From pjotr.public14 at thebird.nl Mon Apr 2 05:49:00 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 2 Apr 2012 11:49:00 +0200 Subject: [BioRuby] GSOC - we are on IRC today and tomorrow Message-ID: <20120402094900.GA12799@thebird.nl> For the Google Summer of Code we are on IRC today (Monday) and tomorrow. The deadline is coming fast, we are there to help. The BioRuby panel (Raoul, Naohisa, Toshiaki, Pjotr & Francesco) From pjotr.public14 at thebird.nl Mon Apr 2 06:06:15 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 2 Apr 2012 12:06:15 +0200 Subject: [BioRuby] BioRuby Constitution (RFC) Message-ID: <20120402100615.GA13035@thebird.nl> In addition to our little FAQ at http://bioruby.open-bio.org/wiki/BioRuby_Panel Gianluca has helped us create a 'BioRuby Constitution' based on that of the Debian project. While it may seem a little like overkill, we see no reason not to have one, assuming it appeals to everyone. The draft is here http://bioruby.open-bio.org/wiki/BioRuby_Constitution Please take a look and tell us to +1 or -1 on the ML. If it gets accepted by the community, I think we make great strides to BioRuby becoming a mature institution. The care-taker BioRuby panel (Raoul, Naohisa, Toshiaki, Pjotr & Francesco) From andrea.nodari91 at gmail.com Tue Apr 3 16:07:54 2012 From: andrea.nodari91 at gmail.com (Andrea Nodari) Date: Tue, 3 Apr 2012 22:07:54 +0200 Subject: [BioRuby] bioruby.org ideas and proposal Message-ID: Hi everybody, I know I am late, but I had some problems with the pc in these days :) Here I have some proposals for bioruby website and soon I'll do my application, again, if you can help me with suggestions and feedback they're very welcome, but I know I'm late: I have three main ideas: 1) Interaction with user. A suggestion could be a sandbox, with some examples of usage of a gem and an interactive environment for try out some features. I think it could be very attractive. (Examples: http://try.redis-db.com/ or http://tryruby.org/) 2) Challanges. As Pjotr said, I think it could be fantastic if some challanges were proposed through github on the main website. 3) A strong integration with github and bioruby.info. I would like to accept the suggestion from the guy who want to do the testing framework. I think it's a good idea to show in the main site the status of various gems. Another thing (easier I think) is the integration of all sources of information such as twitter feed, github issues etc.. The news part in a website is very important :) Well, that's all.. tomorrow I'll come up with some mock ups and more details. Cheers -- Andrea From pjotr.public14 at thebird.nl Wed Apr 4 07:05:38 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 4 Apr 2012 13:05:38 +0200 Subject: [BioRuby] bioruby.org ideas and proposal In-Reply-To: References: Message-ID: <20120404110538.GA30688@thebird.nl> Welcome Andrea, You are late indeed. It will take everything to be in time, for a full proposal. But don't let it discourage you. Your ideas are good, if you send a fleshed out proposal, we can still comment. Pj. On Tue, Apr 03, 2012 at 10:07:54PM +0200, Andrea Nodari wrote: > Hi everybody, > I know I am late, but I had some problems with the pc in these days :) > > Here I have some proposals for bioruby website and soon I'll do my application, > again, if you can help me with suggestions and feedback they're very > welcome, but I know I'm late: > I have three main ideas: > > 1) Interaction with user. > A suggestion could be a sandbox, with some examples of usage of a gem > and an interactive > environment for try out some features. I think it could be very attractive. > (Examples: http://try.redis-db.com/ or http://tryruby.org/) > > 2) Challanges. > As Pjotr said, I think it could be fantastic if some challanges were > proposed through github > on the main website. > > 3) A strong integration with github and bioruby.info. > I would like to accept the suggestion from the guy who want to do the > testing framework. > I think it's a good idea to show in the main site the status of various gems. > > Another thing (easier I think) is the integration of all sources of > information such as twitter feed, > github issues etc.. > The news part in a website is very important :) > > Well, that's all.. tomorrow I'll come up with some mock ups and more details. > > Cheers > -- > Andrea > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Wed Apr 4 17:57:57 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 4 Apr 2012 23:57:57 +0200 Subject: [BioRuby] BioRuby IRC log online Message-ID: <20120404215757.GA1604@thebird.nl> The Perl guys have added a searchable IRC log for us at http://irclog.perlgeek.de/bioruby/today thanks Moritz Lenz for that. From chrisdell at gmail.com Thu Apr 5 13:41:19 2012 From: chrisdell at gmail.com (Chris Dell) Date: Thu, 5 Apr 2012 13:41:19 -0400 Subject: [BioRuby] bioruby.org website problem Message-ID: Hello, It seems that any link with bioruby.org host fails if it doesn't include 'www'. Is this intentional? I don't recall it happening before. Ex: Oops! Google Chrome could not find bioruby.orgSuggestions: - Access a **cached copy of bioruby.?org/?archive/? - Search on Google: Let me know if you need any more information, Chris From pjotr.public14 at thebird.nl Thu Apr 5 13:46:57 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 5 Apr 2012 19:46:57 +0200 Subject: [BioRuby] bioruby.org website problem In-Reply-To: References: Message-ID: <20120405174657.GB12574@thebird.nl> We have recently moved servers. Toshiaki is in charge, but he is travelling now. Patience :) Pj. On Thu, Apr 05, 2012 at 01:41:19PM -0400, Chris Dell wrote: > Hello, > It seems that any link with bioruby.org host fails if it doesn't include > 'www'. Is this intentional? I don't recall it happening before. Ex: > Oops! Google Chrome could not find bioruby.orgSuggestions: > > - Access a **cached > copy > of > bioruby.?org/?archive/? > - Search on Google: > > > > Let me know if you need any more information, > Chris > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From lomereiter at googlemail.com Tue Apr 10 14:50:43 2012 From: lomereiter at googlemail.com (Artem Tarasov) Date: Tue, 10 Apr 2012 22:50:43 +0400 Subject: [BioRuby] Ruby & D shared libraries Message-ID: Hello everybody, Today I started to post some tutorials on how to develop D shared libraries & use them through FFI: http://lomereiter.wordpress.com/tag/ffi Hope it's of interest to some of you. From pjotr.public14 at thebird.nl Tue Apr 10 16:28:06 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 10 Apr 2012 22:28:06 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: References: Message-ID: <20120410202806.GA26494@thebird.nl> Great job Artem :) On Tue, Apr 10, 2012 at 10:50:43PM +0400, Artem Tarasov wrote: > Hello everybody, > > Today I started to post some tutorials on how to develop D shared libraries > & use them through FFI: > http://lomereiter.wordpress.com/tag/ffi > > Hope it's of interest to some of you. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Apr 10 16:54:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 10 Apr 2012 22:54:54 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: References: Message-ID: <20120410205454.GA26717@thebird.nl> >From the blog: (Actually, I would be glad to hear any ideas how to get rid of this extra copying and return just immutable(char)*[] because its layout is the same#) You can enforce a zero byte at the end of the D String, at the point of initialization. That would allow passing s.ptr. Alternatively study Ruby internals - Ruby strings are not zero terminated either, the structure is much like D's... And FFI copies the data in/out of the Ruby String object anyway - I am pretty certain. It sounds costly, but actually, the real cost of FFI is not in data copying, but rather in Ruby object creation (and destruction). To avoid death by object creation, the Narray module may give some clues. Narray maps Ruby array structures directly on C structures. At least, last time I looked. But really, let's not optimize prematurely. A smart API does not need to pump much data... Pj. From pjotr.public14 at thebird.nl Wed Apr 11 01:56:10 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 11 Apr 2012 07:56:10 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: <20120410205454.GA26717@thebird.nl> References: <20120410205454.GA26717@thebird.nl> Message-ID: <20120411055610.GA28834@thebird.nl> Hi Artem, On Tue, Apr 10, 2012 at 10:54:54PM +0200, Pjotr Prins wrote: > But really, let's not optimize prematurely. A smart API does not need > to pump much data... Don't take this as criticism. Your work is very valuable - in fact, I'll use it in the next weeks. I just meant to say that during implementation we'll probably find the transfer of data between the languages is probably not the true bottle neck (based on my experience in BioLib). For example with a GFF3 parser, the file would be read and parsed on the D site. An iterator would pick up results. Copying the buffered results in RAM will not be that expensive, relatively speaking. There is only one way to find out :) Pj. From lomereiter at googlemail.com Wed Apr 11 02:29:33 2012 From: lomereiter at googlemail.com (Artem Tarasov) Date: Wed, 11 Apr 2012 10:29:33 +0400 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: <20120411055610.GA28834@thebird.nl> References: <20120410205454.GA26717@thebird.nl> <20120411055610.GA28834@thebird.nl> Message-ID: > > Don't take this as criticism. Sure, it's just that I like when everything is perfect :) (Btw, I think that criticism is also quite good for this purpose.) > > There is only one way to find out :) > I know. Until it's incorporated in Bio* libraries, there's no way to find out how much all these things cost. Nevertheless, I'll benchmark various ways in the next few days. From bonnal at ingm.org Wed Apr 11 05:40:29 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Wed, 11 Apr 2012 11:40:29 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: Message-ID: https://github.com/SciRuby/nmatrix On 11/04/12 08.29, "Artem Tarasov" wrote: >> >> Don't take this as criticism. > > > Sure, it's just that I like when everything is perfect :) (Btw, I think > that criticism is also quite good for this purpose.) > >> >> There is only one way to find out :) >> > > I know. Until it's incorporated in Bio* libraries, there's no way to find > out how much all these things cost. Nevertheless, I'll benchmark various > ways in the next few days. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Fri Apr 13 05:07:53 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 11:07:53 +0200 Subject: [BioRuby] biogems.info updated In-Reply-To: <20120327115425.GA29301@thebird.nl> References: <20110920165601.GA8933@thebird.nl> <20111014080815.GA25807@thebird.nl> <20120327115425.GA29301@thebird.nl> Message-ID: <20120413090753.GA15000@thebird.nl> Marjan wrote a routine for showing project git commit rate as a colored 'heat map' on http://biogems.info/ the styling is still a bit rough, but I love the functionality! You can see quickly which projects are actively developed. We will do the same for downloads and release date columns. Pj. From bonnal at ingm.org Fri Apr 13 05:53:00 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 13 Apr 2012 11:53:00 +0200 Subject: [BioRuby] biogems.info updated In-Reply-To: <20120413090753.GA15000@thebird.nl> Message-ID: Cool, Is it possible to show the rubygems graph when the mouse is over/cliked the heatmap ? On 13/04/12 11.07, "Pjotr Prins" wrote: > Marjan wrote a routine for showing project git commit rate as a > colored 'heat map' on > > http://biogems.info/ > > the styling is still a bit rough, but I love the functionality! You > can see quickly which projects are actively developed. We will do the > same for downloads and release date columns. > > Pj. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Fri Apr 13 06:02:34 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 12:02:34 +0200 Subject: [BioRuby] biogems.info updated In-Reply-To: References: <20120413090753.GA15000@thebird.nl> Message-ID: <20120413100234.GB16157@thebird.nl> On Fri, Apr 13, 2012 at 11:53:00AM +0200, Raoul Bonnal wrote: > Cool, > Is it possible to show the rubygems graph when the mouse is over/cliked the > heatmap ? Why not. Add it as a feature request to the source repo. Pj. From pjotr.public14 at thebird.nl Fri Apr 13 09:37:45 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 15:37:45 +0200 Subject: [BioRuby] the github effect Message-ID: <20120413133745.GB17752@thebird.nl> The github effect: if you look at the projects on the page - those who do not use github are dropping in the ranks (red arrows on the left). I noticed that before. Not sure why that is. Pj. From pjotr.public14 at thebird.nl Fri Apr 13 09:47:15 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 15:47:15 +0200 Subject: [BioRuby] the github effect In-Reply-To: <20120413133745.GB17752@thebird.nl> References: <20120413133745.GB17752@thebird.nl> Message-ID: <20120413134715.GA18702@thebird.nl> http://biogems.info/ off course. On Fri, Apr 13, 2012 at 03:37:45PM +0200, Pjotr Prins wrote: > The github effect: if you look at the projects on the page - those > who do not use github are dropping in the ranks (red arrows on the > left). I noticed that before. Not sure why that is. > > Pj. > > _______________________________________________ > 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 Sun Apr 15 13:56:37 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sun, 15 Apr 2012 19:56:37 +0200 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: <20120413134715.GA18702@thebird.nl> Message-ID: <20120415175637.992f0920@mail.ingm.it> Finally I got it working. For those who are interested on how to test their gems with 3d party libraries https://github.com/helios/bioruby-samtools/blob/master/.travis.yml language: ruby before_install: - sudo apt-get update - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev before_script: - cd ext - ruby mkrf_conf.rb - rake -f Rakefile - cd ../ rvm: - 1.9.3 _____ From: Pjotr Prins [mailto:pjotr.public14 at thebird.nl] To: bioruby at lists.open-bio.org Sent: Fri, 13 Apr 2012 15:47:15 +0200 Subject: Re: [BioRuby] the github effect http://biogems.info/ off course. On Fri, Apr 13, 2012 at 03:37:45PM +0200, Pjotr Prins wrote: > The github effect: if you look at the projects on the page - those > who do not use github are dropping in the ranks (red arrows on the > left). I noticed that before. Not sure why that is. > > Pj. > > _______________________________________________ > 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 pjotr.public14 at thebird.nl Sun Apr 15 16:30:30 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 15 Apr 2012 22:30:30 +0200 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: <20120415175637.992f0920@mail.ingm.it> References: <20120413134715.GA18702@thebird.nl> <20120415175637.992f0920@mail.ingm.it> Message-ID: <20120415203030.GA28480@thebird.nl> Yes, it is cool they allow adding your own (Debian) packages. On Sun, Apr 15, 2012 at 07:56:37PM +0200, Raoul Bonnal wrote: > Finally I got it working. > For those who are interested on how to test their gems with 3d party libraries > https://github.com/helios/bioruby-samtools/blob/master/.travis.yml > > > > > > language: ruby > before_install: > - sudo apt-get update > - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev > before_script: > - cd ext > - ruby mkrf_conf.rb > - rake -f Rakefile > - cd ../ > rvm: > - 1.9.3 > > > > _____ > > From: Pjotr Prins [mailto:pjotr.public14 at thebird.nl] > To: bioruby at lists.open-bio.org > Sent: Fri, 13 Apr 2012 15:47:15 +0200 > Subject: Re: [BioRuby] the github effect > > http://biogems.info/ off course. > > On Fri, Apr 13, 2012 at 03:37:45PM +0200, Pjotr Prins wrote: > > The github effect: if you look at the projects on the page - those > > who do not use github are dropping in the ranks (red arrows on the > > left). I noticed that before. Not sure why that is. > > > > Pj. > > > > _______________________________________________ > > 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 lomereiter at googlemail.com Mon Apr 16 04:10:54 2012 From: lomereiter at googlemail.com (Artem Tarasov) Date: Mon, 16 Apr 2012 12:10:54 +0400 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: <20120415203030.GA28480@thebird.nl> References: <20120413134715.GA18702@thebird.nl> <20120415175637.992f0920@mail.ingm.it> <20120415203030.GA28480@thebird.nl> Message-ID: They also allow to use 3rd-party PPA repositories, by the way. ( http://about.travis-ci.org/docs/user/build-configuration/) On Mon, Apr 16, 2012 at 12:30 AM, Pjotr Prins wrote: > Yes, it is cool they allow adding your own (Debian) packages. > > On