Re: Teams in changelog trailers

2012-02-19 Thread Charles Plessy
that it is a hint that it should be removed instead. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org

Accepted libbio-graphics-perl 2.26-1 (source all)

2012-02-19 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: libbio-graphics-perl - Generate GD images of Bio::Seq objects Closes: 660481 Changes: libbio-graphics-perl (2.26-1) unstable; urgency=low . * New upstream release (Closes: #660481). Checksums-Sha1

Re: Teams in changelog trailers

2012-02-18 Thread Charles Plessy
with changelogs like the following. r-cran-proto (0.3-9.2-1) unstable; urgency=low * Team upload. [ Carlos Borroto ] * Initial release (Closes: #657994)  -- Charles Plessy ple...@debian.org  Wed, 01 Feb 2012 13:47:24 +0900 At first I worried that it would deprive Carlos

Bug#660165: [new check] Source package names for R libraries (and others if appropriate).

2012-02-16 Thread Charles Plessy
that there is no patch attached... While, if there is agreement to create this new tag, I will try to implement it, everybody is most welcome to be faster than me on this. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan

Accepted permute 0.6-3-1 (source all)

2012-02-16 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-permute - R functions for generating restricted permutations of data Closes: 659689 Changes: permute (0.6-3-1) unstable; urgency=low . * Initial release for Debian (Closes: #659689). Checksums-Sha1

Re: DEP5: minor suggestions - FSF address etc.

2012-02-15 Thread Charles Plessy
illogical. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120215235503.ga14...@falafel.plessy.net

Accepted velvet 1.2.03~nozlibcopy-1 (source all amd64)

2012-02-15 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler Changes: velvet (1.2.03~nozlibcopy-1) unstable; urgency=low . * New upstream

Bug#659863: ITP: vegan -- Community Ecology Package for R

2012-02-14 Thread Charles Plessy
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: vegan Version : 2.0-2 Upstream Author : Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H

Re: Bug#659863: ITP: vegan -- Community Ecology Package for R

2012-02-14 Thread Charles Plessy
Le Tue, Feb 14, 2012 at 10:35:57AM -0800, Don Armstrong a écrit : On Tue, 14 Feb 2012, Charles Plessy wrote: Package name: vegan New R packages shouldn't be added with a source name that does not match the single binary package that they produce. Please consider using r-cran-vegan

Source package names for R libraries (and Perl, Python, Java, …).

2012-02-14 Thread Charles Plessy
?). PS: for the new debian-cran prepository, please consider using the magic tilde in the version numbers. -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject

Accepted r-cran-vcd 1:1.2-12-1 (source all)

2012-02-14 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-vcd - GNU R Visualizing Categorical Data Changes: r-cran-vcd (1:1.2-12-1) unstable; urgency=low . * Team upload. * New upstream release * Corrected Vcs URLs (debian/control). * Using debhelper 8 (debian/control

Bug#659689: ITP: permute -- R functions for generating restricted permutations of data

2012-02-13 Thread Charles Plessy
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: permute Version : 0.6-3 Upstream Author : Gavin L. Simpson gavin.simpson at ucl.ac.uk URL : http://cran.r-project.org/web/packages/permute/ License : GPL-2

Re: DEP5: minor suggestions - FSF address etc.

2012-02-12 Thread Charles Plessy
or delays are asked with a timeline. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120213042825.gc25

Re: DEP5: minor suggestions - FSF address etc.

2012-02-11 Thread Charles Plessy
, and for the next revision, I encourage to propose more in-depth changes as a bug to the debian-policy package. But let's go ahead with the examples as they are now. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org

Accepted ssake 3.8-2 (source all)

2012-02-11 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: ssake - genomics application for assembling millions of very short DNA se ssake-examples - example data for SSAKE, a genomic assembler of short reads Closes: 650469 659428 Changes: ssake (3.8-2) unstable; urgency=low

Re: DEP-5 and files with white spaces

2012-02-10 Thread Charles Plessy
who write the files and the developers who write the parsers. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http

Accepted tophat 1.4.1-1 (source amd64)

