From bugzilla-daemon at portal.open-bio.org Mon Nov 3 10:52:32 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <200311031552.hA3FqWdg002169@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1550 ------- Additional Comments From jchang@biopython.org 2003-11-03 10:52 ------- I do not have easy access to a Linux machine, and I cannot duplicate it on FreeBSD. When I try the command given above (as myself, without root privileges), the installation completes and installs biopython in my home directory. I also get a message that says I've installed biopython in a place Python doesn't know about. springfield:~/remotecvs/biopython>python setup.py install --home=~ [build messages ...] warning: install_biopython: modules installed to '/home/jchang/lib/python/', which is not in Python's module search path (sys.path) -- you'll have to change the search path yourself Are you using a shell that expands ~ correctly? ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From idoerg at burnham.org Mon Nov 3 11:55:46 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <3FA68892.8030605@burnham.org> -------- Original Message -------- Subject: Re: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Date: Mon, 03 Nov 2003 08:53:48 -0800 From: Iddo Friedberg To: bioopython-dev@biopython.org, jchang@biopython.org References: <200311031552.hA3FqWdg002169@portal.open-bio.org> Jeff, I started looking at it (and I've been through the "~" expansion with Tomas, he tried all manners of path specifications). Apparently there is a problem with localinstall in Biopython. I tried to localinstall 1.23 myself, and it didn't work. (In my case, EUtils tried to install in /usr/local/lib/python/site-packages even though I specified --home=/a/local/userdir). bugzilla-daemon@portal.open-bio.org wrote: > http://bugzilla.bioperl.org/show_bug.cgi?id=1550 > > > > > > ------- Additional Comments From jchang@biopython.org 2003-11-03 10:52 ------- > I do not have easy access to a Linux machine, and I cannot duplicate it on > FreeBSD. When I try the command given above (as myself, without root > privileges), the installation completes and installs biopython in my home > directory. I also get a message that says I've installed biopython in a > place Python doesn't know about. > > springfield:~/remotecvs/biopython>python setup.py install --home=~ > [build messages ...] > warning: install_biopython: modules installed to > '/home/jchang/lib/python/', which is not in Python's module search path > (sys.path) -- you'll have to change the search path yourself > > Are you using a shell that expands ~ correctly? > > > > ------- You are receiving this mail because: ------- > You are the assignee for the bug, or are watching the assignee. > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From bugzilla-daemon at portal.open-bio.org Mon Nov 3 11:29:52 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <200311031629.hA3GTqbJ005055@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1550 ------- Additional Comments From tvinar@math.uwaterloo.ca 2003-11-03 11:29 ------- Created an attachment (id=93) --> (http://bugzilla.bioperl.org/attachment.cgi?id=93&action=view) Complete transcript of the failed installation session This is the transcript which I get when running the following command in freshly unpackage biopython-1.23 directory: python2.2 setup.py install --home=/home/tvinar/ The system is Debian Linux Woody (stable) Hope this helps, Tomas ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 3 11:33:15 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <200311031633.hA3GXFJH005458@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1550 ------- Additional Comments From tvinar@math.uwaterloo.ca 2003-11-03 11:33 ------- Created an attachment (id=94) --> (http://bugzilla.bioperl.org/attachment.cgi?id=94&action=view) List of files installed by the failed session ... and here is the list of files which was created in /home/tvinar/lib/python by the session that failed. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 3 11:34:20 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <200311031634.hA3GYK2F005470@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1550 ------- Additional Comments From tvinar@math.uwaterloo.ca 2003-11-03 11:34 ------- Note, that I have tried different combinations of --home= and --prefix= switches; none of which worked properly and they all failed at the same place. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 3 14:18:05 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1462] building Bio.trie fails Message-ID: <200311031918.hA3JI5rd015938@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1462 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2003-11-03 14:18 ------- Fixed some time ago, version 1.20? Did not update database. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Nov 3 14:31:53 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <200311031931.hA3JVrQZ016894@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1550 ------- Additional Comments From jchang@biopython.org 2003-11-03 14:31 ------- OK, I know what is causing this. setup.py wants to install the dtd files under EUtils to python's site-packages. When it doesn't have permission to write under there, the installation fails. Mine was working because distutils noticed that the files were already there and didn't try to copy them again. The proper fix is to see if distutils passes around the root directory (or home), and install the data fiels under there. However, distutils did not do that the last time I checked, so we may have to hack the setup.py file to recognize --home, and use that. Ugh. I'll look into this later this week. The good news is, this appears to only affect the Bio.EUtils package. If you were not plannign on using this, the rest of Biopython should still work corerctly. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From a.perry at pgrad.unimelb.edu.au Mon Nov 3 21:10:56 2003 From: a.perry at pgrad.unimelb.edu.au (Andrew Perry) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] RE: SeqUtils update In-Reply-To: <200311031717.hA3HH3de008246@portal.open-bio.org> References: <200311031717.hA3HH3de008246@portal.open-bio.org> Message-ID: <3FA70AB0.5050300@pgrad.unimelb.edu.au> Cool! Thanks Yair + Iddo . . . I have always meaning to code these myself ... eventually.. They will be useful. >Date: Tue, 28 Oct 2003 11:37:52 +0100 >From: Yair Benita >Subject: [Biopython-dev] Updated SeqUtils > > >Dear All, >The SeqUtils module has been updated with some new functions. > >CodonUsage module: can be used to generate a codon adaptation index for a >set of genes or computer a codon adaptation index from an existing index. > >IsoelectricPoint module: can be used to determine the isoelectric point of a >protein from its sequence. > >ProtParam module: can be used to compute various properties of a protein, >such as: aromaticity, stability, flexibility and more. > >More information is available as docstrings in each module. > >Special thanks to Iddo Friedberg for all the help. > >Yair > ---------------------------------------------- Andrew Perry Department of Biochemistry and Molecular Biology University of Melbourne, Australia ------------------------------------------------ From bugzilla-daemon at portal.open-bio.org Fri Nov 7 12:28:16 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1550] python setup.py install --home=~ fails Message-ID: <200311071728.hA7HSGcr010944@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1550 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2003-11-07 12:28 ------- The setup.py script was trying to save the EUtils dtd data files in the standard locations (under Python site-packages), etc. However, this fails if the user does not have the required privileges, even if they specify an alternate installation path. Thus, I have updated setup.py to be more sensitive to those changes by modifying a hack from the mx.TextTools installation code. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From jeffrey_chang at stanfordalumni.org Tue Nov 11 14:34:48 2003 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] Future Leadership for the Biopython Project Message-ID: <1C80715C-147E-11D8-BA9B-000A956845CE@stanfordalumni.org> Hello Biopythonistas, After 4 years on the Biopython project, I am turning leadership responsibilities over to Brad Chapman. While I've enjoyed working on Biopython, my responsibilities at my day job has grown considerably over the last year, reducing the amount of time I can afford to spend. While I will no longer be the point person on the project, I will still stay involved and help out where I can. Please do not send inquiries about the project or its organization directly to me any longer. Instead, please send them to biopython-dev@biopython.org. What does this mean for the project? Probably good things, since Biopython is in great hands! :) I imagine that for the short term, things will likely continue the same way. In the long run, however, Brad has some exciting ideas about the direction of the project. Also, I'd like to thank everyone who has helped out with Biopython and have become part of the community. Although I, and now Brad, have been nominally "in charge," Biopython is really a community-driven project. It would not have been as successful if not for people who have put in hours of their "free" time in part for altruistic reasons. Let's keep up the good work! I, for one, am eager to see where Biopython goes, and how it supports biology research in the future. Jeff From hoffman at ebi.ac.uk Wed Nov 12 04:27:50 2003 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] Future Leadership for the Biopython Projec In-Reply-To: <1C80715C-147E-11D8-BA9B-000A956845CE@stanfordalumni.org> Message-ID: On Tue, 11 Nov 2003, Jeffrey Chang wrote: > After 4 years on the Biopython project, I am turning leadership > responsibilities over to Brad Chapman. Let me be the first to thank Jeff for all his hard work over the years. You have led something that is truly useful to many people and helps scientific progress everywhere. Congratulations to Brad on his new responsibility! -- Michael Hoffman European Bioinformatics Institute From bugzilla-daemon at portal.open-bio.org Wed Nov 12 13:40:33 2003 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1555] New: # style comments in FASTA format files Message-ID: <200311121840.hACIeXoM010961@portal.