Sun, Apr 15, 2012 at 07:56:37PM +0200, Raoul Bonnal wrote: > > Finally I got it working. > > For those who are interested on how to test their gems with 3d party > libraries > > https://github.com/helios/bioruby-samtools/blob/master/.travis.yml > > > > > > > > > > > > language: ruby > > before_install: > > - sudo apt-get update > > - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev > > before_script: > > - cd ext > > - ruby mkrf_conf.rb > > - rake -f Rakefile > > - cd ../ > > rvm: > > - 1.9.3 > > > From bonnal at ingm.org Mon Apr 16 04:58:14 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 16 Apr 2012 10:58:14 +0200 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: Message-ID: And ... do not forget that travis-ci.org uses 32-bit Ubuntu Linux 11.10 (server edition). http://about.travis-ci.org/docs/user/ci-environment/ On 16/04/12 10.10, "Artem Tarasov" wrote: > They also allow to use 3rd-party PPA repositories, by the way. > (http://about.travis-ci.org/docs/user/build-configuration/) > > On Mon, Apr 16, 2012 at 12:30 AM, Pjotr Prins > wrote: >> Yes, it is cool they allow adding your own (Debian) packages. >> >> On Sun, Apr 15, 2012 at 07:56:37PM +0200, Raoul Bonnal wrote: >>> > Finally I got it working. >>> > For those who are interested on how to test their gems with 3d party >>> libraries >>> > https://github.com/helios/bioruby-samtools/blob/master/.travis.yml >>> > >>> > >>> > >>> > >>> > >>> > language: ruby >>> > before_install: >>> > ? - sudo apt-get update >>> > ? - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev >>> > before_script: >>> > ? - cd ext >>> > ? - ruby mkrf_conf.rb >>> > ? - rake -f Rakefile >>> > ? - cd ../ >>> > rvm: >>> > ? - 1.9.3 >>> > > > From bonnal at ingm.org Mon Apr 16 04:59:20 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 16 Apr 2012 10:59:20 +0200 Subject: [BioRuby] Travis-ci and Bio* TestBoxes Message-ID: We could build our tests VM for each Bio* project https://github.com/travis-ci/travis-boxes -- Ra From p.j.a.cock at googlemail.com Mon Apr 16 07:17:05 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 16 Apr 2012 12:17:05 +0100 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: On Mon, Feb 27, 2012 at 12:41 PM, Peter Cock wrote: > On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: >> 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. > > This issue doesn't happen on two other Ruby 1.9.3 machines > (under Windows XP 32 bit, and a 32 bit Linux Machine). > > Can anyone else reproduce this, or might it be a problem > specific to my 64 bit Linux machine? > > Peter This is still continuing to fail on the nightly tests. If no one else can reproduce it, do you have any suggestions for how I can help you identify the problem? Regards, Peter From pjotr.public14 at thebird.nl Mon Apr 16 07:29:04 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 16 Apr 2012 13:29:04 +0200 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: <20120416112904.GA32746@thebird.nl> I also tried BioRuby on Travis-ci. It fails on all platforms: http://travis-ci.org/#!/pjotrp/bioruby mostly due to libxml. Peter, if you no one picks it up, I may have a go on one of my 64-bit machines. Pj. On Mon, Apr 16, 2012 at 12:17:05PM +0100, Peter Cock wrote: > On Mon, Feb 27, 2012 at 12:41 PM, Peter Cock wrote: > > On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: > >> 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. > > > > This issue doesn't happen on two other Ruby 1.9.3 machines > > (under Windows XP 32 bit, and a 32 bit Linux Machine). > > > > Can anyone else reproduce this, or might it be a problem > > specific to my 64 bit Linux machine? > > > > Peter > > This is still continuing to fail on the nightly tests. If no one else > can reproduce it, do you have any suggestions for how I can > help you identify the problem? > > Regards, > > 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 cjfields at illinois.edu Mon Apr 16 08:41:48 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 16 Apr 2012 12:41:48 +0000 Subject: [BioRuby] Travis-ci and Bio* TestBoxes In-Reply-To: References: Message-ID: <8F01A9D6-F105-4B84-A965-A1C385F2946F@illinois.edu> That's a possibility, but many of the Bio* projects are using buildbot hosted here (by OBF), bioruby was one of them: http://testing.open-bio.org/ Would you prefer to use Travis? chris On Apr 16, 2012, at 3:59 AM, Raoul Bonnal wrote: > We could build our tests VM for each Bio* project > https://github.com/travis-ci/travis-boxes > > -- > Ra > > _______________________________________________ > 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 Apr 16 08:51:33 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 16 Apr 2012 14:51:33 +0200 Subject: [BioRuby] Travis-ci and Bio* TestBoxes In-Reply-To: <8F01A9D6-F105-4B84-A965-A1C385F2946F@illinois.edu> Message-ID: Nono it is just a possibility, that's it. Just because few days ago I was testing native libraries and their VM are 32bit only so I looked for a way to have a 64bit machine with travis. Maybe for biogems plugins we could use custom travis-ci boxes. It's always better to have a backup plan. On 16/04/12 14.41, "Fields, Christopher J" wrote: > That's a possibility, but many of the Bio* projects are using buildbot hosted > here (by OBF), bioruby was one of them: > > http://testing.open-bio.org/ > > Would you prefer to use Travis? > > chris > > On Apr 16, 2012, at 3:59 AM, Raoul Bonnal wrote: > >> We could build our tests VM for each Bio* project >> https://github.com/travis-ci/travis-boxes >> >> -- >> Ra >> >> _______________________________________________ >> 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 Apr 16 09:05:46 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 16 Apr 2012 22:05:46 +0900 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: <201204161314.q3GDESmd030191@portal.open-bio.org> Hi Peter, This may be caused by the order of reading files by using "require" and "autoload", and may be affected by the file order in the directory entry of the file system. I think to avoid cyclic require may solve the problem, and I'll try something later. Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 16 Apr 2012 12:17:05 +0100 Peter Cock wrote: > On Mon, Feb 27, 2012 at 12:41 PM, Peter Cock wrote: > > On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: > >> 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. > > > > This issue doesn't happen on two other Ruby 1.9.3 machines > > (under Windows XP 32 bit, and a 32 bit Linux Machine). > > > > Can anyone else reproduce this, or might it be a problem > > specific to my 64 bit Linux machine? > > > > Peter > > This is still continuing to fail on the nightly tests. If no one else > can reproduce it, do you have any suggestions for how I can > help you identify the problem? > > Regards, > > 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 pjotr.public14 at thebird.nl Sat Apr 21 07:43:58 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 21 Apr 2012 13:43:58 +0200 Subject: [BioRuby] BioRuby Summer of Code (BSoC) Message-ID: <20120421114358.GB16435@thebird.nl> KDE has a program which called Season of KDE http://blog.lydiapintscher.de/2011/04/25/announcing-season-of-kde-2011/ http://dot.kde.org/2010/12/29/season-kde-2010 how about participating a BioRuby Summer of Code this year? You don't have to be a student to take part, as long as you feel like committing some time to the project. It doesn't even have to be coding, it could also be testing and writing documentation and features. Project leaders will be guiding. Pj. From p.j.a.cock at googlemail.com Tue Apr 24 07:24:20 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 24 Apr 2012 12:24:20 +0100 Subject: [BioRuby] OBF GSoC students weekly progress reports Message-ID: Hello all, First, to echo Rob, congratulations to our selected students: http://news.open-bio.org/news/2012/04/students-selected-for-gsoc/ http://lists.open-bio.org/pipermail/gsoc/2012/000049.html Weekly Progress Reports: To encourage community bonding and awareness of what the GSoC 2012 students are doing, this year the OBF is being much clearer about our progress report expectations. We would like every student to setup a blog for the GSoC project (or a category/tag on your existing blog) which you will use to summarize your progress every week, as well as longer posts at the half way