebones server is now > working. it includes ruby 1.8 and 1.9.1 (Debian/Ubuntu). > http://testing.open-bio.org/bioruby > > Honestly I had to read all the ongoing emails superficially, because I > was chasing this silly bug. > > In my view now we have to: > 1. setup slaves > 2. give some of you the password for the admin web interface > 3. get you an area on the testing machine so that you get familiarized > with buildbot. We, of course, will support you during the first times > 4. Think about gems. Excellent stuff. I can add slaves for Debian stable and testing on 64 and 32 bit (interesting to see BioRuby-64 fails on SOAP/WSDL). I propose Naohisa, Raoul and myself to get access to buildbot, so we can maintain and develop the build/integration tests for BioRuby and plugins. This is a big step forward for the Bio* projects, in my opinion. Pj. From p.j.a.cock at googlemail.com Fri Nov 4 15:38:45 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 15:38:45 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 Message-ID: Dear all, I plan to setup one of our servers as a BioRuby buildslave, but it is running CentOS 5.4 which comes with Ruby 1.8.5, and that is too old to use for BioRuby. So, I am installing Ruby 1.9 under the home directory instead, and using that. However, there is a problem with libyaml that I need help with. Note that I have a lot of development tools and libraries already installed (e.g. git), so I'm not mentioning them here - during the configure step nothing seemed to be missing, lucky for me. I did apparently need to install libyaml, $ sudo yum install libyaml $ sudo yum install libyaml-devel This gave 0.1.3-1.el5.rf -------------------------------------------- Step one, download latest stable Ruby 1.9.x and uncompress it, $ cd ~/Downloads $ wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p0.tar.gz $ tar -zxvf ruby-1.9.3-p0.tar.gz $ cd ruby-1.9.3-p0 -------------------------------------------- Step two, compile Ruby, test it, install it Note I tried passing -prefix and --prefix to configure, but it didn't accept it - use prefix with no minus at all, $ ./configure prefix=$HOME $ make $ make test $ make install -------------------------------------------- Step Three, check it Note I have already configured $HOME/bin to be on my $PATH $ which ruby ~/bin/ruby $ ruby -v ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux] $ which gem ~/bin/gem $ gem --version /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': It seems your ruby installation is missing psych (for YAML output). To eliminate this warning, please install libyaml and reinstall your ruby. 1.8.11 Why isn't Ruby finding libyaml? It is installed at system level via yum. Thanks, Peter -------------------------------------------- I went ahead and tried BioRuby, which told me to install libxml-ruby which I did, so I think it is just the libyaml problem to solve.... $ gem install libxml-ruby /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': It seems your ruby installation is missing psych (for YAML output). To eliminate this warning, please install libyaml and reinstall your ruby. Building native extensions. This could take a while... Successfully installed libxml-ruby-2.2.2 1 gem installed Installing ri documentation for libxml-ruby-2.2.2... Installing RDoc documentation for libxml-ruby-2.2.2... From francesco.strozzi at gmail.com Fri Nov 4 15:44:32 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 4 Nov 2011 16:44:32 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: Hi Peter, first of all huge thanks for the work you guys are doing with the automated test! I strongly suggested you to use RVM http://beginrescueend.com/ to compile and install many different versions of Ruby in the home directory or even system wide. Also RVM takes care of Ruby compiling from source and if you have the required libraries it should link them automatically during the installation process. Cheers, Francesco On Fri, Nov 4, 2011 at 16:38, Peter Cock wrote: > Dear all, > > I plan to setup one of our servers as a BioRuby buildslave, but it is > running CentOS 5.4 which comes with Ruby 1.8.5, and that is too old > to use for BioRuby. So, I am installing Ruby 1.9 under the home > directory instead, and using that. However, there is a problem with > libyaml that I need help with. > > Note that I have a lot of development tools and libraries already > installed (e.g. git), so I'm not mentioning them here - during the > configure step nothing seemed to be missing, lucky for me. > > I did apparently need to install libyaml, > > $ sudo yum install libyaml > $ sudo yum install libyaml-devel > > This gave 0.1.3-1.el5.rf > > -------------------------------------------- > > Step one, download latest stable Ruby 1.9.x and uncompress it, > > $ cd ~/Downloads > $ wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p0.tar.gz > $ tar -zxvf ruby-1.9.3-p0.tar.gz > $ cd ruby-1.9.3-p0 > > -------------------------------------------- > > Step two, compile Ruby, test it, install it > > Note I tried passing -prefix and --prefix to configure, but it didn't > accept it - use prefix with no minus at all, > > $ ./configure prefix=$HOME > $ make > $ make test > $ make install > > -------------------------------------------- > > Step Three, check it > > Note I have already configured $HOME/bin to be on my $PATH > > $ which ruby > ~/bin/ruby > $ ruby -v > ruby 1.9.3p0 (2011-10-30 revision 33570) [x86_64-linux] > > $ which gem > ~/bin/gem > $ gem --version > /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': > It seems your ruby installation is missing psych (for YAML output). > To eliminate this warning, please install libyaml and reinstall your ruby. > 1.8.11 > > Why isn't Ruby finding libyaml? It is installed at system level via yum. > > Thanks, > > Peter > > -------------------------------------------- > > I went ahead and tried BioRuby, which told me to install libxml-ruby > which I did, so I think it is just the libyaml problem to solve.... > > $ gem install libxml-ruby > /home/buildslave/lib/ruby/1.9.1/yaml.rb:56:in `': > It seems your ruby installation is missing psych (for YAML output). > To eliminate this warning, please install libyaml and reinstall your ruby. > Building native extensions. This could take a while... > Successfully installed libxml-ruby-2.2.2 > 1 gem installed > Installing ri documentation for libxml-ruby-2.2.2... > Installing RDoc documentation for libxml-ruby-2.2.2... > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From p.j.a.cock at googlemail.com Fri Nov 4 15:54:23 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 15:54:23 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 3:44 PM, Francesco Strozzi wrote: > Hi Peter, > first of all huge thanks for the work you guys are doing with the automated > test! > I strongly suggested you to use RVM?http://beginrescueend.com/ to compile > and install many different versions of Ruby in the home directory or even > system wide. Also RVM takes care of Ruby compiling from source and if you > have the required libraries it should link them automatically during the > installation process. > Cheers, > Francesco Hi Francesco, There is surely value in having a mixture of setups for the buildslaves? So certainly some should use RVM, but it seems wise to have others using a more old fashioned installation? Just my perspective from the outside. For this particular machine, I wasn't planning multiple installations of ruby, just Ruby 1.9.x only. I'll leave setting up and looking after a multi-target BioRuby buildslave to you guys ;) The Ruby website seemed to suggest going with the source code installation for me: "Installing from the source code is a great solution for when you are comfortable enough with your platform and perhaps need specific settings for your environment. It?s also a good solution in the event that there are no other premade packages for your platform." Well there are Ruby 1.8 packages for CentOS 5.4 but that's too old. Any ideas on the libyaml problem? Peter From francesco.strozzi at gmail.com Fri Nov 4 16:07:00 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 4 Nov 2011 17:07:00 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: Try to install libyaml from source, here it seems they have faced the same problem: http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-libyaml-on-centos/ Cheers, Francesco On Fri, Nov 4, 2011 at 16:54, Peter Cock wrote: > On Fri, Nov 4, 2011 at 3:44 PM, Francesco Strozzi > wrote: > > Hi Peter, > > first of all huge thanks for the work you guys are doing with the > automated > > test! > > I strongly suggested you to use RVM http://beginrescueend.com/ to > compile > > and install many different versions of Ruby in the home directory or even > > system wide. Also RVM takes care of Ruby compiling from source and if you > > have the required libraries it should link them automatically during the > > installation process. > > Cheers, > > Francesco > > Hi Francesco, > > There is surely value in having a mixture of setups for the buildslaves? > So certainly some should use RVM, but it seems wise to have others > using a more old fashioned installation? Just my perspective from the > outside. > > For this particular machine, I wasn't planning multiple installations of > ruby, just Ruby 1.9.x only. I'll leave setting up and looking after a > multi-target BioRuby buildslave to you guys ;) > > The Ruby website seemed to suggest going with the source code > installation for me: > > "Installing from the source code is a great solution for when you are > comfortable enough with your platform and perhaps need specific > settings for your environment. It?s also a good solution in the event > that there are no other premade packages for your platform." > > Well there are Ruby 1.8 packages for CentOS 5.4 but that's too old. > > Any ideas on the libyaml problem? > > Peter > -- Francesco From p.j.a.cock at googlemail.com Fri Nov 4 16:34:41 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 16:34:41 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 4:07 PM, Francesco Strozzi wrote: > Try to install libyaml from source, here it seems they have faced the same > problem: > http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-libyaml-on-centos/ > Cheers, > Francesco That didn't seem to work, $ sudo yum erase libyaml-devel $ sudo yum erase libyaml then: $ cd ~/Downloads $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz $ tar -xzvf yaml-0.1.4.tar.gz $ cd yaml-0.1.4 $ ./configure --prefix=$HOME $ make $ make check $ make install Then back to reinstall Ruby as before. Maybe there is a problem in the configure script, or I need to tell it to look for libyaml under $HOME. Peter From francesco.strozzi at gmail.com Fri Nov 4 16:41:00 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 4 Nov 2011 17:41:00 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: Yes maybe try to use --with-opt-dir=path/to/libyaml in configure. Hope it helps in resolving this issue.... Francesco On Fri, Nov 4, 2011 at 17:34, Peter Cock wrote: > On Fri, Nov 4, 2011 at 4:07 PM, Francesco Strozzi > wrote: > > Try to install libyaml from source, here it seems they have faced the > same > > problem: > > > http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-libyaml-on-centos/ > > Cheers, > > Francesco > > That didn't seem to work, > > $ sudo yum erase libyaml-devel > $ sudo yum erase libyaml > > then: > > $ cd ~/Downloads > $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz > $ tar -xzvf yaml-0.1.4.tar.gz > $ cd yaml-0.1.4 > $ ./configure --prefix=$HOME > $ make > $ make check > $ make install > > Then back to reinstall Ruby as before. > > Maybe there is a problem in the configure script, or I need > to tell it to look for libyaml under $HOME. > > Peter > -- Francesco From bonnal at ingm.org Fri Nov 4 16:44:01 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 04 Nov 2011 17:44:01 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: Message-ID: Hi Peter, CentOS 5.4 seems to be very old the lates is 5.7 and I would say it has very old packages. 