Some tasks for people loving Ensembl package
[I keep some additional people in Bcc who might not yet subscribed and I do not know whether their e-mail address should be exposed to spammers] Hi, I just commited a very simple typo in an upstream script which should be reported (otherwise the script might stay broken). Is there any volunteer to report this upstream? For the patch either see below[2] or point upstream to the location in SVN[1]. Further there is another problem which needs clarification from upstream. The script ensembl-variation/scripts/import/run.me is executable and most possibly a shell script but lacking a proper shebang line. I admit it is a bit suspicious because it calls to programs which most probably do not exist: 1. bsub (there are some scripts starting with bsub* but not exactly this string) 2. /usr/local/ensembl/bin/perl --> this should definitely replaced by simply calling perl Is there any volunteer who would take over the job of contacting upstream (possibly on behalf of the Debian Med team if this sounds more convincing) to submit the patch and clarify the issue of the run.me script? Kind regards Andreas. [1] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch?view=markup [2] extract from commit mail: - Forwarded message from Andreas Tille - Date: Wed, 7 Dec 2011 21:06:23 + From: Andreas Tille To: debian-med-com...@lists.alioth.debian.org Subject: r8823 - in trunk/packages/ensembl/ensembl/trunk/debian: . patches Author: tille Date: 2011-12-07 21:06:23 + (Wed, 07 Dec 2011) New Revision: 8823 ... Added: trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch === --- trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch (rev 0) +++ trunk/packages/ensembl/ensembl/trunk/debian/patches/fix_usr_bin_env_typo.patch 2011-12-07 21:06:23 UTC (rev 8823) @@ -0,0 +1,8 @@ +--- ensembl-65.orig/ensembl-variation/scripts/misc/generate_reg_file.pl ensembl-65/ensembl-variation/scripts/misc/generate_reg_file.pl +@@ -1,4 +1,4 @@ +-#!/use/bin/env perl ++#!/usr/bin/env perl + + use strict; + use warnings; ___ - End forwarded message - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20111207212937.gc20...@an3as.eu
Bug#651327: ensembl: dependency from outdated libwww-perl version which conflicts with version in Debian main
Package: ensembl Severity: important Tags: experimental Hi, the long description of ensembl says: libwww-perl5.808 will conflict with the latest libwww-perl installation and thus force a downgrade to 5.808, which will disable many other tools on your system. Therefore it is advisable NOT to install this package in parallel with any other software, and/or use a virtual machine or dedicated machine. . We will work to try and remove these dependencies and allow Ensembl to run fully on an up-do-date machine. Finally this perfectly describes the problem. However, this is now also turned into a bug report to have some record we might update to the current status. Kind regards Andreas. -- System Information: Debian Release: 6.0.3 Architecture: i386 (i686) Kernel: Linux 2.6.36-xenU-4814-i386 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20111207194437.21995.82238.report...@mail.an3as.eu
Re: ITP: agherman, a sleep-research experiment manager, EDF recording viewer/scorer, sleep homeostat modeller
Hi Yaroslav and all, Grooming Aghermann with lintian now comes down to these few warnings: W: aghermann: package-name-doesnt-match-sonames libaghcore0 libexstrom0 libsigfile0 W: aghermann: non-dev-pkg-with-shlib-symlink usr/lib/libsigfile.so.0.0.0 usr/lib/libsigfile.so W: aghermann: non-dev-pkg-with-shlib-symlink usr/lib/libaghcore.so.0.0.0 usr/lib/libaghcore.so W: aghermann: non-dev-pkg-with-shlib-symlink usr/lib/libexstrom.so.0.0.0 usr/lib/libexstrom.so As I could figure from http://lintian.debian.org/tags/*, both warnings are a fairly common issue seen in many packages where a package has some libraries which are for internal use only; and so has mine. One straight solution would be simply to link statically against those libraries so that no .so files need to be installed and shipped in the .deb any longer. And I can indeed do away with libaghcore0 and libexstrom0, but the third one (libsigfile.so) is, actually, shared between aghermann the executable proper, and two smallish accessory "tools" (edfhed and edfhed-gtk). Unless I am enlightened with a better way to achieve a perfect clearance in this matter, I tend to think the solution here would be in splitting the project into three packages, something like libsigfile, aghermann, and aghermann-tools. Or will perhaps "overriding" this warning be sufficient? WRT licenses, all is clean (the only third-party code is under src/libexstrom, and it is clearly stated as GPL-licensed on exstrom.com) and all sources contain proper attribution. Incidentally, I am still a little uncertain about the specific GPL version I want to use. All my sources have "GPL" in the header for a license (that is, no indication whether it be version 2 or 3, or "any later version at your option"). Is such brevity acceptable? Cheers, Andrei On 29 November 2011 21:48, Yaroslav Halchenko wrote: > The first buddy of yours should now be 'lintian' tool -- is it silent if > you give it your generated .changes file? > is debian/copyright file complete? (e.g. nothing additional get found > using licensecheck or simple grep)? ;-) > > On Tue, 29 Nov 2011, andrei zavada wrote: >> > * maintenance "inside Debian Med team" sounds good to me too, since >> > �NeuroDebian team is also a part of it and it would allow more helpful >> > �hands to keep it in good shape ;-) >> Now, what do I do next?� Actually, I routinely do dpkg-buildpackage for >> amd64 and i386 (in a chrooted sid) and post .debs to >> [3]github.com/hmmr/aghermann and [4]sf.net/projects/aghermann.� Perhaps, >> for a start, it would be great if someone knowledgable look into >> debian/control to do QA on my "best effort"? (The tarball includes the >> debian-specific bits, but github makes it really easy.) > > -- > Yaroslav O. Halchenko > Postdoctoral Fellow, Department of Psychological and Brain Sciences > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 > WWW: http://www.linkedin.com/in/yarik -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADRQDB32z7r=q+Z==qt80ssf_8smq1-xb39j41yj+sdcfex...@mail.gmail.com