evaluation, and at the end of the summer. In addition, after publishing each blog post, we expect you to email the URL and the text of the blog (or if important images or formatting would be lost, at least a short summary) to the host project's mailing list(s) (check with your mentors if the project has more than one) AND the gsoc at open-bio.org mailing list. You will be writing under your own name, but with a clear association with your mentors, the OBF and its projects, so please take this seriously and be professional. Remember this will become part of your online presence, and potentially looked at by future employers and colleagues. Please talk to your mentors about this during the "community bonding" stage of the GSoC code (i.e. the next few weeks before you actually start). Thank you, Peter (On behalf of the OBF GSoC mentors and projects) Note: As per Rob's earlier email, could both students and mentors please ensure you have subscribed to the public OBF GSoC email list at http://lists.open-bio.org/mailman/listinfo/gsoc (I have BCC'd you on this email just in case you haven't done this yet). Thanks! From mail at michaelbarton.me.uk Tue Apr 24 09:41:21 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 24 Apr 2012 09:41:21 -0400 Subject: [BioRuby] Calling Java from Ruby Message-ID: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> Hi Everyone, I had a question about using Java from Ruby, specifically packaging up Java code in a gem. Has anyone tried this? What is the best way of going about this? Compile the Java files at install time or include a precompiled .jar with the gem? I'm considering mixing some clojure code into a ruby gem. Thanks Mike From pjotr.public14 at thebird.nl Tue Apr 24 10:18:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 24 Apr 2012 16:18:35 +0200 Subject: [BioRuby] Calling Java from Ruby In-Reply-To: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> References: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> Message-ID: <20120424141835.GA8832@thebird.nl> Hi Michael, On Tue, Apr 24, 2012 at 09:41:21AM -0400, Michael Barton wrote: > Hi Everyone, Great to hear from you again! > I had a question about using Java from Ruby, specifically > packaging up Java code in a gem. Has anyone tried this? What > is the best way of going about this? Compile the Java files > at install time or include a precompiled .jar with the gem? > > I'm considering mixing some clojure code into a ruby gem. I don't see technical issues. It should be possible to include a jar. Or provide a jar together with a gem. Best is probably to ask on the JRuby mailing list - there must be people thinking about or doing it. Make sure to publish it as a bio-gem! At least, if you want people to find it. Pj. From mail at michaelbarton.me.uk Tue Apr 24 22:47:25 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 24 Apr 2012 22:47:25 -0400 Subject: [BioRuby] Calling Java from Ruby In-Reply-To: <20120424141835.GA8832@thebird.nl> References: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> <20120424141835.GA8832@thebird.nl> Message-ID: <20120425024725.GA14803@bartonh-mbp-01> > > Great to hear from you again! > Thank you. I've been following the bioruby list and the progress on the website is excellent. I think this will be very positive for BioRuby. > > I had a question about using Java from Ruby, > > specifically packaging up Java code in a gem. Has anyone > > tried this? What is the best way of going about this? > > Compile the Java files at install time or include a > > precompiled .jar with the gem? > > > > I'm considering mixing some clojure code into a ruby > > gem. > > I don't see technical issues. It should be possible to > include a jar. Or provide a jar together with a gem. Best > is probably to ask on the JRuby mailing list - there must > be people thinking about or doing it. OK. Thank you for the suggestion. I will try this. > Make sure to publish it as a bio-gem! At least, if you > want people to find it. Still a germ of an idea at the moment, but I will of course. :) Mike From marian.povolny at gmail.com Wed Apr 25 13:17:01 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Wed, 25 Apr 2012 19:17:01 +0200 Subject: [BioRuby] OBF GSoC students weekly progress reports In-Reply-To: References: Message-ID: Hi Peter, Another excited GSoC student here :) I think the idea with a blog for status updates a great idea, I would have done it probably even if it wasn't a requirement. I didn't have a blog before, so I created one at tumblr, and it should be possible for the visitors to leave comments too. But I do agree with you that the ML is a better place for discussions about our GSoC projects. Here is a link to my new blog: http://blog.mpthecoder.com/ GSoC related posts will be tagged with #gsoc ( http://blog.mpthecoder.com/tagged/gsoc). @Lenna Tumblr lets you use your Disqus account if you want to enable comments on your tumblr blog. However, not all themes support it. See the first q&a here for more info: http://www.tumblr.com/help It took me about 2 minutes to create an account on Disqus and link it to my blog. -- Marjan On Tue, Apr 24, 2012 at 1:24 PM, Peter Cock wrote: > Hello all, > > First, to echo Rob, congratulations to our selected students: > http://news.open-bio.org/news/2012/04/students-selected-for-gsoc/ > http://lists.open-bio.org/pipermail/gsoc/2012/000049.html > > Weekly Progress Reports: > > To encourage community bonding and awareness of what the > GSoC 2012 students are doing, this year the OBF is being much > clearer about our progress report expectations. > > We would like every student to setup a blog for the GSoC project > (or a category/tag on your existing blog) which you will use to > summarize your progress every week, as well as longer posts > at the half way evaluation, and at the end of the summer. > > In addition, after publishing each blog post, we expect you to > email the URL and the text of the blog (or if important images > or formatting would be lost, at least a short summary) to the > host project's mailing list(s) (check with your mentors if the > project has more than one) AND the gsoc at open-bio.org > mailing list. > > You will be writing under your own name, but with a clear > association with your mentors, the OBF and its projects, so > please take this seriously and be professional. Remember > this will become part of your online presence, and potentially > looked at by future employers and colleagues. > > Please talk to your mentors about this during the "community > bonding" stage of the GSoC code (i.e. the next few weeks > before you actually start). > > Thank you, > > Peter > > (On behalf of the OBF GSoC mentors and projects) > > Note: As per Rob's earlier email, could both students and mentors > please ensure you have subscribed to the public OBF GSoC email > list at http://lists.open-bio.org/mailman/listinfo/gsoc (I have BCC'd > you on this email just in case you haven't done this yet). Thanks! > From francesco.strozzi at gmail.com Fri Apr 27 10:40:37 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 27 Apr 2012 16:40:37 +0200 Subject: [BioRuby] Bio::Faster update version 0.4.4 Message-ID: Hi all, I have updated the Bio::Faster gem for BioRuby. This gem allows for a fast parsing of FastQ files and it's based on a C extension. Many updates were done since the last version. The gem has been completely rewritten, both the C extension and the Ruby code. The C extension is now called through FFI, so this new gem works fine also with alternative Ruby interpreter, like JRuby. In particular, this new version can handle correctly the formatting errors that may be present in FastQ files, something that was not possible with the previous version due to the external C library used at the time. The RSpecs to build this new version were defined using the test files available from the official FastQ format paper (http://nar.oxfordjournals.org/content/38/6/1767.abstract). The code is available here: https://github.com/fstrozzi/bioruby-faster The new version of the gem is available on RubyGems: gem install bio-faster If you have the chance, please check this new version at let me know of any bugs or problems you may find. Please note that since version 0.4.0 bio-faster does not support parsing FastA files anymore. The code is now only focused on FastQ format. Cheers -- Francesco From pjotr.public14 