2012-02-10 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: tophat - fast splice junction mapper for RNA-Seq reads Changes: tophat (1.4.1-1) unstable; urgency=low . * Team upload. * Initial upload to Debian archive. . [ Carlos Borroto ] * New upstream release . [ Charles Plessy

Accepted r-cran-rsqlite 0.11.1-1 (source amd64)

2012-02-10 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-rsqlite - Database Interface R driver for SQLite Closes: 657995 Changes: r-cran-rsqlite (0.11.1-1) unstable; urgency=low . * Team upload. . [ Carlos Borroto ] * Initial release (Closes: #657995) Checksums

Re: Please test gzip -9n - related to dpkg with multiarch support

2012-02-08 Thread Charles Plessy
previously to effect a version change. Hi, I think that it is important for maintainers that who decided the binNMU and the reason for it are recorded in the changelog, because often these changes are not triggred or coordinated by the maintainers themselves. Have a nice day, -- Charles Plessy

Accepted mummer 3.23~dfsg-1 (source all amd64)

2012-02-06 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: mummer - Efficient sequence alignment of full genomes mummer-doc - Documentation for MUMmer Changes: mummer (3.23~dfsg-1) unstable; urgency=low . * New upstream release adding -D and --banded option to nucmer

Re: DEP-5 and files with white spaces

2012-02-03 Thread Charles Plessy
Le Thu, Feb 02, 2012 at 09:50:09AM +0900, Charles Plessy a écrit : 1) DEP 5 and directory/file names with spaces (http://lists.debian.org/debian-devel/2009/06/msg00155.html) My summary is that the participants were quite divided on whether separating the list of files by spaces

Accepted r-cran-proto 0.3-9.2-1 (source amd64)

2012-02-02 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-proto - Prototype object-based programming Closes: 657994 Changes: r-cran-proto (0.3-9.2-1) unstable; urgency=low . * Team upload. . [ Carlos Borroto ] * Initial release (Closes: #657994) Checksums-Sha1

Re: Patch Tagging Guidelines: DEP-3 moved to ACCEPTED status

2012-02-01 Thread Charles Plessy
that the best way to close the debate is to finish that work. Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org

Re: DEP-5 and files with white spaces

2012-02-01 Thread Charles Plessy
1.0 that we are preparing. What I propose, if you think it is worth, is to open a bug, to track that request for the next revision. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe

Accepted gedit-r-plugin 0.7.1.2-Gtk3-1 (source all)

2012-01-31 Thread Charles Plessy
Plessy ple...@debian.org Description: gedit-r-plugin - Gedit plugin for R statistical computing language Changes: gedit-r-plugin (0.7.1.2-Gtk3-1) unstable; urgency=low . * Team upload. . [ Tobias Hansen ] * New upstream release . [ Charles Plessy ] * Set DM-Upload-Allowed: yes

Bug#657825: ITP: umegaya -- Umegaya is a MEtadata GAtherer using YAml

2012-01-29 Thread Charles Plessy
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: umegaya Version : 0 Upstream Author : Charles Plessy ple...@debian.org URL : http://upstream-metadata.debian.net/ License : BOLA-1.1 Programming Lang: Perl

Accepted grinder 0.4.4-2 (source all)

2012-01-29 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: grinder- Versatile omics shotgun and amplicon sequencing read simulator Closes: 654394 Changes: grinder (0.4.4-2) unstable; urgency=low . * Team upload. . [ Florent Angly ] * Added copyright information for files in inc

Accepted libbio-samtools-perl 1.33-1 (source amd64)

2012-01-28 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing Changes: libbio-samtools-perl (1.33-1) unstable; urgency=low . * [5fd8406] New upstream release 1.33 . [ Nathan Handler ] * [4058f51] Add

Re: Patch Tagging Guidelines: DEP-3 moved to ACCEPTED status

2012-01-19 Thread Charles Plessy
. I admit that as DEP admins, we have not done a good job at pinging DEP drivers. Because of the current confusion of roles on DEP 5, that I push as a driver, I am waiting for its completion before pinging other DEPs as admin. Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan

Re: Releasing DEP 5 in two weeks in the absence of blocking bugs.