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1555 Summary: # style comments in FASTA format files Product: Biopython Version: Not Applicable Platform: Sun OS/Version: SunOS Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: ktdiedrich@yahoo.com Many FASTA format files have comments of the style # The Bio.Fasta.RecordParser and Bio.Fasta.SequenceParser should skip these lines. Thanks, ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From idoerg at burnham.org Wed Nov 12 14:44:28 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:28 2005 Subject: [Biopython-dev] [Bug 1555] New: # style comments in FASTA format files In-Reply-To: <200311121840.hACIeXoM010961@portal.open-bio.org> References: <200311121840.hACIeXoM010961@portal.open-bio.org> Message-ID: <3FB28D9C.9050203@burnham.org> Can you point to a source of #-commented FASTA files? I don't think that's in any ``official'' specification, but if it's commonplace enough we can work the # thing in. bugzilla-daemon@portal.open-bio.org wrote: > http://bugzilla.bioperl.org/show_bug.cgi?id=1555 > > Summary: # style comments in FASTA format files > Product: Biopython > Version: Not Applicable > Platform: Sun > OS/Version: SunOS > Status: NEW > Severity: normal > Priority: P2 > Component: Main Distribution > AssignedTo: biopython-dev@biopython.org > ReportedBy: ktdiedrich@yahoo.com > > > Many FASTA format files have comments of the style # > The Bio.Fasta.RecordParser and Bio.Fasta.SequenceParser should skip these lines. > Thanks, > > > > ------- You are receiving this mail because: ------- > You are the assignee for the bug, or are watching the assignee. > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From idoerg at burnham.org Sun Nov 16 16:26:04 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:29 2005 Subject: [Biopython-dev] CVS problem Message-ID: <3FB7EB6C.4060203@burnham.org> Hi, Trying to update from CVS, but I cannot seem to get some of the latest stuff. I'm pointing to: pub.open-bio.org And I am tring to update from the top directory using: cvs update . Any ideas? ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From hoffman at ebi.ac.uk Mon Nov 17 04:35:26 2003 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Sat Mar 5 14:43:29 2005 Subject: [Biopython-dev] CVS problem In-Reply-To: <3FB7EB6C.4060203@burnham.org> References: <3FB7EB6C.4060203@burnham.org> Message-ID: On Sun, 16 Nov 2003, Iddo Friedberg wrote: > Trying to update from CVS, but I cannot seem to get some of the latest > stuff. > > [...] > > cvs update . If you use "cvs update -d" it will also checkout new files, not just files already existing in your local copy. HTH, -- Michael Hoffman European Bioinformatics Institute From cm33 at njit.edu Thu Nov 20 21:06:14 2003 From: cm33 at njit.edu (cm33@njit.edu) Date: Sat Mar 5 14:43:29 2005 Subject: [Biopython-dev] installing numeric pyhton for biopython Message-ID: <1069380374.3fbd731633511@webmail.njit.edu> hi does biopython work on python 2.3.2 or only on 2.2.3 I have redhat linux 9 on my system i cannot install numerical pyhton can anyone help me to install the numerical python on linux. I have installed all the other modules it is working fine. i installed numeric pythoon it installs but when iam trying to test it gives me an error no module found. iam eagerly waiting for someones reply. Thanx chidambaram Muthappan From chapmanb at uga.edu Mon Nov 24 11:57:45 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:29 2005 Subject: [Biopython-dev] installing numeric pyhton for biopython In-Reply-To: <1069380374.3fbd731633511@webmail.njit.edu> References: <1069380374.3fbd731633511@webmail.njit.edu> Message-ID: <20031124165745.GC27502@evostick.agtec.uga.edu> Hello; > does biopython work on python 2.3.2 or only on 2.2.3 It works without any problem on python 2.3.2. > I have redhat linux 9 on my system i cannot install numerical pyhton can > anyone help me to install the numerical python on linux. > > I have installed all the other modules it is working fine. > > i installed numeric pythoon it installs but when iam trying to test it gives > me an error no module found. You'll probably have to provide a bit more information before we can help you. Are you installing from source or using rpms? What exactly did you do to install it? What exactly is the error you are getting? The biopython installation instructions at: http://www.biopython.org/docs/install/Installation.html describe installation from source with all of the dependencies. Have you had a look at this? If so, letting us know exactly where problems occur would be very helpful. Hope this helps. Brad From idoerg at burnham.org Thu Nov 27 14:21:11 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat Mar 5 14:43:29 2005 Subject: [Biopython-dev] Spam Filtering? Message-ID: <3FC64EA7.1010809@burnham.org> Should we put a spam filter on our lists? Or start non-member moderation? ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From jeffrey.chang at duke.edu Thu Nov 27 14:29:19 2003 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Sat Mar 5 14:43:29 2005 Subject: [Biopython-dev] Spam Filtering? In-Reply-To: <3FC64EA7.1010809@burnham.org> References: <3FC64EA7.1010809@burnham.org> Message-ID: We already have one! You're just seeing the 10% of the spams that make it through the filters. :) Chris Dagdigian and I get emails about the other ones that the filter holds for moderation, and I actually spend a bit of time every day deleting them from the queue. :( Chris, what do you think? Is it time to revisit the spam filter issue? Jeff On Nov 27, 2003, at 2:21 PM, Iddo Friedberg wrote: > Should we put a spam filter on our lists? Or start non-member > moderation? > > ./I > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > Biopython-dev mailing list > Biopython-dev@biopython.org > http://biopython.org/mailman/listinfo/biopython-dev