at thebird.nl Mon Apr 2 09:49:00 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 2 Apr 2012 11:49:00 +0200 Subject: [BioRuby] GSOC - we are on IRC today and tomorrow Message-ID: <20120402094900.GA12799@thebird.nl> For the Google Summer of Code we are on IRC today (Monday) and tomorrow. The deadline is coming fast, we are there to help. The BioRuby panel (Raoul, Naohisa, Toshiaki, Pjotr & Francesco) From pjotr.public14 at thebird.nl Mon Apr 2 10:06:15 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 2 Apr 2012 12:06:15 +0200 Subject: [BioRuby] BioRuby Constitution (RFC) Message-ID: <20120402100615.GA13035@thebird.nl> In addition to our little FAQ at http://bioruby.open-bio.org/wiki/BioRuby_Panel Gianluca has helped us create a 'BioRuby Constitution' based on that of the Debian project. While it may seem a little like overkill, we see no reason not to have one, assuming it appeals to everyone. The draft is here http://bioruby.open-bio.org/wiki/BioRuby_Constitution Please take a look and tell us to +1 or -1 on the ML. If it gets accepted by the community, I think we make great strides to BioRuby becoming a mature institution. The care-taker BioRuby panel (Raoul, Naohisa, Toshiaki, Pjotr & Francesco) From andrea.nodari91 at gmail.com Tue Apr 3 20:07:54 2012 From: andrea.nodari91 at gmail.com (Andrea Nodari) Date: Tue, 3 Apr 2012 22:07:54 +0200 Subject: [BioRuby] bioruby.org ideas and proposal Message-ID: Hi everybody, I know I am late, but I had some problems with the pc in these days :) Here I have some proposals for bioruby website and soon I'll do my application, again, if you can help me with suggestions and feedback they're very welcome, but I know I'm late: I have three main ideas: 1) Interaction with user. A suggestion could be a sandbox, with some examples of usage of a gem and an interactive environment for try out some features. I think it could be very attractive. (Examples: http://try.redis-db.com/ or http://tryruby.org/) 2) Challanges. As Pjotr said, I think it could be fantastic if some challanges were proposed through github on the main website. 3) A strong integration with github and bioruby.info. I would like to accept the suggestion from the guy who want to do the testing framework. I think it's a good idea to show in the main site the status of various gems. Another thing (easier I think) is the integration of all sources of information such as twitter feed, github issues etc.. The news part in a website is very important :) Well, that's all.. tomorrow I'll come up with some mock ups and more details. Cheers -- Andrea From pjotr.public14 at thebird.nl Wed Apr 4 11:05:38 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 4 Apr 2012 13:05:38 +0200 Subject: [BioRuby] bioruby.org ideas and proposal In-Reply-To: References: Message-ID: <20120404110538.GA30688@thebird.nl> Welcome Andrea, You are late indeed. It will take everything to be in time, for a full proposal. But don't let it discourage you. Your ideas are good, if you send a fleshed out proposal, we can still comment. Pj. On Tue, Apr 03, 2012 at 10:07:54PM +0200, Andrea Nodari wrote: > Hi everybody, > I know I am late, but I had some problems with the pc in these days :) > > Here I have some proposals for bioruby website and soon I'll do my application, > again, if you can help me with suggestions and feedback they're very > welcome, but I know I'm late: > I have three main ideas: > > 1) Interaction with user. > A suggestion could be a sandbox, with some examples of usage of a gem > and an interactive > environment for try out some features. I think it could be very attractive. > (Examples: http://try.redis-db.com/ or http://tryruby.org/) > > 2) Challanges. > As Pjotr said, I think it could be fantastic if some challanges were > proposed through github > on the main website. > > 3) A strong integration with github and bioruby.info. > I would like to accept the suggestion from the guy who want to do the > testing framework. > I think it's a good idea to show in the main site the status of various gems. > > Another thing (easier I think) is the integration of all sources of > information such as twitter feed, > github issues etc.. > The news part in a website is very important :) > > Well, that's all.. tomorrow I'll come up with some mock ups and more details. > > Cheers > -- > Andrea > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Wed Apr 4 21:57:57 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 4 Apr 2012 23:57:57 +0200 Subject: [BioRuby] BioRuby IRC log online Message-ID: <20120404215757.GA1604@thebird.nl> The Perl guys have added a searchable IRC log for us at http://irclog.perlgeek.de/bioruby/today thanks Moritz Lenz for that. From chrisdell at gmail.com Thu Apr 5 17:41:19 2012 From: chrisdell at gmail.com (Chris Dell) Date: Thu, 5 Apr 2012 13:41:19 -0400 Subject: [BioRuby] bioruby.org website problem Message-ID: Hello, It seems that any link with bioruby.org host fails if it doesn't include 'www'. Is this intentional? I don't recall it happening before. Ex: Oops! Google Chrome could not find bioruby.orgSuggestions: - Access a **cached copy of bioruby.?org/?archive/? - Search on Google: Let me know if you need any more information, Chris From pjotr.public14 at thebird.nl Thu Apr 5 17:46:57 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 5 Apr 2012 19:46:57 +0200 Subject: [BioRuby] bioruby.org website problem In-Reply-To: References: Message-ID: <20120405174657.GB12574@thebird.nl> We have recently moved servers. Toshiaki is in charge, but he is travelling now. Patience :) Pj. On Thu, Apr 05, 2012 at 01:41:19PM -0400, Chris Dell wrote: > Hello, > It seems that any link with bioruby.org host fails if it doesn't include > 'www'. Is this intentional? I don't recall it happening before. Ex: > Oops! Google Chrome could not find bioruby.orgSuggestions: > > - Access a **cached > copy > of > bioruby.?org/?archive/? > - Search on Google: > > > > Let me know if you need any more information, > Chris > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From lomereiter at googlemail.com Tue Apr 10 18:50:43 2012 From: lomereiter at googlemail.com (Artem Tarasov) Date: Tue, 10 Apr 2012 22:50:43 +0400 Subject: [BioRuby] Ruby & D shared libraries Message-ID: Hello everybody, Today I started to post some tutorials on how to develop D shared libraries & use them through FFI: http://lomereiter.wordpress.com/tag/ffi Hope it's of interest to some of you. From pjotr.public14 at thebird.nl Tue Apr 10 20:28:06 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 10 Apr 2012 22:28:06 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: References: Message-ID: <20120410202806.GA26494@thebird.nl> Great job Artem :) On Tue, Apr 10, 2012 at 10:50:43PM +0400, Artem Tarasov wrote: > Hello everybody, > > Today I started to post some tutorials on how to develop D shared libraries > & use them through FFI: > http://lomereiter.wordpress.com/tag/ffi > > Hope it's of interest to some of you. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Apr 10 20:54:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 10 Apr 2012 22:54:54 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: References: Message-ID: <20120410205454.GA26717@thebird.nl> >From the blog: (Actually, I would be glad to hear any ideas how to get rid of this extra copying and return just immutable(char)*[] because its layout is the same#) You can enforce a zero byte at the end of the D String, at the point of initialization. That would allow passing s.ptr. Alternatively study Ruby internals - Ruby strings are not zero terminated either, the structure is much like D's... And FFI copies the data in/out of the Ruby String object anyway - I am pretty certain. It sounds costly, but actually, the real cost of FFI is not in data copying, but rather in Ruby object creation (and destruction). To avoid death by object creation, the Narray module may give some clues. Narray maps Ruby array structures directly on C structures. At least, last time I looked. But really, let's not optimize prematurely. A smart API does not need to pump much data... Pj. From pjotr.public14 at thebird.nl Wed Apr 11 05:56:10 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 11 Apr 2012 07:56:10 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: <20120410205454.GA26717@thebird.nl> References: <20120410205454.GA26717@thebird.nl> Message-ID: <20120411055610.GA28834@thebird.nl> Hi Artem, On Tue, Apr 10, 2012 at 10:54:54PM +0200, Pjotr Prins wrote: > But really, let's not optimize prematurely. A smart API does not need > to pump much data... Don't take this as criticism. Your work is very valuable - in fact, I'll use it in the next weeks. I just meant to say that during implementation we'll probably find the transfer of data between the languages is probably not the true bottle neck (based on my experience in BioLib). For example with a GFF3 parser, the file would be read and parsed on the D site. An iterator would pick up results. Copying the buffered results in RAM will not be that expensive, relatively speaking. There is only one way to find out :) Pj. From lomereiter at googlemail.com Wed Apr 11 06:29:33 2012 From: lomereiter at googlemail.com (Artem Tarasov) Date: Wed, 11 Apr 2012 10:29:33 +0400 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: <20120411055610.GA28834@thebird.nl> References: <20120410205454.GA26717@thebird.nl> <20120411055610.GA28834@thebird.nl> Message-ID: > > Don't take this as criticism. Sure, it's just that I like when everything is perfect :) (Btw, I think that criticism is also quite good for this purpose.) > > There is only one way to find out :) > I know. Until it's incorporated in Bio* libraries, there's no way to find out how much all these things cost. Nevertheless, I'll benchmark various ways in the next few days. From bonnal at ingm.org Wed Apr 11 09:40:29 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Wed, 11 Apr 2012 11:40:29 +0200 Subject: [BioRuby] Ruby & D shared libraries In-Reply-To: Message-ID: https://github.com/SciRuby/nmatrix On 11/04/12 08.29, "Artem Tarasov" wrote: >> >> Don't take this as criticism. > > > Sure, it's just that I like when everything is perfect :) (Btw, I think > that criticism is also quite good for this purpose.) > >> >> There is only one way to find out :) >> > > I know. Until it's incorporated in Bio* libraries, there's no way to find > out how much all these things cost. Nevertheless, I'll benchmark various > ways in the next few days. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Fri Apr 13 09:07:53 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 11:07:53 +0200 Subject: [BioRuby] biogems.info updated In-Reply-To: <20120327115425.GA29301@thebird.nl> References: <20110920165601.GA8933@thebird.nl> <20111014080815.GA25807@thebird.nl> <20120327115425.GA29301@thebird.nl> Message-ID: <20120413090753.GA15000@thebird.nl> Marjan wrote a routine for showing project git commit rate as a colored 'heat map' on http://biogems.info/ the styling is still a bit rough, but I love the functionality! You can see quickly which projects are actively developed. We will do the same for downloads and release date columns. Pj. From bonnal at ingm.org Fri Apr 13 09:53:00 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 13 Apr 2012 11:53:00 +0200 Subject: [BioRuby] biogems.info updated In-Reply-To: <20120413090753.GA15000@thebird.nl> Message-ID: Cool, Is it possible to show the rubygems graph when the mouse is over/cliked the heatmap ? On 13/04/12 11.07, "Pjotr Prins" wrote: > Marjan wrote a routine for showing project git commit rate as a > colored 'heat map' on > > http://biogems.info/ > > the styling is still a bit rough, but I love the functionality! You > can see quickly which projects are actively developed. We will do the > same for downloads and release date columns. > > Pj. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Fri Apr 13 10:02:34 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 12:02:34 +0200 Subject: [BioRuby] biogems.info updated In-Reply-To: References: <20120413090753.GA15000@thebird.nl> Message-ID: <20120413100234.GB16157@thebird.nl> On Fri, Apr 13, 2012 at 11:53:00AM +0200, Raoul Bonnal wrote: > Cool, > Is it possible to show the rubygems graph when the mouse is over/cliked the > heatmap ? Why not. Add it as a feature request to the source repo. Pj. From pjotr.public14 at thebird.nl Fri Apr 13 13:37:45 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 15:37:45 +0200 Subject: [BioRuby] the github effect Message-ID: <20120413133745.GB17752@thebird.nl> The github effect: if you look at the projects on the page - those who do not use github are dropping in the ranks (red arrows on the left). I noticed that before. Not sure why that is. Pj. From pjotr.public14 at thebird.nl Fri Apr 13 13:47:15 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Apr 2012 15:47:15 +0200 Subject: [BioRuby] the github effect In-Reply-To: <20120413133745.GB17752@thebird.nl> References: <20120413133745.GB17752@thebird.nl> Message-ID: <20120413134715.GA18702@thebird.nl> http://biogems.info/ off course. On Fri, Apr 13, 2012 at 03:37:45PM +0200, Pjotr Prins wrote: > The github effect: if you look at the projects on the page - those > who do not use github are dropping in the ranks (red arrows on the > left). I noticed that before. Not sure why that is. > > Pj. > > _______________________________________________ > 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 Sun Apr 15 17:56:37 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sun, 15 Apr 2012 19:56:37 +0200 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: <20120413134715.GA18702@thebird.nl> Message-ID: <20120415175637.992f0920@mail.ingm.it> Finally I got it working. For those who are interested on how to test their gems with 3d party libraries https://github.com/helios/bioruby-samtools/blob/master/.travis.yml language: ruby before_install: - sudo apt-get update - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev before_script: - cd ext - ruby mkrf_conf.rb - rake -f Rakefile - cd ../ rvm: - 1.9.3 _____ From: Pjotr Prins [mailto:pjotr.public14 at thebird.nl] To: bioruby at lists.open-bio.org Sent: Fri, 13 Apr 2012 15:47:15 +0200 Subject: Re: [BioRuby] the github effect http://biogems.info/ off course. On Fri, Apr 13, 2012 at 03:37:45PM +0200, Pjotr Prins wrote: > The github effect: if you look at the projects on the page - those > who do not use github are dropping in the ranks (red arrows on the > left). I noticed that before. Not sure why that is. > > Pj. > > _______________________________________________ > 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 pjotr.public14 at thebird.nl Sun Apr 15 20:30:30 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 15 Apr 2012 22:30:30 +0200 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: <20120415175637.992f0920@mail.ingm.it> References: <20120413134715.GA18702@thebird.nl> <20120415175637.992f0920@mail.ingm.it> Message-ID: <20120415203030.GA28480@thebird.nl> Yes, it is cool they allow adding your own (Debian) packages. On Sun, Apr 15, 2012 at 07:56:37PM +0200, Raoul Bonnal wrote: > Finally I got it working. > For those who are interested on how to test their gems with 3d party libraries > https://github.com/helios/bioruby-samtools/blob/master/.travis.yml > > > > > > language: ruby > before_install: > - sudo apt-get update > - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev > before_script: > - cd ext > - ruby mkrf_conf.rb > - rake -f Rakefile > - cd ../ > rvm: > - 1.9.3 > > > > _____ > > From: Pjotr Prins [mailto:pjotr.public14 at thebird.nl] > To: bioruby at lists.open-bio.org > Sent: Fri, 13 Apr 2012 15:47:15 +0200 > Subject: Re: [BioRuby] the github effect > > http://biogems.info/ off course. > > On Fri, Apr 13, 2012 at 03:37:45PM +0200, Pjotr Prins wrote: > > The github effect: if you look at the projects on the page - those > > who do not use github are dropping in the ranks (red arrows on the > > left). I noticed that before. Not sure why that is. > > > > Pj. > > > > _______________________________________________ > > 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 lomereiter at googlemail.com Mon Apr 16 08:10:54 2012 From: lomereiter at googlemail.com (Artem Tarasov) Date: Mon, 16 Apr 2012 12:10:54 +0400 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: <20120415203030.GA28480@thebird.nl> References: <20120413134715.GA18702@thebird.nl> <20120415175637.992f0920@mail.ingm.it> <20120415203030.GA28480@thebird.nl> Message-ID: They also allow to use 3rd-party PPA repositories, by the way. ( http://about.travis-ci.org/docs/user/build-configuration/) On Mon, Apr 16, 2012 at 12:30 AM, Pjotr Prins wrote: > Yes, it is cool they allow adding your own (Debian) packages. > > On