1 Day ago I installed sqlite3 and the default version in 5.7 was too old as well, it's odd but I don't think CentOS is the right distro for these stuffs. This is what I did to update sqlite " I had an old sqlite package installed on my CentOS box and sqlite3-ruby wouldnt install without atleast sqlite 3.6.16 So for installing from source wget http://www.sqlite.org/sqlite-autoconf-3070500.tar.gz tar xvzf sqlite-autoconf-3070500.tar.gz cd sqlite-autoconf-3070500 ./configure make sudo make install *Modifica del percorso di ricerca delle librerie: - create file /etc/ld.conf.d/aaa.conf - add row: /usr/local/lib - ldconf (per ricaricare i percorsi di ricerca delle librerie) Now you also need to install the sqlite-devel packages, that is a yum install so sudo yum install sqlite-devel To install the gem sudo gem install sqlite3-ruby Probably the best thing to do is to help Peter in setting up a VM with a pre installed Ruby environment, what about using CloudBioLinux as base distro for testing ? On 04/11/11 17.34, "Peter Cock" wrote: > On Fri, Nov 4, 2011 at 4:07 PM, Francesco Strozzi > wrote: >> Try to install libyaml from source, here it seems they have faced the same >> problem: >> http://collectiveidea.com/blog/archives/2011/10/31/install-ruby-193-with-liby >> aml-on-centos/ >> Cheers, >> Francesco > > That didn't seem to work, > > $ sudo yum erase libyaml-devel > $ sudo yum erase libyaml > > then: > > $ cd ~/Downloads > $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz > $ tar -xzvf yaml-0.1.4.tar.gz > $ cd yaml-0.1.4 > $ ./configure --prefix=$HOME > $ make > $ make check > $ make install > > Then back to reinstall Ruby as before. > > Maybe there is a problem in the configure script, or I need > to tell it to look for libyaml under $HOME. > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Fri Nov 4 16:48:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 16:48:18 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 4:44 PM, Raoul Bonnal wrote: > Hi Peter, CentOS 5.4 seems to be very old the lates is 5.7 and I would say > it has very old packages. I agree that CenOS 5.4 is very old, but we're stuck with it I'm afraid :( > Probably the best thing to do is to help Peter in setting up a VM with a pre > installed Ruby environment, what about using CloudBioLinux as base distro > for testing ? As I've said before, having (at least one) CloudBioLinux installation as a buildslave is a wonderful idea. But one of my aims in having a pool of buildslaves is to cover as many likely end user configurations as possible. So I think is it sensible to include BioRuby and Ruby installed from source on an otherwise solid/old Linux distribution. Peter From p.j.a.cock at googlemail.com Fri Nov 4 17:14:01 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 4 Nov 2011 17:14:01 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: On Fri, Nov 4, 2011 at 4:41 PM, Francesco Strozzi wrote: > Yes maybe try to use --with-opt-dir=path/to/libyaml in configure. Hope it > helps in resolving this issue.... > Francesco $ ./configure prefix=$HOME --with-opt-dir=$HOME/lib ... $ make ... configuring objspace configuring openssl Failed to configure openssl. It will not be installed. configuring pathname configuring psych yaml.h is missing. Please install libyaml. Failed to configure psych. It will not be installed. configuring pty ... Clues! But quite what is going wrong any why configure failed to complain is a puzzle. I came up with a plan B, installing ruby-1.9.2-p290.tar.gz instead. This worked, and I could run the BioRuby test suite: $ ruby test/runner.rb Loaded suite test/runner Started .....................................................................................EEEE............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Finished in 86.123565 seconds. 1) Error: test_log(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 2) Error: test_set_log(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 3) Error: test_set_wsdl(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 4) Error: test_wsdl(Bio::FuncTestSOAPWSDL): NameError: uninitialized constant Bio::SOAPWSDL::SOAP /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:63:in `create_driver' /home/buildslave/repositories/bioruby/lib/bio/io/soapwsdl.rb:57:in `initialize' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `new' /home/buildslave/repositories/bioruby/test/functional/bio/io/test_soapwsdl.rb:26:in `setup' 3704 tests, 21447 assertions, 0 failures, 4 errors, 0 skips Test run options: --seed 21073 Anyone care to comment on this NameError? Peter From ngoto at gen-info.osaka-u.ac.jp Sat Nov 5 12:10:57 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sat, 05 Nov 2011 21:10:57 +0900 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > Note I tried passing -prefix and --prefix to configure, but it didn't > accept it - use prefix with no minus at all, This seems to be very strange. I'm afraid if the machine might have serious trouble. > $ cd ~/Downloads > $ wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz > $ tar -xzvf yaml-0.1.4.tar.gz > $ cd yaml-0.1.4 > $ ./configure --prefix=$HOME > $ make > $ make check > $ make install The above process seems completely right. In addition, install libffi is recommended. $ cd ~/Downloads $ wget ftp://sourceware.org/pub/libffi/libffi-3.0.10.tar.gz $ tar zxvf libffi-3.0.10.tar.gz $ cd libffi-3.0.10 $ ./configure --prefix=$HOME $ make $ make check $ make install "yum install openssl-devel" is also strongly recommended. And then, configureing Ruby. For using libraries installed other than system-wide directory, additional options to specify paths of C header files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. $ tar zxvf ruby-1.9.3-p0.tar.gz $ cd ruby-1.9.3-p0 $ ./configure --prefix=$HOME \ CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" $ make $ make check $ make install If you think the gcc in CentOS 5.4 is buggy, adding optflags="-O2" to supress optimize level is suggested. During make check, few error would be happened, due to incomplete IPv6 network settings, kernel and glibc bug, older libraries bug, etc. FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully installed ruby-1.9.3-p0 in my home directory without root privilege. RedHat 4.6 uses gcc 3.4.6 that may have bug about symbol visibility options, and the following error happened during make process. Generating RDoc documentation ./ruby: symbol lookup error: /XXXXX/src/ruby-1.9.3-p0/.ext/ x86_64-linux/enc/encdb.so: undefined symbol: rb_encdb_declare For the workaround of the (very old gcc's) bug, editing Makefile is needed. after configure before make. $ cp Makefile Makefile.bak $ sed -e "s/-fvisibility=hidden/-fvisibility=default/" Makefile.bak > Makefile $ make clean $ make Note that the workaround is needed only when you see the symbol lookup error. On, CentOS 5.4, it seems the workaround is not needed (and it may have bad effect for systems without the problem). -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp From ngoto at gen-info.osaka-u.ac.jp Sat Nov 5 17:16:49 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Sun, 06 Nov 2011 02:16:49 +0900 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: Message-ID: <20111106021649.20EF.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > 1) Error: > test_log(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > 2) Error: > test_set_log(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > 3) Error: > test_set_wsdl(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > 4) Error: > test_wsdl(Bio::FuncTestSOAPWSDL): > NameError: uninitialized constant Bio::SOAPWSDL::SOAP (snip) > > 3704 tests, 21447 assertions, 0 failures, 4 errors, 0 skips > > Test run options: --seed 21073 > > Anyone care to comment on this NameError? These 4 errors are caused by the drop of SOAP4R from the standard bundled library since Ruby 1.9. It is written in KNOWN_ISSUES.rdoc. "gem install soap4r-ruby1.9" should solve the problem. This is described in the latest (unreleased) README.rdoc. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp From pjotr.public14 at thebird.nl Sat Nov 5 17:34:34 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 5 Nov 2011 18:34:34 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: <20111106021649.20EF.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111106021649.20EF.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111105173434.GB2541@thebird.nl> It is a dependency. Should it not be in the BioRuby gemspec? On Sun, Nov 06, 2011 at 02:16:49AM +0900, Naohisa Goto wrote: > Hi Peter, > > > 1) Error: > > test_log(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > 2) Error: > > test_set_log(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > 3) Error: > > test_set_wsdl(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > 4) Error: > > test_wsdl(Bio::FuncTestSOAPWSDL): > > NameError: uninitialized constant Bio::SOAPWSDL::SOAP > (snip) > > > > 3704 tests, 21447 assertions, 0 failures, 4 errors, 0 skips > > > > Test run options: --seed 21073 > > > > Anyone care to comment on this NameError? > > These 4 errors are caused by the drop of SOAP4R from the standard > bundled library since Ruby 1.9. It is written in KNOWN_ISSUES.rdoc. > > "gem install soap4r-ruby1.9" should solve the problem. > This is described in the latest (unreleased) README.rdoc. > > -- > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Mon Nov 7 09:59:17 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 09:59:17 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Sat, Nov 5, 2011 at 12:10 PM, Naohisa Goto wrote: >> Note I tried passing -prefix and --prefix to configure, but it didn't >> accept it - use prefix with no minus at all, > > This seems to be very strange. I'm afraid if the machine might have > serious trouble. Odd - it worked today. Maybe it wasn't a minus sign last week, but a different dash if I copied and pasted it from a webpage? Not sure. > In addition, install libffi is recommended. > ?