2012-01-19 Thread Charles Plessy
Le Wed, Jan 18, 2012 at 06:13:05PM -0800, Russ Allbery a écrit : Charles Plessy ple...@debian.org writes: I do not intend to push a document on which persons disagree, so please, if you think that there are serious problems with the current wording DEP 5, or if you found an important bug

Re: Clarifying the mandatory contents of the Debian copyright file.

2012-01-18 Thread Charles Plessy
, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120118113113.gd26...@merveille.plessy.net

Re: Releasing DEP 5 in two weeks in the absence of blocking bugs.

2012-01-18 Thread Charles Plessy
, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120119005013.gb11...@merveille.plessy.net

Re: status of DEP5: Machine-readable debian/copyright (was: Patch Tagging Guidelines: DEP-3 moved to ACCEPTED status)

2012-01-17 Thread Charles Plessy
requirements for copyright file.”). Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120117115904.gr24

Re: proposed new pseudo-package 'debian-mentors' for handling sponsoring requests

2012-01-17 Thread Charles Plessy
a dedicated pseudo-package would definitely be superior. Another point of my proposal was to ask that developers who call for sponsorship try to review at least another package. Please do not hesitate to take the idea of you like it. http://wiki.debian.org/PackageReview Have a nice day, -- Charles

Clarifying the mandatory contents of the Debian copyright file.

2012-01-17 Thread Charles Plessy
? Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120118004925.gc26...@merveille.plessy.net

Re: Patch Tagging Guidelines: DEP-3 moved to ACCEPTED status

2012-01-16 Thread Charles Plessy
as inspiration the RFCs 822, 2822 and then 5322), or outside the DEP process. Have a nice day, -- Charles Plessy Debian Enhancement Process team, http://dep.debian.net Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble

Using debian/upstream to document things about Upstream with “umegaya”.

2012-01-16 Thread Charles Plessy
/upstream for this purpose, it will make it unavailable for other current or planned purposes. Can we take ‘upstream’ in the ‘debian/’ namespace ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email

Re: Using debian/upstream to document things about Upstream with “umegaya”.

2012-01-16 Thread Charles Plessy
the advantage that is a good mechanism to share the metadata between distributions by sending patches upstream. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org

Re: Ownership issue when repacking source in get-orig-source target

2012-01-14 Thread Charles Plessy
the branches by default; requested in http://bugs.debian.org/625940. But this does not completely solve the problem, as when working on the master branch, ‘git pull’ will not automatically fast-forward the pristine-tar branch. Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan … by the way, how about

Accepted mafft 6.864-1 (source amd64)

2012-01-12 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (6.864-1) unstable; urgency=low . * New upstream release. * Pre-Depends on dpkg (= 1.15.6) for xz compression support (debian/control

Accepted r-cran-genabel 1.7-0-1 (source amd64)

2012-01-12 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-genabel - GNU R package for genome-wide SNP association analysis Changes: r-cran-genabel (1.7-0-1) unstable; urgency=low . * New upstream release. * Depends and Suggests packages according to DESCRIPTION (debian

Accepted bedtools 2.15.0-1 (source amd64)

2012-01-10 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.15.0-1) unstable; urgency=low . [3f8e754] Upstream version 2.15.0. [f27b295] Build-depend on python because of scripts/makeBashScripts.py

Accepted sra-sdk 2.1.7a-1 (source amd64)

2012-01-09 Thread Charles Plessy
debian-med-packag...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: sra-toolkit - utilities for the NCBI Sequence Read Archive sra-toolkit-libs-dev - Development files for the NCBI SRA Toolkit's libraries sra-toolkit-libs0 - Libraries for the SRA Toolkit Closes

Accepted seaview 1:4.3.2-1 (source amd64)

2012-01-08 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: seaview- Multiplatform interface for sequence alignment and phylogeny Changes: seaview (1:4.3.2-1) unstable; urgency=low . * New upstream release. * Moved help file to /usr/share/seaview and left a symbolic link. Checksums-Sha1