Sun, Apr 15, 2012 at 07:56:37PM +0200, Raoul Bonnal wrote: > > Finally I got it working. > > For those who are interested on how to test their gems with 3d party > libraries > > https://github.com/helios/bioruby-samtools/blob/master/.travis.yml > > > > > > > > > > > > language: ruby > > before_install: > > - sudo apt-get update > > - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev > > before_script: > > - cd ext > > - ruby mkrf_conf.rb > > - rake -f Rakefile > > - cd ../ > > rvm: > > - 1.9.3 > > > From bonnal at ingm.org Mon Apr 16 08:58:14 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 16 Apr 2012 10:58:14 +0200 Subject: [BioRuby] Bio-samtools & travis-ci & native libraries In-Reply-To: Message-ID: And ... do not forget that travis-ci.org uses 32-bit Ubuntu Linux 11.10 (server edition). http://about.travis-ci.org/docs/user/ci-environment/ On 16/04/12 10.10, "Artem Tarasov" wrote: > They also allow to use 3rd-party PPA repositories, by the way. > (http://about.travis-ci.org/docs/user/build-configuration/) > > On Mon, Apr 16, 2012 at 12:30 AM, Pjotr Prins > wrote: >> Yes, it is cool they allow adding your own (Debian) packages. >> >> On Sun, Apr 15, 2012 at 07:56:37PM +0200, Raoul Bonnal wrote: >>> > Finally I got it working. >>> > For those who are interested on how to test their gems with 3d party >>> libraries >>> > https://github.com/helios/bioruby-samtools/blob/master/.travis.yml >>> > >>> > >>> > >>> > >>> > >>> > language: ruby >>> > before_install: >>> > ? - sudo apt-get update >>> > ? - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev >>> > before_script: >>> > ? - cd ext >>> > ? - ruby mkrf_conf.rb >>> > ? - rake -f Rakefile >>> > ? - cd ../ >>> > rvm: >>> > ? - 1.9.3 >>> > > > From bonnal at ingm.org Mon Apr 16 08:59:20 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 16 Apr 2012 10:59:20 +0200 Subject: [BioRuby] Travis-ci and Bio* TestBoxes Message-ID: We could build our tests VM for each Bio* project https://github.com/travis-ci/travis-boxes -- Ra From p.j.a.cock at googlemail.com Mon Apr 16 11:17:05 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 16 Apr 2012 12:17:05 +0100 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: On Mon, Feb 27, 2012 at 12:41 PM, Peter Cock wrote: > On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: >> 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. > > This issue doesn't happen on two other Ruby 1.9.3 machines > (under Windows XP 32 bit, and a 32 bit Linux Machine). > > Can anyone else reproduce this, or might it be a problem > specific to my 64 bit Linux machine? > > Peter This is still continuing to fail on the nightly tests. If no one else can reproduce it, do you have any suggestions for how I can help you identify the problem? Regards, Peter From pjotr.public14 at thebird.nl Mon Apr 16 11:29:04 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 16 Apr 2012 13:29:04 +0200 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: <20120416112904.GA32746@thebird.nl> I also tried BioRuby on Travis-ci. It fails on all platforms: http://travis-ci.org/#!/pjotrp/bioruby mostly due to libxml. Peter, if you no one picks it up, I may have a go on one of my 64-bit machines. Pj. On Mon, Apr 16, 2012 at 12:17:05PM +0100, Peter Cock wrote: > On Mon, Feb 27, 2012 at 12:41 PM, Peter Cock wrote: > > On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: > >> 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. > > > > This issue doesn't happen on two other Ruby 1.9.3 machines > > (under Windows XP 32 bit, and a 32 bit Linux Machine). > > > > Can anyone else reproduce this, or might it be a problem > > specific to my 64 bit Linux machine? > > > > Peter > > This is still continuing to fail on the nightly tests. If no one else > can reproduce it, do you have any suggestions for how I can > help you identify the problem? > > Regards, > > 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 cjfields at illinois.edu Mon Apr 16 12:41:48 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 16 Apr 2012 12:41:48 +0000 Subject: [BioRuby] Travis-ci and Bio* TestBoxes In-Reply-To: References: Message-ID: <8F01A9D6-F105-4B84-A965-A1C385F2946F@illinois.edu> That's a possibility, but many of the Bio* projects are using buildbot hosted here (by OBF), bioruby was one of them: http://testing.open-bio.org/ Would you prefer to use Travis? chris On Apr 16, 2012, at 3:59 AM, Raoul Bonnal wrote: > We could build our tests VM for each Bio* project > https://github.com/travis-ci/travis-boxes > > -- > Ra > > _______________________________________________ > 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 Apr 16 12:51:33 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 16 Apr 2012 14:51:33 +0200 Subject: [BioRuby] Travis-ci and Bio* TestBoxes In-Reply-To: <8F01A9D6-F105-4B84-A965-A1C385F2946F@illinois.edu> Message-ID: Nono it is just a possibility, that's it. Just because few days ago I was testing native libraries and their VM are 32bit only so I looked for a way to have a 64bit machine with travis. Maybe for biogems plugins we could use custom travis-ci boxes. It's always better to have a backup plan. On 16/04/12 14.41, "Fields, Christopher J" wrote: > That's a possibility, but many of the Bio* projects are using buildbot hosted > here (by OBF), bioruby was one of them: > > http://testing.open-bio.org/ > > Would you prefer to use Travis? > > chris > > On Apr 16, 2012, at 3:59 AM, Raoul Bonnal wrote: > >> We could build our tests VM for each Bio* project >> https://github.com/travis-ci/travis-boxes >> >> -- >> Ra >> >> _______________________________________________ >> 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 Apr 16 13:05:46 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 16 Apr 2012 22:05:46 +0900 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: <201204161314.q3GDESmd030191@portal.open-bio.org> Hi Peter, This may be caused by the order of reading files by using "require" and "autoload", and may be affected by the file order in the directory entry of the file system. I think to avoid cyclic require may solve the problem, and I'll try something later. Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 16 Apr 2012 12:17:05 +0100 Peter Cock wrote: > On Mon, Feb 27, 2012 at 12:41 PM, Peter Cock wrote: > > On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: > >> 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. > > > > This issue doesn't happen on two other Ruby 1.9.3 machines > > (under Windows XP 32 bit, and a 32 bit Linux Machine). > > > > Can anyone else reproduce this, or might it be a problem > > specific to my 64 bit Linux machine? > > > > Peter > > This is still continuing to fail on the nightly tests. If no one else > can reproduce it, do you have any suggestions for how I can > help you identify the problem? > > Regards, > > 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 pjotr.public14 at thebird.nl Sat Apr 21 11:43:58 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 21 Apr 2012 13:43:58 +0200 Subject: [BioRuby] BioRuby Summer of Code (BSoC) Message-ID: <20120421114358.GB16435@thebird.nl> KDE has a program which called Season of KDE http://blog.lydiapintscher.de/2011/04/25/announcing-season-of-kde-2011/ http://dot.kde.org/2010/12/29/season-kde-2010 how about participating a BioRuby Summer of Code this year? You don't have to be a student to take part, as long as you feel like committing some time to the project. It doesn't even have to be coding, it could also be testing and writing documentation and features. Project leaders will be guiding. Pj. From p.j.a.cock at googlemail.com Tue Apr 24 11:24:20 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 24 Apr 2012 12:24:20 +0100 Subject: [BioRuby] OBF GSoC students weekly progress reports Message-ID: Hello all, First, to echo Rob, congratulations to our selected students: http://news.open-bio.org/news/2012/04/students-selected-for-gsoc/ http://lists.open-bio.org/pipermail/gsoc/2012/000049.html Weekly Progress Reports: To encourage community bonding and awareness of what the GSoC 2012 students are doing, this year the OBF is being much clearer about our progress report expectations. We would like every student to setup a blog for the GSoC project (or a category/tag on your existing blog) which you will use to summarize your progress every week, as well as longer posts at