$ cd ~/Downloads > ?$ wget ftp://sourceware.org/pub/libffi/libffi-3.0.10.tar.gz > ?$ tar zxvf libffi-3.0.10.tar.gz > ?$ cd libffi-3.0.10 > ?$ ./configure --prefix=$HOME > ?$ make > ?$ make check > ?$ make install Done > "yum install openssl-devel" is also strongly recommended. > Done, I'm surprised that wasn't installed on this server already. > And then, configureing Ruby. For using libraries installed other than > system-wide directory, additional options to specify paths of C header > files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. > > ?$ tar zxvf ruby-1.9.3-p0.tar.gz > ?$ cd ruby-1.9.3-p0 > ?$ ./configure --prefix=$HOME \ > ? CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ > ? LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" > ?$ make > ?$ make check > ?$ make install > > If you think the gcc in CentOS 5.4 is buggy, adding optflags="-O2" > to supress optimize level is suggested. > > During make check, few error would be happened, due to incomplete IPv6 > network settings, kernel and glibc bug, older libraries bug, etc. > > FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully > installed ruby-1.9.3-p0 in my home directory without root privilege. That was very encouraging, as it is almost exactly what I'm trying to do :) I think it was the flags that I was missing. I also did "gem install soap4r-ruby1.9" as you suggested, and now BioRuby's test pass using ruby-1.9.3-p0: $ ruby test/runner.rb /home/buildslave/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: .......................................................................................ignored attr: {}arrayType ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Finished tests in 130.295656s, 28.4277 tests/s, 164.6333 assertions/s. 3704 tests, 21451 assertions, 0 failures, 0 errors, 0 skips Do you need to look at this iconv deprecation warning, and the "ignored attr: {}arrayType" message? > RedHat 4.6 uses gcc 3.4.6 that may have bug about symbol visibility > options, and the following error happened during make process. > > ?Generating RDoc documentation > ?./ruby: symbol lookup error: /XXXXX/src/ruby-1.9.3-p0/.ext/ > ?x86_64-linux/enc/encdb.so: undefined symbol: rb_encdb_declare > > For the workaround of ?the (very old gcc's) bug, editing Makefile is > needed. after configure before make. > > ?$ cp Makefile Makefile.bak > ?$ sed -e "s/-fvisibility=hidden/-fvisibility=default/" Makefile.bak > Makefile > ?$ make clean > ?$ make > > Note that the workaround is needed only when you see the symbol > lookup error. On, CentOS 5.4, it seems the workaround is not needed > (and it may have bad effect for systems without the problem). I didn't see that error, so didn't apply this change to the Makefile. Thank you very much Goto-san :) Peter From p.j.a.cock at googlemail.com Mon Nov 7 10:49:38 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 10:49:38 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Mon, Nov 7, 2011 at 9:59 AM, Peter Cock wrote: > On Sat, Nov 5, 2011 at 12:10 PM, Naohisa Goto >> And then, configureing Ruby. For using libraries installed other than >> system-wide directory, additional options to specify paths of C header >> files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. >> >> ?$ tar zxvf ruby-1.9.3-p0.tar.gz >> ?$ cd ruby-1.9.3-p0 >> ?$ ./configure --prefix=$HOME \ >> ? CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ >> ? LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" >> ?$ make >> ?$ make check >> ?$ make install >> >> ... >> >> FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully >> installed ruby-1.9.3-p0 in my home directory without root privilege. > > That was very encouraging, as it is almost exactly what I'm trying to do :) > I think it was the flags that I was missing. > > I also did "gem install soap4r-ruby1.9" as you suggested, and now > BioRuby's test pass using ruby-1.9.3-p0: This 64 bit Linux machine and a 32bit Linux box are now setup and running as buildslaves for BioRuby, bringing us to three slaves so far: http://testing.open-bio.org/bioruby/buildslaves Next up: My Windows machine... Peter From p.j.a.cock at googlemail.com Mon Nov 7 11:26:53 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:26:53 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows Message-ID: Hi all, Again I thought it would be useful to write down what I did to get BioRuby running on my Windows XP 32 bit machine (which will be a buildslave). Note I have some things already installed, like git. 1. Download http://rubyforge.org/frs/download.php/75465/rubyinstaller-1.9.3-p0.exe 2. Run it, using default options except I ticked "Add Ruby executables to your PATH" Otherwise the path installed to will be C:\Ruby193 or similar, and thus version dependent, which I anticipate will complicate things for the buildbot setup. I then tried the BioRuby tests which confirmed it was missing the next two gems (although there were some other errors, e.g. in the sanger_chromatogram example). 3. gem install libxml-ruby 4. gem install soap4r-ruby1.9 5. git clone git://github.com/bioruby/bioruby.git 6. cd bioruby 7. ruby test/runner.rb Error message popped up three times, typed in by hand: ruby.exe - Unable to Locate Component This application has failed to start because libxml2-2.dll was not found. Re-installing the application my fix this problem. [OK] Perhaps the gem install wasn't quite right? Or it doesn't actually link to the DLL properly? I could find the DLL here, C:\Ruby193\lib\ruby\gems\1.9.1\gems\libxml-ruby-2.2.2-x86-mingw32\lib\libs\libxml2-2.dll The following StackOverflow question looked relevant, although on a much older version of Ruby: http://stackoverflow.com/questions/4323234/ I tried the work around mentioned and copied the 3 DLL files in that folder to C:\Ruby193\bin - that solved the missing DLL error message, but seems like a hack. After that there were 4 failures and 7 errors, which I will cover in the next email. Peter -------------------------------------------------- C:\repositories\bioruby>gem install libxml-ruby Fetching: libxml-ruby-2.2.2-x86-mingw32.gem (100%) Successfully installed libxml-ruby-2.2.2-x86-mingw32 1 gem installed Installing ri documentation for libxml-ruby-2.2.2-x86-mingw32... Installing RDoc documentation for libxml-ruby-2.2.2-x86-mingw32... C:\repositories\bioruby>gem install soap4r-ruby1.9 Fetching: soap4r-ruby1.9-2.0.3.gem (100%) Successfully installed soap4r-ruby1.9-2.0.3 1 gem installed Installing ri documentation for soap4r-ruby1.9-2.0.3... Installing RDoc documentation for soap4r-ruby1.9-2.0.3... From pjotr.public14 at thebird.nl Mon Nov 7 11:31:28 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 7 Nov 2011 12:31:28 +0100 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111107113128.GA12989@thebird.nl> Very cool. Would it be possible to show the builder names including the distro? So instead of the too generic Linux 32 - Ruby 1.9 show Linux CentOS 4.6 32bits - Ruby 1.9 so the output is immediately self descriptive? Pj. On Mon, Nov 07, 2011 at 10:49:38AM +0000, Peter Cock wrote: > On Mon, Nov 7, 2011 at 9:59 AM, Peter Cock wrote: > > On Sat, Nov 5, 2011 at 12:10 PM, Naohisa Goto > >> And then, configureing Ruby. For using libraries installed other than > >> system-wide directory, additional options to specify paths of C header > >> files and libraries shoud be given to CPPFLAGS, LDFLAGS, etc. > >> > >> ?$ tar zxvf ruby-1.9.3-p0.tar.gz > >> ?$ cd ruby-1.9.3-p0 > >> ?$ ./configure --prefix=$HOME \ > >> ? CPPFLAGS="-I$HOME/lib/libffi-3.0.10/include -I$HOME/include" \ > >> ? LDFLAGS="-L$HOME/lib -Wl,-rpath,$HOME/lib" > >> ?$ make > >> ?$ make check > >> ?$ make install > >> > >> ... > >> > >> FYI, I have very very old RedHat 4.6 (x86_64), and I've successfully > >> installed ruby-1.9.3-p0 in my home directory without root privilege. > > > > That was very encouraging, as it is almost exactly what I'm trying to do :) > > I think it was the flags that I was missing. > > > > I also did "gem install soap4r-ruby1.9" as you suggested, and now > > BioRuby's test pass using ruby-1.9.3-p0: > > This 64 bit Linux machine and a 32bit Linux box are now setup and > running as buildslaves for BioRuby, bringing us to three slaves so far: > > http://testing.open-bio.org/bioruby/buildslaves > > Next up: My Windows machine... > > Peter > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Mon Nov 7 11:38:28 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:38:28 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock wrote: > Hi all, > > Again I thought it would be useful to write down what I did to get > BioRuby running on my Windows XP 32 bit machine (which will > be a buildslave). > ... > After that there were 4 failures and 7 errors, which I will cover in the > next email. Full details at end of email, here is my attempt to summarise and guess what is wrong: Errors (1), (2) and (3) are permission failures in testing calling commands. My guess is this is something about the batch file being used, C:\repositories\bioruby>test/data/command/echoarg2.bat Hello test: missing argument after `Hello' C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World test: Hello: binary operator expected Errors (4) and (5) may be transient network problems with efetch? Errors (6), (7) and (8) are all from Bio::TestAbif about NoMethodError: undefined method `match' for nil:NilClass Errors (9) and (10) look like a path name escape test being too strict and/or unaware of cross platform path separators. Error (11) looks like it could be an error removing a file - note you can't do this on Windows if there is an open handle to the file If any of these are specific to my Windows setup, with some guidance we can try to work out what is different. Peter --------------------------------------------------------- C:\repositories\bioruby>ruby test/runner.rb C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: ...................E.EE................................................F......F. .......ignored attr: {}arrayType ................................................................................ ..............EEE............................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ...........................................................................F.... ....F........................................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ....................................................................E........... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................. Finished tests in 145.575330s, 25.4439 tests/s, 147.2434 assertions/s. 1) Error: test_call_command(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call _command' 2) Error: test_call_command_open3(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/test/functional/bio/test_command.rb:71:in `test_call _command_open3' test/runner.rb:27:in `