Accepted r-cran-randomforest 4.6-6-1 (source amd64)

2012-01-08 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-randomforest - GNU R package implementing the random forest classificator Changes: r-cran-randomforest (4.6-6-1) unstable; urgency=low . * New upstream release. * Suggest r-cran-mass in debian/control

Accepted mira 3.4.0.1-2 (source all amd64)

2012-01-06 Thread Charles Plessy
-packag...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: mira-assembler - Whole Genome Shotgun and EST Sequence Assembler mira-doc - documentation for the mira assembler mira-examples - files to experiment with the mira assembler Closes: 654884 Changes: mira

Re: Source package without a binary

2012-01-05 Thread Charles Plessy
of automatic as-installed package testing, see http://dep.debian.net/deps/dep8/. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive

Accepted cufflinks 1.3.0-1 (source amd64)

2012-01-05 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: cufflinks - Transcript assembly, differential expression and regulation for R Changes: cufflinks (1.3.0-1) unstable; urgency=low . [ Alexandre Mestiashvili ] * New upstream release * Fixed spelling error. * Updated source

Accepted njplot 2.4-1 (source amd64)

2012-01-04 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: njplot - phylogenetic tree drawing program Changes: njplot (2.4-1) unstable; urgency=low . * New upstream release integrating Debian patches. * Removed debian/patches. * Updated debian/copyright to latest format and removed

Re: many packages fail to build twice in a row again

2011-12-21 Thread Charles Plessy
direct evidence that it is unsuitable, see http://bugs.debian.org/642801. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http

Accepted cufflinks 1.2.1-1 (source amd64)

2011-12-11 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: cufflinks - Transcript assembly, differential expression and regulation for R Closes: 627799 Changes: cufflinks (1.2.1-1) unstable; urgency=low . [ Alexandre Mestiashvili ] * New upstream release * added patch to fix bam.h

Accepted velvet 1.1.07~nozlibcopy-1 (source all amd64)

2011-12-08 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler Closes: 647415 Changes: velvet (1.1.07~nozlibcopy-1) unstable; urgency=low

Accepted phyml 2:20110919-1 (source amd64)

2011-12-04 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: phyml - Phylogenetic estimation using Maximum Likelihood Changes: phyml (2:20110919-1) unstable; urgency=low . * New upstream version. * Kept manual's old name with no date (debian/docs, debian/rules). * Do not compress PDFs

Accepted seaview 1:4.3.1-1 (source amd64)

2011-12-02 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: seaview- Multiplatform interface for sequence alignment and phylogeny Changes: seaview (1:4.3.1-1) unstable; urgency=low . * New upstream release incorporating debian/patches/format-security.patch. * Build seaview on armel

Accepted bwa 0.6.1-1 (source amd64)

2011-11-30 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: bwa- Burrows-Wheeler Aligner Closes: 648803 Changes: bwa (0.6.1-1) unstable; urgency=low . [b794564] New upstream release. [fc9894b] Pass -D_NO_SSE2 everywhere except on amd64 (Closes: #648803). [52312b6] Corrected changelog: 0.6.0

Accepted perlprimer 1.1.21-1 (source all)

2011-11-24 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: perlprimer - Graphical design of primers for PCR perlprimer-doc - Tutorial to perlprimer Changes: perlprimer (1.1.21-1) unstable; urgency=low . [0b963e8] New upstream release restoring Ensembl compatibility

Accepted libbio-samtools-perl 1.32-1 (source amd64)

2011-11-23 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files Changes: libbio-samtools-perl (1.32-1) unstable; urgency=low . [36ac64b] New upstream release. [dfb9312] Depend on BioPerl 1.6.901

Accepted bwa 0.6.0-2 (source amd64)

2011-11-21 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: bwa- Burrows-Wheeler Aligner Closes: 648803 Changes: bwa (0.6.0-2) experimental; urgency=low . [9410de3] Disable SSE2 everywhere except on amd64 (Closes: #648803). [fb4c559] Reimplementation of Standard SW for when SSE2

Re: directory under /usr/bin -- Ok or not?

