Bug#964850: Splitting mime-support into mailcap and media-types (Re: Bug#964850: ITP: mailcap -- Debian's mailcap system, and support programs)
Le Sat, Jul 11, 2020 at 01:48:55PM +0900, Charles Plessy a écrit : > > I plan to split the mime-support package into "mailcap" (this WNPP bug) > that will provide the mailcap system, optionally, and "media-types" > (ITP later), which will provide /etc/mime.types (Priority: standard). > > My goal is to allow for evolution of this package, or alternative > implementations if we need to satisfy at the same time those who would > like some change and those who would not. Lastly, the split will also > allow us to explore the complete replacement of mailcap entries by > information flowing from the FreeDesktop menu system. Dear all, I made progress in preparing the split: `mime-support` will become dummy and depend on `media-types`, providing /etc/mime.types, priority Stanard, and `mailcap`, providing the mailcap system, priority optional. Before I upload to experimental, I would be happy to hear your comments. The source packages are on Salsa. - https://salsa.debian.org/debian/mime-support - https://salsa.debian.org/debian/media-types - https://salsa.debian.org/debian/mailcap Please CC me and the bug; I am not subscribed to debian-devel. Have a nice day, Charles -- Charles Plessy Akano, Uruma, Okinawa, Japan
Bug#964850: ITP: mailcap -- Debian's mailcap system, and support programs
Package: wnpp Severity: wishlist Owner: Charles Plessy * Package name: mailcap Version : 3.65 Upstream Author : the authors of the current mime-support package * URL : Will be hosted on Salsa * License : Public domain Programming Lang: Perl Description : Debian's mailcap system, and support programs Priority: optional Provides: run-mailcap The mailcap system associates media types with programs that can handle them, using system and user configuration files. A file's media type is determined by its extension or by running the "file" command if available. . Other packages register their programs as viewers/editors/composers/etc by placing mailcap entry files or FreeDesktop menu entries in predetermined directories monitored by this package's dpkg triggers. . This package provides a "run-mailcap" program to open arbitrary files, and in addition the "see", "edit", "compose", and "print" aliases to display, alter, create, and print (respectively). I plan to split the mime-support package into "mailcap" (this WNPP bug) that will provide the mailcap system, optionally, and "media-types" (ITP later), which will provide /etc/mime.types (Priority: standard). My goal is to allow for evolution of this package, or alternative implementations if we need to satisfy at the same time those who would like some change and those who would not. Lastly, the split will also allow us to explore the complete replacement of mailcap entries by information flowing from the FreeDesktop menu system. Have a nice week-end, Charles (mime-support maintainer) -- Charles Plessy Akano, Okinawa, Japan
Bug#731599: About the license of the locfit package.
Dear CRAN administrators, following a license review of the locfit R package helped in 2013 by its current maintainer [1], we concluded that: - The original C source code of locfit had a README file where the copyright holders gave a license that forbids to redistribute the work for a fee, and that forbids to benchmark the code against other algorithms, and of course, forbids to remove the license itself[1,2]. - When the locfit R package was initially submitted by one of its authors, the README file was omitted. - Nevertheless, there is nothing that indicates that the license does not apply, as the copyright statements that remain directly refer to the README file. For redistributors such as Debian or Fedora, which only include Free software, the license of locfit C code also precludes redistribution because it is not Free. Moreover, for binary redistribution by third parties, the license of the C code is not compatible with the license of the R code (GPL-2+). Unfortunately, an increasing number of CRAN or Bioconductor package depend directly or transitively on locfit, which is a problem for us. We would like to clarify the license of locfit and if necessary to convince the authors to use alternatives. Our first question to you is if you could clarify what, in your point of view, is the license of the locfit package that CRAN distributes. During the initial submitssion to CRAN, did you have some explicit comments from the authors (who are not the sole copyright holders) that the C code was relicensed to the GPL2+ license, as the DESCRIPTION file might suggest ? Did the original submitters comment on the absent README file ? Then, if the license of locfit is not clearly GPL, can CRAN add (or ask the maintainer) to add back the original license in the soure directory of the C code, and reflect it in the README ? Best regards, [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=731599#27 [2] https://web.archive.org/web/20080925025140/http://cm.bell-labs.com/cm/ms/departments/sia/project/locfit/index.html [3] https://cran.r-project.org/web/packages/locfit/index.html (Please note that the bug address CCed is publicly archived) Charles Plessy and Andreas Tille, for the Debian Med project.