' 3) Error: test_call_command_popen(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/test/functional/bio/test_command.rb:48:in `test_call _command_popen' 4) Failure: test_efetch_multiple_xml(Bio::FuncTestPubmed) [C:/repositories/bioruby/test/func tional/bio/io/test_pubmed.rb:108]: Failed assertion, no message given. 5) Failure: test_efetch_multiple(Bio::FuncTestPubmedClassMethod) [C:/repositories/bioruby/te st/functional/bio/io/test_pubmed.rb:91]: <3> expected but was <47>. 6) Error: test_complement(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 7) Error: test_seq(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 8) Error: test_to_biosequence(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 9) Failure: test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_ command.rb:59]: <"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 10) Failure: test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/ test_command.rb:76]: <"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 11) Error: test_simple_xml(Bio::TestPhyloXMLWriter): Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-1116-m0djng/example_ tree1.xml C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure' C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback' C:/repositories/bioruby/lib/bio/command.rb:607:in `call' C:/repositories/bioruby/lib/bio/command.rb:607:in `close!' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test _passed' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea rdown' test/runner.rb:27:in `
' 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips From p.j.a.cock at googlemail.com Mon Nov 7 11:43:54 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:43:54 +0000 Subject: [BioRuby] Installing Ruby 1.9 on CentOS 5.4 In-Reply-To: <20111107113128.GA12989@thebird.nl> References: <20111105211057.20EC.EEF6E030@gen-info.osaka-u.ac.jp> <20111107113128.GA12989@thebird.nl> Message-ID: On Mon, Nov 7, 2011 at 11:31 AM, Pjotr Prins wrote: > Very cool. Would it be possible to show the builder names including > the distro? So instead of the too generic > > ?Linux 32 - Ruby 1.9 > > show > > ?Linux CentOS 4.6 32bits - Ruby 1.9 > > so the output is immediately self descriptive? > > Pj. That short name is configurable, but it would be used for multiple buildslaves supporting that target. The question is do you want to lump together all your 32 bit Linux machines testing Ruby 1.9 under one group (as it is now, although currently with just one buildslave for this grouping), or have a more fine grained listing? i.e. More build targets which will show up as more rows or columns here: http://testing.open-bio.org/bioruby/grid http://testing.open-bio.org/bioruby/tgrid http://testing.open-bio.org/bioruby/waterfall This is what we were trying to ask earlier about the build targets, and initially we agreed to go for Ruby 1.8 and 1.9 on a range of operating systems - Windows 32, Win 64, Linux 32, Linux 64, Mac OS Snow Leopard (64 bit), etc Hopefully this is starting to become clearer now. Peter From p.j.a.cock at googlemail.com Mon Nov 7 11:48:06 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 11:48:06 +0000 Subject: [BioRuby] Buildbot target platforms Message-ID: Retitling thread On Mon, Nov 7, 2011 at 11:43 AM, Peter Cock wrote: > On Mon, Nov 7, 2011 at 11:31 AM, Pjotr Prins wrote: >> Very cool. Would it be possible to show the builder names including >> the distro? So instead of the too generic >> >> ?Linux 32 - Ruby 1.9 >> >> show >> >> ?Linux CentOS 4.6 32bits - Ruby 1.9 >> >> so the output is immediately self descriptive? >> >> Pj. > > That short name is configurable, but it would be used for multiple > buildslaves supporting that target. > > The question is do you want to lump together all your 32 bit > Linux machines testing Ruby 1.9 under one group (as it is > now, although currently with just one buildslave for this > grouping), or have a more fine grained listing? > > i.e. More build targets which will show up as more rows or > columns here: > > http://testing.open-bio.org/bioruby/grid > http://testing.open-bio.org/bioruby/tgrid > http://testing.open-bio.org/bioruby/waterfall > > This is what we were trying to ask earlier about the build > targets, and initially we agreed to go for Ruby 1.8 and 1.9 > on a range of operating systems - Windows 32, Win 64, > Linux 32, Linux 64, Mac OS Snow Leopard (64 bit), etc > Hopefully this is starting to become clearer now. These are the Biopython targets, 23 of them right now: testing.open-bio.org/biopython/grid testing.open-bio.org/biopython/tgrid For us since we test several variants of Python, having the OS broken down into anything finer would be too much. Note that I am beginning to think that on Ruby the revision number seems to be much more important than in Python. i.e. Maybe we should have separate testing for Ruby 1.9.1, 1.9.2, 1.9.3 etc rather than just bundling them together under Ruby 1.9? Peter From p.j.a.cock at googlemail.com Mon Nov 7 12:35:07 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 12:35:07 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: On Mon, Nov 7, 2011 at 11:38 AM, Peter Cock wrote: > On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock wrote: >> Hi all, >> >> Again I thought it would be useful to write down what I did to get >> BioRuby running on my Windows XP 32 bit machine (which will >> be a buildslave). >> ... >> After that there were 4 failures and 7 errors, which I will cover in the >> next email. > > Full details at end of email, here is my attempt to summarise and guess > what is wrong: > > Errors (1), (2) and (3) are permission failures in testing calling commands. > My guess is this is something about the batch file being used, > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello > test: missing argument after `Hello' > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World > test: Hello: binary operator expected > Wrong slashes - that would have been cygwin's echo rather than Window's, C:\repositories\bioruby>test\data\command\echoarg2.bat Hello ECHO is on. C:\repositories\bioruby>test\data\command\echoarg2.bat Hello World World So there isn't a problem with the batch file itself. Peter From p.j.a.cock at googlemail.com Mon Nov 7 13:48:48 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 7 Nov 2011 13:48:48 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: On Mon, Nov 7, 2011 at 11:38 AM, Peter Cock wrote: > > C:\repositories\bioruby>ruby test/runner.rb > C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will > ?be deprecated in the future, use String#encode instead. > Run options: > > # Running tests: > > ...................E.EE................................................F......F. > .......ignored attr: {}arrayType > ................................................................................ > etc > 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips Interestingly I gave Ruby the path name with Windows style slashes, and the pattern is a little different, 3 failures, 8 errors. However, some of these seem to be network related or stochastic, so a direct comparison is not fair. On closer inspection it looks like the same problems. We've got a couple of stochastic tests in Biopython and even after relaxing the test criteria they still can fail every so often, which is annoying. Peter -- C:\repositories\bioruby>ruby test\runner.rb C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: ...................E.EE...................................................E..... .......ignored attr: {}arrayType ................................................................................ ..............EEE............................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ...........................................................................F.... ....F........................................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ....................................................................E........... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ..........................................................................F..... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................. Finished tests in 214.230262s, 17.2898 tests/s, 99.9765 assertions/s. 1) Error: test_call_command(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call _command' 2) Error: test_call_command_open3(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/test/functional/bio/test_command.rb:71:in `test_call _command_open3' test/runner.rb:27:in `
' 3) Error: test_call_command_popen(Bio::FuncTestCommandCall): Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/test/functional/bio/test_command.rb:48:in `test_call _command_popen' 4) Error: test_esearch(Bio::FuncTestPubmed): Errno::ETIMEDOUT: A connection attempt failed because the connected party did no t properly respond after a period of time, or established connection failed beca use connected host has failed to respond. - connect(2) C:/repositories/bioruby/lib/bio/command.rb:649:in `start_http' C:/repositories/bioruby/lib/bio/command.rb:735:in `post_form' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:131:in `ncbi_post_form' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:268:in `block in esearch' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:265:in `step' C:/repositories/bioruby/lib/bio/io/ncbirest.rb:265:in `esearch' C:/repositories/bioruby/lib/bio/io/pubmed.rb:96:in `esearch' C:/repositories/bioruby/test/functional/bio/io/test_pubmed.rb:26:in `test_es earch' test/runner.rb:27:in `
' 5) Error: test_complement(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 6) Error: test_seq(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 7) Error: test_to_biosequence(Bio::TestAbif): NoMethodError: undefined method `match' for nil:NilClass C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e ntry_data' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block in get_directory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di rectory_entries' C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia lize' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `new' C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 :in `setup' 8) Failure: test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_ command.rb:59]: <"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 9) Failure: test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/ test_command.rb:76]: <"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was <"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">. 10) Error: test_simple_xml(Bio::TestPhyloXMLWriter): Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-3360-1ksuohs/example _tree1.xml C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure' C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback' C:/repositories/bioruby/lib/bio/command.rb:607:in `call' C:/repositories/bioruby/lib/bio/command.rb:607:in `close!' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test _passed' C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea rdown' test/runner.rb:27:in `