2011-11-17 Thread Charles Plessy
, then we need easy mechanisms for our users to switch namespaces. Perhaps the Debian Pure Blends are a good tool for this… Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel

Accepted r-bioc-edger 2.4.0~dfsg-1 (source all)

2011-11-17 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-bioc-edger - Empirical analysis of digital gene expression data in R Changes: r-bioc-edger (2.4.0~dfsg-1) unstable; urgency=low . [16d49d0] Bioconductor release 2.9. [0e79ff9] Removed User's Guide (no source

Re: Two groups of users, one distro in the middle

2011-11-15 Thread Charles Plessy
could be provided by a third package. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/2015094358.ge27

Accepted clustalx 2.1+lgpl-2 (source amd64)

2011-11-15 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: clustalx - Multiple alignment of nucleic acid and protein sequences (graphic Closes: 648812 Changes: clustalx (2.1+lgpl-2) unstable; urgency=low . [8b9662e] Update providing upgrade path to backports (Closes: #648812). [727f540

Accepted bwa 0.6.0-1 (source amd64)

2011-11-14 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: bwa- Burrows-Wheeler Aligner Changes: bwa (0.6.0-1) experimental; urgency=low . [9ce640c] New upstream release (not to use in a production pipeline). [e641dd6] Corrected the name of the file downloaded by uscan. [4ada685] Pass Dpkg

Accepted muscle 1:3.8.31-1 (source amd64)

2011-11-13 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: muscle - Multiple alignment program of protein sequences Closes: 643443 Changes: muscle (1:3.8.31-1) unstable; urgency=low . [ Charles Plessy ] * New upstream release (Closes: #643443). * debian/control: Enhances: t-coffee

Accepted bwa 0.5.10-1 (source amd64)

2011-11-13 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: bwa- Burrows-Wheeler Aligner Changes: bwa (0.5.10-1) unstable; urgency=low . [a01f6ca] New upstream release. [6d7bc7f] Conforms with Debian Policy version 3.9.2. [125c73d] Corrected Vcs-Git URL. [37f43c9] Normalised machine

Accepted bedtools 2.14.3-1 (source amd64)

2011-11-04 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.14.3-1) unstable; urgency=low . [04f6aa3] Bugfix release. Checksums-Sha1: f7160e8ca716de33a5dda76b8f154c5ba09cb431 1967 bedtools_2.14.3-1.dsc

Accepted r-bioc-limma 3.10.0-1 (source amd64)

2011-11-03 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-bioc-limma - linear models for microarray data Changes: r-bioc-limma (3.10.0-1) unstable; urgency=low . [eebb062] New upstream release (Bioconductor 2.9). [c1a8767] Include 7 digits of the commit ID in the changelog entry

Accepted bedtools 2.14.1-1 (source amd64)

2011-11-02 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.14.1-1) unstable; urgency=low . [bce732c] New upstream release and new tool, multiBedIntersect. Checksums-Sha1

Accepted bedtools 2.14.2-1 (source amd64)

2011-11-02 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.14.2-1) unstable; urgency=low . [356313d] Bugfix release. Checksums-Sha1: 097fc5899be2e89d150dbc3524083c40e024e315 1967 bedtools_2.14.2-1.dsc

Accepted libbio-samtools-perl 1.31-1 (source amd64)

2011-11-01 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files Changes: libbio-samtools-perl (1.31-1) unstable; urgency=low . [abb8487] New upstream release 1.31 [e222e9f] New upstream release 1.30

Accepted r-bioc-biobase 2.14.0-1 (source amd64)

2011-11-01 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-bioc-biobase - base functions for Bioconductor Changes: r-bioc-biobase (2.14.0-1) unstable; urgency=low . [cb6b786] Bioconductor release 2.9. [d70e490] Build-Depend on R = 2.10 according to DESCRIPTION. [ae99e35

Re: Advocating the use of RDF for Debian's published metadata - Was: Re: Proposal for additional metadata in Debian archives (DEP-11)

2011-10-31 Thread Charles Plessy
of the Free software ecosystem. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20111031143235.ga18