Bug#804007: [Debian-med-packaging] Bug#804007: pre-existing git repository for bcftools
> On Tue, Nov 03, 2015 at 11:22:53PM -0800, Afif Elghraoui wrote: > > > > As I've already made good progress on the package starting anew, would > > it be alright if I discard the old repository on Alioth? That attempt > > targets a much older upstream release. Le Wed, Nov 04, 2015 at 08:59:18AM +0100, Andreas Tille a écrit : > > Keeping Charles in CC to enable him to insist: From my perspective it > is fine to keep the "most promising" repository. If your progress is > larger than the old repository I would not mind about its history. Thanks for the ping; no problem on my side. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan
Bug#798872: [Debian-med-packaging] Bug#798872: RFS: python-pbcommand (NEW)
Le Mon, Oct 26, 2015 at 12:57:58AM -0700, Afif Elghraoui a écrit : > Hi, all, > I've finished preparing the python-pbcommand package. This is part of > the smrtanalysis suite for long-read DNA sequencing data analysis. > > git+ssh://git.debian.org/git/debian-med/python-pbcommand.git > http://anonscm.debian.org/cgit/debian-med/python-pbcommand.git > > Many thanks and regards Uploaded, compressed build logs attached. Cheers, -- Charles python-pbcommand_0.2.16-1_amd64.build.xz Description: application/xz
Bug#802041: [Debian-med-packaging] Bug#802041: RFS: python-avro
Le Sat, Oct 24, 2015 at 05:51:54PM -0700, Afif Elghraoui a écrit : > Hi, team, > I have finished preparing the python-avro package. I need this one > because it's a dependency of python-pbcommand, which is part of the > dependency chain in smrtanalysis. > > git+ssh://git.debian.org/git/debian-med/python-avro.git > http://anonscm.debian.org/cgit/debian-med/python-avro.git > > Would someone please upload to unstable? Uploaded; compressed build logs attached. Cheers, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan python-avro_1.8.0~rc0+dfsg-1_amd64.build.xz Description: application/xz
Bug#794447: [Debian-med-packaging] Bug#794447: RFS: pbgenomicconsensus (NEW)
Le Tue, Oct 13, 2015 at 10:04:27PM -0700, Afif Elghraoui a écrit : > Hi, team, > I finished preparing pbgenomicconsensus. Could someone please upload to > unstable? > > http://anonscm.debian.org/cgit/debian-med/pbgenomicconsensus.git/ > ssh://git.debian.org/git/debian-med/pbgenomicconsensus.git Uploaded; compressed build logs attached. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan pbgenomicconsensus_1.0.0-1_amd64.build.xz Description: application/xz
Bug#726262: Accepted m2crypto 0.21.1-4 (source amd64) into unstable
Le Sat, Sep 12, 2015 at 10:20:25AM +, Emanuele Rocca a écrit : > Urgency: low > Maintainer: Debian QA Group <packa...@qa.debian.org> > Changed-By: Emanuele Rocca <e...@debian.org> > Description: > python-m2crypto - Crypto and SSL toolkit for Python > Changes: > m2crypto (0.21.1-4) unstable; urgency=low > . >* QA upload. >* Maintainer field set to QA Group. >* Bump Standards-Version to 3.9.6. >* Remove Uploaders field. >* Fix debian/watch by using pypi.debian.net. >* Do not start synopsis with an article. Hi Emanuele, thank you for formally relieving me from the maintenance of m2crypto. In #726262, where I ophaned it, a few people offered their help, but did not follow up. Have you considered re-contacting them or the Debian Python Applications or Modules Teams, that maintain some packages depending on m2crypto ? The reason I ask is that, as the name indicates, m2crypto might be involved in security issues anytime, and it would obviously better if we found a person or a team knowledgeable in at least python or cryptography, to increase Debian's chances of reacting quickly. One painful alternative is to remove m2crypto, and therefore its dependency chain, given the concerns of not being able to deal with potential problems in the future. Anyway, thanks for your intervention, and have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan
Bug#787982: [Debian-med-packaging] Bug#787982: python-pbh5tools ready to upload
Le Sat, Aug 15, 2015 at 03:26:54PM -0700, Afif Elghraoui a écrit : I've finished preparing the first version of the pbh5tools package. Could someone upload to unstable please? Hi Afif, I uploaded it. Here are the build logs. Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan python-pbh5tools_0.8.0+dfsg-1_amd64.build.xz Description: application/xz
Bug#786889: ITP: media-types -- List of media types associated to file suffixes