' 11) Failure: test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandom ize) [C:/repositories/bioruby/test/unit/bio/sequence/test_common.rb:286]: test of chi2 < 21.666 failed (25.8). Expected 21.666 to be > 25.8. 3704 tests, 21418 assertions, 3 failures, 8 errors, 0 skips From rob.syme at gmail.com Mon Nov 14 06:07:47 2011 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 14 Nov 2011 14:07:47 +0800 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection Message-ID: Hi all, Full details are up at: http://gist.github.com/1363302 This might just be the result of a schema change in BioSQL, but my SQL knowledge doesn't extend quite far enough. Has anyone come across this before? When connecting to an empty postgres BioSQL db, I get an ActiveRecord::StatementInvalid error: PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" HINT: You need an unconditional ON INSERT DO INSTEAD rule with a RETURNING clause. : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) RETURNING "ontology_id" ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" HINT: You need an unconditional ON INSERT DO INSTEAD rule with a RETURNING clause. : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) RETURNING "ontology_id" from /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/connection_adapters/postgresql_adapter.rb:1009:in `prepare' from /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/biosql.rb:31:in `establish_connection' The offending SQL was: SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') LIMIT 1 # This works fine INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) RETURNING "ontology_id" [["definition", nil], ["name", "Annotation Tags"]] # This fails Relevant gems installed: activerecord (3.1.1) composite_primary_keys (4.1.1) pg (0.11.0) bio (1.4.2.5000) Using: psql (PostgreSQL) 9.1.1 BioSQL schema version 1.0.1 and ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] -r From bonnal at ingm.org Mon Nov 14 10:43:51 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 14 Nov 2011 11:43:51 +0100 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: Message-ID: Hi Rob, may be a problem of my biosql implementation, I suppose. I didn't update the library and I didn't check compatibility with new active record stuff and composite primary keys. Now, I can not take care of this, if there is someone wants to take care of I'll be happy to support him/her. On 14/11/11 07.07, "Rob Syme" wrote: > Hi all, > Full details are up at: http://gist.github.com/1363302 > > This might just be the result of a schema change in BioSQL, but my SQL > knowledge doesn't extend quite far enough. Has anyone come across this > before? > > When connecting to an empty postgres BioSQL db, I get an > ActiveRecord::StatementInvalid error: > > PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > RETURNING clause. > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > RETURNING "ontology_id" > ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT > RETURNING on relation "ontology" > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > RETURNING clause. > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > RETURNING "ontology_id" > from > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/ > connection_adapters/postgresql_adapter.rb:1009:in > `prepare' > > from > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios > ql.rb:31:in > `establish_connection' > > > The offending SQL was: > > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') > LIMIT 1 # This works fine > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > RETURNING "ontology_id" [["definition", nil], ["name", "Annotation > Tags"]] # This fails > > Relevant gems installed: > activerecord (3.1.1) > composite_primary_keys (4.1.1) > pg (0.11.0) > bio (1.4.2.5000) > > Using: > psql (PostgreSQL) 9.1.1 > BioSQL schema version 1.0.1 and > ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] > > -r > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From rob.syme at gmail.com Mon Nov 14 13:03:13 2011 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 14 Nov 2011 21:03:13 +0800 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: References: Message-ID: Cool. Just checking that I wasn't struggling with something that was already known. I'll have a poke around tomorrow. -r On 14 Nov 2011 18:43, "Raoul Bonnal" wrote: > Hi Rob, > may be a problem of my biosql implementation, I suppose. > I didn't update the library and I didn't check compatibility with new > active > record stuff and composite primary keys. > Now, I can not take care of this, if there is someone wants to take care of > I'll be happy to support him/her. > > > On 14/11/11 07.07, "Rob Syme" wrote: > > > Hi all, > > Full details are up at: http://gist.github.com/1363302 > > > > This might just be the result of a schema change in BioSQL, but my SQL > > knowledge doesn't extend quite far enough. Has anyone come across this > > before? > > > > When connecting to an empty postgres BioSQL db, I get an > > ActiveRecord::StatementInvalid error: > > > > PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT > > RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > from > > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/ > > connection_adapters/postgresql_adapter.rb:1009:in > > `prepare' > > > > from > > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios > > ql.rb:31:in > > `establish_connection' > > > > > > The offending SQL was: > > > > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') > > LIMIT 1 # This works fine > > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" [["definition", nil], ["name", "Annotation > > Tags"]] # This fails > > > > Relevant gems installed: > > activerecord (3.1.1) > > composite_primary_keys (4.1.1) > > pg (0.11.0) > > bio (1.4.2.5000) > > > > Using: > > psql (PostgreSQL) 9.1.1 > > BioSQL schema version 1.0.1 and > > ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] > > > > -r > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > From ngoto at gen-info.osaka-u.ac.jp Mon Nov 14 13:14:22 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 14 Nov 2011 22:14:22 +0900 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: References: Message-ID: <20111114131423.6D6F61CBC513@idnmail.gen-info.osaka-u.ac.jp> Hi Raoul, Which version of ActiveRecord is suitable with the current BioRuby's biosql implementation? With RubyGems and (optionally) with Bundler, we can specify specific version number to be used. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 14 Nov 2011 11:43:51 +0100 Raoul Bonnal wrote: > Hi Rob, > may be a problem of my biosql implementation, I suppose. > I didn't update the library and I didn't check compatibility with new active > record stuff and composite primary keys. > Now, I can not take care of this, if there is someone wants to take care of > I'll be happy to support him/her. > > > On 14/11/11 07.07, "Rob Syme" wrote: > > > Hi all, > > Full details are up at: http://gist.github.com/1363302 > > > > This might just be the result of a schema change in BioSQL, but my SQL > > knowledge doesn't extend quite far enough. Has anyone come across this > > before? > > > > When connecting to an empty postgres BioSQL db, I get an > > ActiveRecord::StatementInvalid error: > > > > PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT > > RETURNING on relation "ontology" > > HINT: You need an unconditional ON INSERT DO INSTEAD rule with a > > RETURNING clause. > > : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" > > from > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_record/ > > connection_adapters/postgresql_adapter.rb:1009:in > > `prepare' > > > > from > > /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bios > > ql.rb:31:in > > `establish_connection' > > > > > > The offending SQL was: > > > > SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') > > LIMIT 1 # This works fine > > INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) > > RETURNING "ontology_id" [["definition", nil], ["name", "Annotation > > Tags"]] # This fails > > > > Relevant gems installed: > > activerecord (3.1.1) > > composite_primary_keys (4.1.1) > > pg (0.11.0) > > bio (1.4.2.5000) > > > > Using: > > psql (PostgreSQL) 9.1.1 > > BioSQL schema version 1.0.1 and > > ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] > > > > -r > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnal at ingm.org Mon Nov 14 13:34:25 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 14 Nov 2011 14:34:25 +0100 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: <20111114131423.6D6F61CBC513@idnmail.gen-info.osaka-u.ac.jp> Message-ID: It should work with versions prior to Rails 3.x. But if you are not in a rush after paper submission I'll look into it, let'say 2 weeks ? There was another BioSQL issue around, i didn't answer because I was busy. @Rob: could you give me the script to replicate the error ? We could extract BioSQL from BioRuby and create a plugin, is something I'm considering. On 14/11/11 14.14, "Naohisa GOTO" wrote: > Hi Raoul, > > Which version of ActiveRecord is suitable with the current > BioRuby's biosql implementation? > > With RubyGems and (optionally) with Bundler, we can specify > specific version number to be used. > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Mon, 14 Nov 2011 11:43:51 +0100 > Raoul Bonnal wrote: > >> Hi Rob, >> may be a problem of my biosql implementation, I suppose. >> I didn't update the library and I didn't check compatibility with new active >> record stuff and composite primary keys. >> Now, I can not take care of this, if there is someone wants to take care of >> I'll be happy to support him/her. >> >> >> On 14/11/11 07.07, "Rob Syme" wrote: >> >>> Hi all, >>> Full details are up at: http://gist.github.com/1363302 >>> >>> This might just be the result of a schema change in BioSQL, but my SQL >>> knowledge doesn't extend quite far enough. Has anyone come across this >>> before? >>> >>> When connecting to an empty postgres BioSQL db, I get an >>> ActiveRecord::StatementInvalid error: >>> >>> PGError: ERROR: cannot perform INSERT RETURNING on relation "ontology" >>> HINT: You need an unconditional ON INSERT DO INSTEAD rule with a >>> RETURNING clause. >>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>> RETURNING "ontology_id" >>> ActiveRecord::StatementInvalid: PGError: ERROR: cannot perform INSERT >>> RETURNING on relation "ontology" >>> HINT: You need an unconditional ON INSERT DO INSTEAD rule with a >>> RETURNING