Accepted bedtools 2.13.4-1 (source amd64)

2011-10-28 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.13.4-1) unstable; urgency=low . [e553c37] New upstream release. Checksums-Sha1: f726dd0ed96d54e8c7cba259fad2230be201475a 1967 bedtools_2.13.4-1.dsc

Re: Minified files and source code requirement

2011-10-26 Thread Charles Plessy
message here – we could reach it considering all the packages that are part of the same release, by using the dpkg source format 3.0 (git), which would be an efficient way to distribute past source versions and point at the preferred one at the same time. Have a nice day, -- Charles Plessy

Accepted last-align 189-1 (source amd64)

2011-10-22 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: last-align - genome-scale comparison of biological sequences Changes: last-align (189-1) unstable; urgency=low . * New upstream release. * Autogenerate a manual page for last-merge-batches (debian/rules). Checksums-Sha1

Accepted r-cran-rocr 1.0-4-3 (source all)

2011-10-21 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-rocr - GNU R package to prepare and display ROC curves Closes: 646157 Changes: r-cran-rocr (1.0-4-3) unstable; urgency=low . * Support depending on R pre-releases (debian/rules, Closes: #646157). * Machine-readable debian

Accepted r-bioc-edger 2.2.6-1 (source all)

2011-10-19 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-bioc-edger - Empirical analysis of digital gene expression data in R Changes: r-bioc-edger (2.2.6-1) unstable; urgency=low . [c9512e2] New upstream release. [40876f8] Compress binary package with xz. Checksums-Sha1

Accepted catools 1.12-2 (source amd64)

2011-10-18 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: r-cran-catools - GNU R package providing various utility functions Closes: 645832 Changes: catools (1.12-2) unstable; urgency=low . * Uploaded to rebuild against R 2.14 (Closes: #645832) * Corrected Vcs-Browser field in debian

Re: DEP-5 for Upstream

2011-10-15 Thread Charles Plessy
an unversionned URL, it will be fine. The URL chosen in #640737 will probably available by the next upload of the Policy, but that upload is decided taking other factors than the DEP into account, so I can not give a timeline, as I am not a maintainer of the Policy. Have a nice day, -- Charles

Re: Move all to /usr

2011-10-13 Thread Charles Plessy
in practice ? Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20111013230915.ge20...@merveille.plessy.net

Accepted bedtools 2.13.3-1 (source amd64)

2011-10-05 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.13.3-1) unstable; urgency=low . [ea1c596] New upstream release. Checksums-Sha1: d7882e5d74df2e20d9e2b28705add9cb53638413 1967 bedtools_2.13.3-1.dsc

Accepted paml 4.4e-1 (source all amd64)

2011-09-30 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: paml - Phylogenetic Analysis by Maximum Likelihood (PAML) paml-doc - Documentation for PAML Closes: 643843 Changes: paml (4.4e-1) unstable; urgency=low . * Team upload. * New upstream release. * Upload to unstable

Re: Bits from dpkg developers - dpkg 1.16.1

2011-09-28 Thread Charles Plessy
the recommendation of Policy's §10.2 to not build static libraries with -fPIC ? http://www.debian.org/doc/debian-policy/ch-files.html#s-libraries Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject

Accepted velvet 1.1.06~nozlibcopy-1 (source all amd64)

2011-09-27 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: velvet - Nucleic acid sequence assembler for very short reads velvet-example - Example data for the Velvet sequence assembler Changes: velvet (1.1.06~nozlibcopy-1) unstable; urgency=low . [ Andreas Tille

Accepted altree 1.0.1-5 (source all amd64)

2011-09-26 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: altree - program to perform phylogeny-based association and localization a altree-examples - example files for ALTree Closes: 643045 Changes: altree (1.0.1-5) unstable; urgency=low . * Upload source package without

Bug#642801: ftp.debian.org: Please support dpkg-source format 3.0 (git) in our archive.