the half way evaluation, and at the end of the summer. In addition, after publishing each blog post, we expect you to email the URL and the text of the blog (or if important images or formatting would be lost, at least a short summary) to the host project's mailing list(s) (check with your mentors if the project has more than one) AND the gsoc at open-bio.org mailing list. You will be writing under your own name, but with a clear association with your mentors, the OBF and its projects, so please take this seriously and be professional. Remember this will become part of your online presence, and potentially looked at by future employers and colleagues. Please talk to your mentors about this during the "community bonding" stage of the GSoC code (i.e. the next few weeks before you actually start). Thank you, Peter (On behalf of the OBF GSoC mentors and projects) Note: As per Rob's earlier email, could both students and mentors please ensure you have subscribed to the public OBF GSoC email list at http://lists.open-bio.org/mailman/listinfo/gsoc (I have BCC'd you on this email just in case you haven't done this yet). Thanks! From mail at michaelbarton.me.uk Tue Apr 24 13:41:21 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 24 Apr 2012 09:41:21 -0400 Subject: [BioRuby] Calling Java from Ruby Message-ID: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> Hi Everyone, I had a question about using Java from Ruby, specifically packaging up Java code in a gem. Has anyone tried this? What is the best way of going about this? Compile the Java files at install time or include a precompiled .jar with the gem? I'm considering mixing some clojure code into a ruby gem. Thanks Mike From pjotr.public14 at thebird.nl Tue Apr 24 14:18:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 24 Apr 2012 16:18:35 +0200 Subject: [BioRuby] Calling Java from Ruby In-Reply-To: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> References: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> Message-ID: <20120424141835.GA8832@thebird.nl> Hi Michael, On Tue, Apr 24, 2012 at 09:41:21AM -0400, Michael Barton wrote: > Hi Everyone, Great to hear from you again! > I had a question about using Java from Ruby, specifically > packaging up Java code in a gem. Has anyone tried this? What > is the best way of going about this? Compile the Java files > at install time or include a precompiled .jar with the gem? > > I'm considering mixing some clojure code into a ruby gem. I don't see technical issues. It should be possible to include a jar. Or provide a jar together with a gem. Best is probably to ask on the JRuby mailing list - there must be people thinking about or doing it. Make sure to publish it as a bio-gem! At least, if you want people to find it. Pj. From mail at michaelbarton.me.uk Wed Apr 25 02:47:25 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Tue, 24 Apr 2012 22:47:25 -0400 Subject: [BioRuby] Calling Java from Ruby In-Reply-To: <20120424141835.GA8832@thebird.nl> References: <20120424134121.GC22341@bartonh-mbp-01.uanet.edu> <20120424141835.GA8832@thebird.nl> Message-ID: <20120425024725.GA14803@bartonh-mbp-01> > > Great to hear from you again! > Thank you. I've been following the bioruby list and the progress on the website is excellent. I think this will be very positive for BioRuby. > > I had a question about using Java from Ruby, > > specifically packaging up Java code in a gem. Has anyone > > tried this? What is the best way of going about this? > > Compile the Java files at install time or include a > > precompiled .jar with the gem? > > > > I'm considering mixing some clojure code into a ruby > > gem. > > I don't see technical issues. It should be possible to > include a jar. Or provide a jar together with a gem. Best > is probably to ask on the JRuby mailing list - there must > be people thinking about or doing it. OK. Thank you for the suggestion. I will try this. > Make sure to publish it as a bio-gem! At least, if you > want people to find it. Still a germ of an idea at the moment, but I will of course. :) Mike From marian.povolny at gmail.com Wed Apr 25 17:17:01 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Wed, 25 Apr 2012 19:17:01 +0200 Subject: [BioRuby] OBF GSoC students weekly progress reports In-Reply-To: References: Message-ID: Hi Peter, Another excited GSoC student here :) I think the idea with a blog for status updates a great idea, I would have done it probably even if it wasn't a requirement. I didn't have a blog before, so I created one at tumblr, and it should be possible for the visitors to leave comments too. But I do agree with you that the ML is a better place for discussions about our GSoC projects. Here is a link to my new blog: http://blog.mpthecoder.com/ GSoC related posts will be tagged with #gsoc ( http://blog.mpthecoder.com/tagged/gsoc). @Lenna Tumblr lets you use your Disqus account if you want to enable comments on your tumblr blog. However, not all themes support it. See the first q&a here for more info: http://www.tumblr.com/help It took me about 2 minutes to create an account on Disqus and link it to my blog. -- Marjan On Tue, Apr 24, 2012 at 1:24 PM, Peter Cock wrote: > Hello all, > > First, to echo Rob, congratulations to our selected students: > http://news.open-bio.org/news/2012/04/students-selected-for-gsoc/ > http://lists.open-bio.org/pipermail/gsoc/2012/000049.html > > Weekly Progress Reports: > > To encourage community bonding and awareness of what the > GSoC 2012 students are doing, this year the OBF is being much > clearer about our progress report expectations. > > We would like every student to setup a blog for the GSoC project > (or a category/tag on your existing blog) which you will use to > summarize your progress every week, as well as longer posts > at the half way evaluation, and at the end of the summer. > > In addition, after publishing each blog post, we expect you to > email the URL and the text of the blog (or if important images > or formatting would be lost, at least a short summary) to the > host project's mailing list(s) (check with your mentors if the > project has more than one) AND the gsoc at open-bio.org > mailing list. > > You will be writing under your own name, but with a clear > association with your mentors, the OBF and its projects, so > please take this seriously and be professional. Remember > this will become part of your online presence, and potentially > looked at by future employers and colleagues. > > Please talk to your mentors about this during the "community > bonding" stage of the GSoC code (i.e. the next few weeks > before you actually start). > > Thank you, > > Peter > > (On behalf of the OBF GSoC mentors and projects) > > Note: As per Rob's earlier email, could both students and mentors > please ensure you have subscribed to the public OBF GSoC email > list at http://lists.open-bio.org/mailman/listinfo/gsoc (I have BCC'd > you on this email just in case you haven't done this yet). Thanks! > From francesco.strozzi at gmail.com Fri Apr 27 14:40:37 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 27 Apr 2012 16:40:37 +0200 Subject: [BioRuby] Bio::Faster update version 0.4.4 Message-ID: Hi all, I have updated the Bio::Faster gem for BioRuby. This gem allows for a fast parsing of FastQ files and it's based on a C extension. Many updates were done since the last version. The gem has been completely rewritten, both the C extension and the Ruby code. The C extension is now called through FFI, so this new gem works fine also with alternative Ruby interpreter, like JRuby. In particular, this new version can handle correctly the formatting errors that may be present in FastQ files, something that was not possible with the previous version due to the external C library used at the time. The RSpecs to build this new version were defined using the test files available from the official FastQ format paper (http://nar.oxfordjournals.org/content/38/6/1767.abstract). The code is available here: https://github.com/fstrozzi/bioruby-faster The new version of the gem is available on RubyGems: gem install bio-faster If you have the chance, please check this new version at let me know of any bugs or problems you may find. Please note that since version 0.4.0 bio-faster does not support parsing FastA files anymore. The code is now only focused on FastQ format. Cheers -- Francesco