clause. >>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>> RETURNING "ontology_id" >>> from >>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_recor >>> d/ >>> connection_adapters/postgresql_adapter.rb:1009:in >>> `prepare' >>> >>> from >>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bi >>> os >>> ql.rb:31:in >>> `establish_connection' >>> >>> >>> The offending SQL was: >>> >>> SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') >>> LIMIT 1 # This works fine >>> INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>> RETURNING "ontology_id" [["definition", nil], ["name", "Annotation >>> Tags"]] # This fails >>> >>> Relevant gems installed: >>> activerecord (3.1.1) >>> composite_primary_keys (4.1.1) >>> pg (0.11.0) >>> bio (1.4.2.5000) >>> >>> Using: >>> psql (PostgreSQL) 9.1.1 >>> BioSQL schema version 1.0.1 and >>> ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] >>> >>> -r >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > From bonnal at ingm.org Mon Nov 14 15:08:08 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 14 Nov 2011 16:08:08 +0100 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: Message-ID: Hi Rob, Thanks, I'll try to replicate the issue later this week. Having this dependencies perhaps is better to extract biosql from bioruby. On 14/11/11 15.37, "Rob Syme" wrote: > The script is very simple, just try and connect to the db. Replication > is easiest when your postgres install includes a database $USER with > permissions such that you can create databases with `createdb` without > sudo. Instructions up at https://help.ubuntu.com/community/PostgreSQL > under "Alternative Setup". If you have a more secure postgres setup, > just supply the username password in the final line: > > # Setup the postgres db > git clone https://github.com/biosql/biosql.git > createdb biosql > psql biosql < biosql/sql/biosqldb-pg.sql > > # Grab all the gems > gem install activerecord bio composite_primary_keys pg > activerecord-postgres-adapter > > # Try and establish the db connection > # The connection hash is minimal, username defaults to the $USER, and > hostname defaults to localhost. > ruby -r bio -e "Bio::SQL.establish_connection({'development'=>{ > 'database'=>'biosql','adapter'=>'postgresql' }},'development')" > > > > > On Mon, Nov 14, 2011 at 9:34 PM, Raoul Bonnal wrote: >> It should work with versions prior to Rails 3.x. >> But if you are not in a rush after paper submission I'll look into it, >> let'say 2 weeks ?? There was another BioSQL issue around, i didn't answer >> because I was busy. >> >> @Rob: could you give me the script to replicate the error ? >> >> We could extract BioSQL from BioRuby and create a plugin, is something I'm >> considering. >> >> On 14/11/11 14.14, "Naohisa GOTO" wrote: >> >>> Hi Raoul, >>> >>> Which version of ActiveRecord is suitable with the current >>> BioRuby's biosql implementation? >>> >>> With RubyGems and (optionally) with Bundler, we can specify >>> specific version number to be used. >>> >>> Naohisa Goto >>> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org >>> >>> On Mon, 14 Nov 2011 11:43:51 +0100 >>> Raoul Bonnal wrote: >>> >>>> Hi Rob, >>>> may be a problem of my biosql implementation, I suppose. >>>> I didn't update the library and I didn't check compatibility with new >>>> active >>>> record stuff and composite primary keys. >>>> Now, I can not take care of this, if there is someone wants to take care of >>>> I'll be happy to support him/her. >>>> >>>> >>>> On 14/11/11 07.07, "Rob Syme" wrote: >>>> >>>>> Hi all, >>>>> Full details are up at: http://gist.github.com/1363302 >>>>> >>>>> This might just be the result of a schema change in BioSQL, but my SQL >>>>> knowledge doesn't extend quite far enough. Has anyone come across this >>>>> before? >>>>> >>>>> When connecting to an empty postgres BioSQL db, I get an >>>>> ActiveRecord::StatementInvalid error: >>>>> >>>>> PGError: ERROR: ?cannot perform INSERT RETURNING on relation "ontology" >>>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>>> RETURNING clause. >>>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>>> RETURNING "ontology_id" >>>>> ActiveRecord::StatementInvalid: PGError: ERROR: ?cannot perform INSERT >>>>> RETURNING on relation "ontology" >>>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>>> RETURNING clause. >>>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>>> RETURNING "ontology_id" >>>>> from >>>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_rec >>>>> or >>>>> d/ >>>>> connection_adapters/postgresql_adapter.rb:1009:in >>>>> `prepare' >>>>> >>>>> from >>>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/ >>>>> bi >>>>> os >>>>> ql.rb:31:in >>>>> `establish_connection' >>>>> >>>>> >>>>> The offending SQL was: >>>>> >>>>> SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') >>>>> LIMIT 1 # This works fine >>>>> INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>>> RETURNING "ontology_id" ?[["definition", nil], ["name", "Annotation >>>>> Tags"]] # This fails >>>>> >>>>> Relevant gems installed: >>>>> ? activerecord (3.1.1) >>>>> ? composite_primary_keys (4.1.1) >>>>> ? pg (0.11.0) >>>>> ? bio (1.4.2.5000) >>>>> >>>>> Using: >>>>> ? psql (PostgreSQL) 9.1.1 >>>>> ? BioSQL schema version 1.0.1 and >>>>> ? ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] >>>>> >>>>> -r >>>>> _______________________________________________ >>>>> BioRuby Project - http://www.bioruby.org/ >>>>> BioRuby mailing list >>>>> BioRuby at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> From rob.syme at gmail.com Mon Nov 14 14:37:55 2011 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 14 Nov 2011 22:37:55 +0800 Subject: [BioRuby] BioSQL - postgres refusing SQL generated by Bio::SQL::establish_connection In-Reply-To: References: <20111114131423.6D6F61CBC513@idnmail.gen-info.osaka-u.ac.jp> Message-ID: The script is very simple, just try and connect to the db. Replication is easiest when your postgres install includes a database $USER with permissions such that you can create databases with `createdb` without sudo. Instructions up at https://help.ubuntu.com/community/PostgreSQL under "Alternative Setup". If you have a more secure postgres setup, just supply the username password in the final line: # Setup the postgres db git clone https://github.com/biosql/biosql.git createdb biosql psql biosql < biosql/sql/biosqldb-pg.sql # Grab all the gems gem install activerecord bio composite_primary_keys pg activerecord-postgres-adapter # Try and establish the db connection # The connection hash is minimal, username defaults to the $USER, and hostname defaults to localhost. ruby -r bio -e "Bio::SQL.establish_connection({'development'=>{ 'database'=>'biosql','adapter'=>'postgresql' }},'development')" On Mon, Nov 14, 2011 at 9:34 PM, Raoul Bonnal wrote: > It should work with versions prior to Rails 3.x. > But if you are not in a rush after paper submission I'll look into it, > let'say 2 weeks ?? There was another BioSQL issue around, i didn't answer > because I was busy. > > @Rob: could you give me the script to replicate the error ? > > We could extract BioSQL from BioRuby and create a plugin, is something I'm > considering. > > On 14/11/11 14.14, "Naohisa GOTO" wrote: > >> Hi Raoul, >> >> Which version of ActiveRecord is suitable with the current >> BioRuby's biosql implementation? >> >> With RubyGems and (optionally) with Bundler, we can specify >> specific version number to be used. >> >> Naohisa Goto >> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org >> >> On Mon, 14 Nov 2011 11:43:51 +0100 >> Raoul Bonnal wrote: >> >>> Hi Rob, >>> may be a problem of my biosql implementation, I suppose. >>> I didn't update the library and I didn't check compatibility with new active >>> record stuff and composite primary keys. >>> Now, I can not take care of this, if there is someone wants to take care of >>> I'll be happy to support him/her. >>> >>> >>> On 14/11/11 07.07, "Rob Syme" wrote: >>> >>>> Hi all, >>>> Full details are up at: http://gist.github.com/1363302 >>>> >>>> This might just be the result of a schema change in BioSQL, but my SQL >>>> knowledge doesn't extend quite far enough. Has anyone come across this >>>> before? >>>> >>>> When connecting to an empty postgres BioSQL db, I get an >>>> ActiveRecord::StatementInvalid error: >>>> >>>> PGError: ERROR: ?cannot perform INSERT RETURNING on relation "ontology" >>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>> RETURNING clause. >>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>> RETURNING "ontology_id" >>>> ActiveRecord::StatementInvalid: PGError: ERROR: ?cannot perform INSERT >>>> RETURNING on relation "ontology" >>>> HINT: ?You need an unconditional ON INSERT DO INSTEAD rule with a >>>> RETURNING clause. >>>> : INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>> RETURNING "ontology_id" >>>> from >>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/activerecord-3.1.1/lib/active_recor >>>> d/ >>>> connection_adapters/postgresql_adapter.rb:1009:in >>>> `prepare' >>>> >>>> from >>>> /home/rob/.rvm/gems/ruby-1.9.2-p290/gems/bio-1.4.2.5000/lib/bio/io/biosql/bi >>>> os >>>> ql.rb:31:in >>>> `establish_connection' >>>> >>>> >>>> The offending SQL was: >>>> >>>> SELECT "ontology".* FROM "ontology" WHERE (name = 'Annotation Tags') >>>> LIMIT 1 # This works fine >>>> INSERT INTO "ontology" ("definition", "name") VALUES ($1, $2) >>>> RETURNING "ontology_id" ?[["definition", nil], ["name", "Annotation >>>> Tags"]] # This fails >>>> >>>> Relevant gems installed: >>>> ? activerecord (3.1.1) >>>> ? composite_primary_keys (4.1.1) >>>> ? pg (0.11.0) >>>> ? bio (1.4.2.5000) >>>> >>>> Using: >>>> ? psql (PostgreSQL) 9.1.1 >>>> ? BioSQL schema version 1.0.1 and >>>> ? ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-linux] >>>> >>>> -r >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ngoto at gen-info.osaka-u.ac.jp Mon Nov 21 08:09:13 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Mon, 21 Nov 2011 17:09:13 +0900 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: Message-ID: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, Sorry very late. On my Windows 7 (32-bit, Business or Enterprise) machines, with Ruby 1.9.3-p0 downloaded from rubyinstaller.org, the 1), 2), and 3) "Errno::EACCES: Permission denied" cannot be reproduced. Instead, failure occur due to the change of command-line escaping in Ruby 1.9, which would be the same as 9) and 10). The "Errno::EACCESS" might occurr when using other shell than cmd.exe e.g. Cygwin's Bash, execution prohibition by security software, or by access controll on NTFS. For 9) and 10): In Windows, command-line escaping is treated by each software, and no "general" escaping way exists. This means the test is bad for Windows. With Ruby 1.8.x, current BioRuby uses its internal command-line string builder, but with Ruby 1.9.x, it uses Ruby's. 6), 7), and 8) may be due to text mode that is default file reading mode when Ruby on windows and that may break things when reading binary files. 