2011-09-25 Thread Charles Plessy
Package: ftp.debian.org Severity: wishlist Dear FTP team, There are now 4,921 source packages maintained in Git repositories (http://upsilon.cc/~zack/stuff/vcs-usage/), and for some of them the dpkg-source format 3.0 (git), for which support is available in Squeeze, would be natural and

Format 3.0 (git) (was: Re: single-debian-patch (was Re: Bits from dpkg developers - dpkg 1.16.1))

2011-09-24 Thread Charles Plessy
? Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110924063002.gh13...@merveille.plessy.net

Re: Format 3.0 (git)

2011-09-24 Thread Charles Plessy
as intermediate revisions are available. To this paraphrasing of our Social Contract, I would add that 3.0 (git) also fits with another Debian ideal, technical excellence. Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject

Accepted bedtools 2.13.2-1 (source amd64)

2011-09-23 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.13.2-1) unstable; urgency=low . [1930a26] New upstream release. Checksums-Sha1: 46ff4b743bad81eafebd2b5b9302b3fe3edd3c78 1967 bedtools_2.13.2-1.dsc

Re: About DEP-5 Format URL

2011-09-18 Thread Charles Plessy
is not changing much. What I personally do with my packages is to use http://dep.debian.net/deps/dep5/ without mentionning any revision. You can also read more opinions in the following thread: http://lists.debian.org/debian-devel/2011/09/msg00084.html Have a nice day, -- Charles Plessy

Accepted mafft 6.860-1 (source amd64)

2011-09-18 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (6.860-1) unstable; urgency=low . * New upstream release. * Simplified debian/watch. * Updated Homepage (debian/control). * Compress

Accepted last-align 184-1 (source amd64)

2011-09-17 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: last-align - genome-scale comparison of biological sequences Changes: last-align (184-1) unstable; urgency=low . * New upstream release. * Corrected VCS URLs (debian/control). * Compress source and binary package with xz

Accepted seqan 1.3-1 (source all amd64)

2011-09-15 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: seqan-apps - C++ library for the analysis of biological sequences seqan-dev - C++ library for the analysis of biological sequences Closes: 640302 Changes: seqan (1.3-1) unstable; urgency=low . * Team upload. * New

Accepted wise 2.4.1-9 (source all amd64)

2011-09-14 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: wise - comparison of biopolymers, commonly DNA and protein sequences wise-doc - documentation for the wise package Closes: 641333 Changes: wise (2.4.1-9) unstable; urgency=low . * Correct src/models/makefile to link

Accepted bedtools 2.13.1-1 (source amd64)

2011-09-10 Thread Charles Plessy
Changed-By: Charles Plessy ple...@debian.org Description: bedtools - suite of utilities for comparing genomic features Changes: bedtools (2.13.1-1) unstable; urgency=low . [2e3fe5e] New upstream release. [ff5450e] Compress source and binary packages with xz. [ef58a33] Suggest filo

Accepted samtools 0.1.18-1 (source amd64)

2011-09-06 Thread Charles Plessy
...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format samtools - processing sequence alignments in SAM and BAM formats Changes: samtools (0.1.18-1) unstable; urgency=low . [b990d9d3] New upstream

Re: Maintainers, porters, and burden of porting

2011-09-01 Thread Charles Plessy
on architectures unless there is evidence that somebody will actually use these particular packages. Charles -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Re: Maintainers, porters, and burden of porting

2011-08-31 Thread Charles Plessy
in their users community. I think we would benefit of a system that acknowledges this, and should have more flexibility for taking it into account when deciding where we spend our time. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa

Re: Bug#639535: ITP: libdebian-copyright-perl -- perl module to parse, merge and write Debian copyright files

2011-08-27 Thread Charles Plessy
extensively the word “paragraph” instead of “stanza”, perhaps you could either update the terminology in your documentation or add a note that stanza and parargraph are synonymous. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-devel-requ

Accepted mafft 6.859-1 (source amd64)

2011-08-26 Thread Charles Plessy
-By: Charles Plessy ple...@debian.org Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (6.859-1) unstable; urgency=low . * New upstream release. * Converted debian/copyright to machine-readable (DEP 5) format. Checksums-Sha1

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