11) may be the problem of removing a file before closing, as you said. Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > 1) Error: > test_call_command(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call > _command' > On Mon, Nov 7, 2011 at 11:26 AM, Peter Cock wrote: > > Hi all, > > > > Again I thought it would be useful to write down what I did to get > > BioRuby running on my Windows XP 32 bit machine (which will > > be a buildslave). > > ... > > After that there were 4 failures and 7 errors, which I will cover in the > > next email. > > Full details at end of email, here is my attempt to summarise and guess > what is wrong: > > Errors (1), (2) and (3) are permission failures in testing calling commands. > My guess is this is something about the batch file being used, > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello > test: missing argument after `Hello' > > C:\repositories\bioruby>test/data/command/echoarg2.bat Hello World > test: Hello: binary operator expected > > > Errors (4) and (5) may be transient network problems with efetch? > > > Errors (6), (7) and (8) are all from Bio::TestAbif about > NoMethodError: undefined method `match' for nil:NilClass > > > Errors (9) and (10) look like a path name escape test being too > strict and/or unaware of cross platform path separators. > > > Error (11) looks like it could be an error removing a file - note you > can't do this on Windows if there is an open handle to the file > > > If any of these are specific to my Windows setup, with some guidance we > can try to work out what is different. > > Peter > > --------------------------------------------------------- > > C:\repositories\bioruby>ruby test/runner.rb > C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will > be deprecated in the future, use String#encode instead. > Run options: > > # Running tests: > > ...................E.EE................................................F......F. > .......ignored attr: {}arrayType > ................................................................................ > ..............EEE............................................................... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ...........................................................................F.... > ....F........................................................................... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ....................................................................E........... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................. > > Finished tests in 145.575330s, 25.4439 tests/s, 147.2434 assertions/s. > > 1) Error: > test_call_command(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/test/functional/bio/test_command.rb:40:in `test_call > _command' > > 2) Error: > test_call_command_open3(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/test/functional/bio/test_command.rb:71:in `test_call > _command_open3' > test/runner.rb:27:in `
' > > 3) Error: > test_call_command_popen(Bio::FuncTestCommandCall): > Errno::EACCES: Permission denied - C:/repositories/bioruby/test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/test/functional/bio/test_command.rb:48:in `test_call > _command_popen' > > 4) Failure: > test_efetch_multiple_xml(Bio::FuncTestPubmed) [C:/repositories/bioruby/test/func > tional/bio/io/test_pubmed.rb:108]: > Failed assertion, no message given. > > 5) Failure: > test_efetch_multiple(Bio::FuncTestPubmedClassMethod) [C:/repositories/bioruby/te > st/functional/bio/io/test_pubmed.rb:91]: > <3> expected but was > <47>. > > 6) Error: > test_complement(Bio::TestAbif): > NoMethodError: undefined method `match' for nil:NilClass > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e > ntry_data' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block > in get_directory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' > > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di > rectory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia > lize' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `new' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `setup' > > 7) Error: > test_seq(Bio::TestAbif): > NoMethodError: undefined method `match' for nil:NilClass > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e > ntry_data' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block > in get_directory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' > > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di > rectory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia > lize' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `new' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `setup' > > 8) Error: > test_to_biosequence(Bio::TestAbif): > NoMethodError: undefined method `match' for nil:NilClass > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:107:in `get_e > ntry_data' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:83:in `block > in get_directory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `times' > > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:77:in `get_di > rectory_entries' > C:/repositories/bioruby/lib/bio/db/sanger_chromatogram/abif.rb:42:in `initia > lize' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `new' > C:/repositories/bioruby/test/unit/bio/db/sanger_chromatogram/test_abif.rb:42 > :in `setup' > > 9) Failure: > test_escape_shell(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/test_ > command.rb:59]: > <"bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was > <"\"bio'\"\"r u\"\"b\\y123 at 456:789\"">. > > 10) Failure: > test_make_command_line(Bio::TestCommand) [C:/repositories/bioruby/test/unit/bio/ > test_command.rb:76]: > <"ruby test.rb atgcatgc bio\\'\\\"r\\ u\\\"b\\\\y123 at 456:789"> expected but was > <"ruby test.rb atgcatgc \"bio'\"\"r u\"\"b\\y123 at 456:789\"">. > > 11) Error: > test_simple_xml(Bio::TestPhyloXMLWriter): > Errno::EACCES: Permission denied - C:/Temp/PhyloXML20111107-1116-m0djng/example_ > tree1.xml > C:/repositories/bioruby/lib/bio/command.rb:479:in `remove_entry_secure' > C:/repositories/bioruby/lib/bio/command.rb:569:in `block in callback' > C:/repositories/bioruby/lib/bio/command.rb:607:in `call' > C:/repositories/bioruby/lib/bio/command.rb:607:in `close!' > C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:77:in `test > _passed' > C:/repositories/bioruby/test/unit/bio/db/test_phyloxml_writer.rb:105:in `tea > rdown' > test/runner.rb:27:in `
' > > 3704 tests, 21435 assertions, 4 failures, 7 errors, 0 skips Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From p.j.a.cock at googlemail.com Mon Nov 21 09:42:45 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 21 Nov 2011 09:42:45 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Mon, Nov 21, 2011 at 8:09 AM, Naohisa Goto wrote: > Hi Peter, > > Sorry very late. > > On my Windows 7 (32-bit, Business or Enterprise) machines, > with Ruby 1.9.3-p0 downloaded from rubyinstaller.org, the 1), 2), and 3) > "Errno::EACCES: Permission denied" cannot be reproduced. > Instead, failure occur due to the change of command-line escaping in > Ruby 1.9, which would be the same as 9) and 10). > > The "Errno::EACCESS" might occurr when using other shell than cmd.exe > e.g. Cygwin's Bash, execution prohibition by security software, or by > access controll on NTFS. > > For 9) and 10): In Windows, command-line escaping is treated by each > software, and no "general" escaping way exists. This means the test is > bad for Windows. With Ruby 1.8.x, current BioRuby uses its internal > command-line string builder, but with Ruby 1.9.x, it uses Ruby's. > > 6), 7), and 8) may be due to text mode that is default file reading mode > when Ruby on windows and that ?may break things when reading binary > files. > > 11) may be the problem of removing a file before closing, as you said. > > Thanks, > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org Hi Goto-san, Hmm. Can you mark some of these as known failures under Windows, or skip those tests under Windows? Otherwise right now having a nightly build on Windows will always fail, and always send an error email. So It won't be helpful. Regards, Peter From ngoto at gen-info.osaka-u.ac.jp Wed Nov 23 06:34:21 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Wed, 23 Nov 2011 15:34:21 +0900 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> Hi, I've fixed all of the test failures/errors which are reproduced on my Windows machines. Now 0 failures 0 errors, with latest git version, on Windows 7 Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32). Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at biourby.org > On Mon, Nov 21, 2011 at 8:09 AM, Naohisa Goto > wrote: > > Hi Peter, > > > > Sorry very late. > > > > On my Windows 7 (32-bit, Business or Enterprise) machines, > > with Ruby 1.9.3-p0 downloaded from rubyinstaller.org, the 1), 2), and 3) > > "Errno::EACCES: Permission denied" cannot be reproduced. > > Instead, failure occur due to the change of command-line escaping in > > Ruby 1.9, which would be the same as 9) and 10). > > > > The "Errno::EACCESS" might occurr when using other shell than cmd.exe > > e.g. Cygwin's Bash, execution prohibition by security software, or by > > access controll on NTFS. > > > > For 9) and 10): In Windows, command-line escaping is treated by each > > software, and no "general" escaping way exists. This means the test is > > bad for Windows. With Ruby 1.8.x, current BioRuby uses its internal > > command-line string builder, but with Ruby 1.9.x, it uses Ruby's. > > > > 6), 7), and 8) may be due to text mode that is default file reading mode > > when Ruby on windows and that ?may break things when reading binary > > files. > > > > 11) may be the problem of removing a file before closing, as you said. > > > > Thanks, > > > > Naohisa Goto > > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > Hi Goto-san, > > Hmm. Can you mark some of these as known failures under > Windows, or skip those tests under Windows? > > Otherwise right now having a nightly build on Windows will always > fail, and always send an error email. So It won't be helpful. > > Regards, > > Peter Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From p.j.a.cock at googlemail.com Thu Nov 24 09:41:09 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 24 Nov 2011 09:41:09 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111121170911.3975.EEF6E030@gen-info.osaka-u.ac.jp> <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: 2011/11/23 Naohisa Goto : > Hi, > > I've fixed all of the test failures/errors which are reproduced on my > Windows machines. > > Now 0 failures 0 errors, with latest git version, on Windows 7 > Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32). Great. I ran the tests again on my machine, using commit d2d66f833d0b20647e8d761d2a240b99b206eaa8 and things have improved a lot - I'm only seeing some kind of permissions problem calling batch files now: Note my machine is Windows XP (32 bit), whereas you have Windows 7 Enterprise 32 bit. This may be important. I have the same version of Ruby (I think): C:\repositories\bioruby>ruby -v ruby 1.9.3p0 (2011-10-30) [i386-mingw32] C:\repositories\bioruby>ruby Test\runner.rb C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will be deprecated in the future, use String#encode instead. Run options: # Running tests: ...........E.EEE.EEE.EE......................................................... ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ................................................................................ ...................................................... Finished tests in 25.234052s, 144.8043 tests/s, 832.0503 assertions/s. 1) Error: test_call_command(Bio::FuncTestCommandCallMisc1): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call _command' 2) Error: test_call_command_open3(Bio::FuncTestCommandCallMisc1): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call _command_open3' Test/runner.rb:36:in `
' 3) Error: test_call_command_popen(Bio::FuncTestCommandCallMisc1): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call _command_popen' 4) Error: test_call_command(Bio::FuncTestCommandCallSimple): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call _command' 5) Error: test_call_command_open3(Bio::FuncTestCommandCallSimple): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call _command_open3' Test/runner.rb:36:in `
' 6) Error: test_call_command_popen(Bio::FuncTestCommandCallSimple): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call _command_popen' 7) Error: test_call_command(Bio::FuncTestCommandCallWithSpace): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call _command' 8) Error: test_call_command_open3(Bio::FuncTestCommandCallWithSpace): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call _command_open3' Test/runner.rb:36:in `
' 9) Error: test_call_command_popen(Bio::FuncTestCommandCallWithSpace): Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech oarg2.bat C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call _command_popen' 3654 tests, 20996 assertions, 0 failures, 9 errors, 0 skips C:\repositories\bioruby> Thanks, Peter From ngoto at gen-info.osaka-u.ac.jp Fri Nov 25 04:50:35 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 25 Nov 2011 13:50:35 +0900 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: References: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <20111125135033.3B84.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, I think the failure may be due to the setting of permission for the file or the folder. Please look at the permisson for the file C:\repositories\bioruby\Test\data\command\echoarg2.bat By using explorer, right click the file and see "Property" -- "Security" and see details. Please confirm if the ACL "Traverse Folder/Execute File" is allowed and is not denyed. http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/acl_special_permissions.mspx?mfr=true The file permission can also be viewed by using cacls command on Windows. Please show the output of the command. C:\> cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat If the special ACL "FILE_EXECUTE" is shown as "DENY", its execution is denyed and thus the tests failed. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > 2011/11/23 Naohisa Goto : > > Hi, > > > > I've fixed all of the test failures/errors which are reproduced on my > > Windows machines. > > > > Now 0 failures 0 errors, with latest git version, on Windows 7 > > Enterprise 32-bit with Ruby 1.9.3-p0 (mingw32). > > Great. I ran the tests again on my machine, using commit > d2d66f833d0b20647e8d761d2a240b99b206eaa8 and things > have improved a lot - I'm only seeing some kind of permissions > problem calling batch files now: > > Note my machine is Windows XP (32 bit), whereas you have > Windows 7 Enterprise 32 bit. This may be important. > > I have the same version of Ruby (I think): > > C:\repositories\bioruby>ruby -v > ruby 1.9.3p0 (2011-10-30) [i386-mingw32] > > C:\repositories\bioruby>ruby Test\runner.rb > C:/Ruby193/lib/ruby/1.9.1/rubygems/custom_require.rb:36:in `require': iconv will > be deprecated in the future, use String#encode instead. > Run options: > > # Running tests: > > ...........E.EEE.EEE.EE......................................................... > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ................................................................................ > ...................................................... > > Finished tests in 25.234052s, 144.8043 tests/s, 832.0503 assertions/s. > > 1) Error: > test_call_command(Bio::FuncTestCommandCallMisc1): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call > _command' > > 2) Error: > test_call_command_open3(Bio::FuncTestCommandCallMisc1): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call > _command_open3' > Test/runner.rb:36:in `
' > > 3) Error: > test_call_command_popen(Bio::FuncTestCommandCallMisc1): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call > _command_popen' > > 4) Error: > test_call_command(Bio::FuncTestCommandCallSimple): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call > _command' > > 5) Error: > test_call_command_open3(Bio::FuncTestCommandCallSimple): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call > _command_open3' > Test/runner.rb:36:in `
' > > 6) Error: > test_call_command_popen(Bio::FuncTestCommandCallSimple): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call > _command_popen' > > 7) Error: > test_call_command(Bio::FuncTestCommandCallWithSpace): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/lib/bio/command.rb:198:in `call_command' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:44:in `test_call > _command' > > 8) Error: > test_call_command_open3(Bio::FuncTestCommandCallWithSpace): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:343:in `call_command_open3' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:75:in `test_call > _command_open3' > Test/runner.rb:36:in `
' > > 9) Error: > test_call_command_popen(Bio::FuncTestCommandCallWithSpace): > Errno::EACCES: Permission denied - C:/repositories/bioruby/Test/data/command/ech > oarg2.bat > C:/repositories/bioruby/lib/bio/command.rb:243:in `popen' > C:/repositories/bioruby/lib/bio/command.rb:243:in `call_command_popen' > C:/repositories/bioruby/Test/functional/bio/test_command.rb:52:in `test_call > _command_popen' > > 3654 tests, 20996 assertions, 0 failures, 9 errors, 0 skips > > C:\repositories\bioruby> > > Thanks, > > Peter From p.j.a.cock at googlemail.com Fri Nov 25 11:25:35 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 25 Nov 2011 11:25:35 +0000 Subject: [BioRuby] Installing & testing BioRuby on Windows In-Reply-To: <20111125135033.3B84.EEF6E030@gen-info.osaka-u.ac.jp> References: <20111123153248.3862.EEF6E030@gen-info.osaka-u.ac.jp> <20111125135033.3B84.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: On Fri, Nov 25, 2011 at 4:50 AM, Naohisa Goto wrote: > Hi Peter, > > I think the failure may be due to the setting of permission for the file > or the folder. Yes, you are right :) > Please look at the permisson for the file > C:\repositories\bioruby\Test\data\command\echoarg2.bat > > By using explorer, right click the file and see "Property" -- "Security" > and see details. Please confirm if the ACL "Traverse Folder/Execute File" > is allowed and is not denyed. > http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/acl_special_permissions.mspx?mfr=true I see the following table, with two columns of tick boxes: Permissions for XXX: Allow? Deny? Full Control: Neither ticked Modify: Neither ticked Read and Execute: Neither ticked Read: Allow ticked Write: Allow ticked for me, not everyone or administrators Special Permissions: Greyed out Via the advanced settings button, it seems allow permissions are not inherited. > The file permission can also be viewed by using cacls command > on Windows. ?Please show the output of the command. > C:\> cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat > > If the special ACL "FILE_EXECUTE" is shown as "DENY", its execution is > denyed and thus the tests failed. > I've had to edit the line wrapping because otherwise it was unreadable, but there is no mention of FILE_EXECUTE at all. C:\repositories\bioruby>cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat C:\repositories\bioruby\Test\data\command\echoarg2.bat XXX:(special access:) STANDARD_RIGHTS_ALL DELETE READ_CONTROL WRITE_DAC WRITE_OWNER SYNCHRONIZE STANDARD_RIGHTS_REQUIRED FILE_GENERIC_READ FILE_GENERIC_WRITE FILE_READ_DATA FILE_WRITE_DATA FILE_APPEND_DATA FILE_READ_EA FILE_WRITE_EA FILE_READ_ATTRIBUTES FILE_WRITE_ATTRIBUTES BUILTIN\Administrators:(special access:) READ_CONTROL SYNCHRONIZE FILE_GENERIC_READ FILE_READ_DATA FILE_READ_EA FILE_READ_ATTRIBUTES Everyone:(special access:) READ_CONTROL SYNCHRONIZE FILE_GENERIC_READ FILE_READ_DATA FILE_READ_EA FILE_READ_ATTRIBUTES C:\repositories\bioruby> Via the cygwin's ls command the execute permission is not set for echoarg2.bat or echoarg2.sh The following seems to fix it, and the tests then pass on my machine: https://github.com/peterjc/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d https://github.com/bioruby/bioruby/pull/42 If you can commit that (or something similar), we can set this machine up as a buildslave :) Regards, Peter From p.j.a.cock at googlemail.com Fri Nov 25 14:32:50 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 25 Nov 2011 14:32:50 +0000 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) Message-ID: Hello all, There seems to have been a new test failure or regression in Linux 64 Ruby 1.9, Revision 48bd150a6180d59879872bd85dd95c7ddf1a19c0 passed, http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/22/steps/test/logs/stdio commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0 Author: Naohisa Goto Date: Tue Nov 22 17:32:23 2011 +0900 Test bug fix: fixed incomplete Windows platform detection. https://github.com/bioruby/bioruby/commit/48bd150a6180d59879872bd85dd95c7ddf1a19c0 Revision 688779e71a27e861fb01e07f816384561b8cfe45 failed, http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/23/steps/test/logs/stdio commit 688779e71a27e861fb01e07f816384561b8cfe45 Author: Naohisa Goto Date: Thu Nov 24 11:49:30 2011 +0900 Rakefile: new tasks: test-all to run all tests, etc. https://github.com/bioruby/bioruby/commit/688779e71a27e861fb01e07f816384561b8cfe45 1) Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) [/home/buildslave/BuildBot_BioRuby/lin1964/build/test/functional/bio/sequence/test_output_embl.rb:47]: Exception raised: <#>. I hope that helps and that someone can reproduce the failure locally. If need be I can try to bisect the failure here. Peter