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: media-types Version : 2.1.44 Upstream Author : Mostly Ville Skyttä ville.sky...@iki.fi, for Fedora URL : https://git.fedorahosted.org/cgit/mailcap.git/tree/mime.types License : Public domain Programming Lang: Just a text file Description : List of media types associated to file suffixes The IANA [Internet Assigned Numbers Authority] maintains a list of media types (see [RFC 6838]) and their detailed descriptions that indicate which file name suffixes, if any, are used to signal that a given file is of the given type. On Unix systems, the file `/etc/mime.types` summarises this information in a plain text tabular format (media types were formerly called MIME types). . The IANA does not provide directly a `mime.types`f ile. To keep it up to date, one has to regularly monitor changes on the IANA website. This is done very well by the maintainer of Fedora's `mailcap` package. This Debian package provides Fedora's `/etc/mime.types` in Debian systems. . [Internet Assigned Numbers Authority]: https://www.iana.org/assignments/media-types [RFC 6838]: https://tools.ietf.org/html/rfc4855 Further comments: Currently, /etc/mime.types is provided by the mime-support package, which I maintain. This package also provides Debian's implementation of the Mailcap system (https://tools.ietf.org/html/rfc1524). However, the /etc/mime.types files is consumed by other systems, like Apache, and not all computers need to have the Mailcap system installed. Moreover, maintaing the /etc/mime.types is time-consuming (see above), so I plan to track Fedora's file. Since it lives in a Git repository it is tempting to base a Debian source package on it, but this Debian package would only distribute a single file. Alternatively, /etc/mime.types could be moved to a different package, for instance base-files, but this would increase the work load of the package maintainer. Your comments are welcome. Please CC this ITP as I am not subscribed to debian-devel. Cheers, Charles -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150526131841.22093.98692.reportbug@falafel
Bug#726262: Will help packaging
Le Fri, Apr 11, 2014 at 01:42:40PM -0600, Mike Place a écrit : I'm on the SaltStack core development team. I will volunteer to maintain the m2crypto package going forward. Whom do I need to contact to help to manage the transition? Dear Mike, I am worried that I forgot to answer your proposition for taking over the package… You are of course very welcome to do so, there is no extra permission to ask for. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140923102357.GA2435@aqwa.igloo
Bug#762412: ITP: paraclu -- Parametric clustering of genomic and transcriptomic features
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org * Package name: paraclu Version : 9 Upstream Author : Martin C. Frith * URL : http://www.cbrc.jp/paraclu/ * License : GPL-3+ Programming Lang: C++ Description : Parametric clustering of genomic and transcriptomic features Paraclu finds clusters in data attached to sequences. It was first applied to transcription start counts in genome sequences, but it could be applied to other things too. . Paraclu is intended to explore the data, imposing minimal prior assumptions, and letting the data speak for itself. . One consequence of this is that paraclu can find clusters within clusters. Real data sometimes exhibits clustering at multiple scales: there may be large, rarefied clusters; and within each large cluster there may be several small, dense clusters. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140922014634.32408.15482.reportbug@localhost.localdomain
Bug#729203: Reintroducing FFmpeg to Debian
user debian-le...@lists.debian.org usertags 729203 one-copyright-review thanks Le Fri, Aug 08, 2014 at 01:53:15AM +0200, Andreas Cadhalpun a écrit : Now, could anyone review the debian/copyright file of ffmpeg? The sources are available in this repository: https://anonscm.debian.org/cgit/collab-maint/ffmpeg.git Hi Andreas, I searched for license information missing from your debian/copyright and could find only one case, libavutil/x86/x86inc.asm, which is under the ISC license. The debian/copyright file of your package looks comprehensive to me. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140809094503.ga24...@falafel.plessy.net
Bug#753704: ITP: amap -- Next-generation scanning tool for pentesters
Le Sun, Jul 06, 2014 at 10:33:35AM +0200, Andreas Tille a écrit : On Sat, Jul 05, 2014 at 04:37:16PM +0200, Ralf Treinen wrote: This violates the Policy's section 10.1, but it is still my favorite solution for the reason that you explained above. I don't agree, packages should not be in conflict when it can be easily avoided by renaming files. +1 Hi Andreas, Feel free to rename yourself, but do not forget to remove me from the uploaders list. On my side I find these renamings harmful and illogical. The probability that people want to use both amaps on the same machine is close to zero, and the probability that users of both amaps will be annoyed by the rename is close to one. I think that these renamings are applied dogmatically in a way that makes Debian inferior. I do not want to participate to this. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140706134930.ga2...@falafel.plessy.net
Bug#753704: ITP: amap -- Next-generation scanning tool for pentesters
Le Fri, Jul 04, 2014 at 02:20:12PM +0100, Gianfranco Costamagna a écrit : Package: wnpp Severity: wishlist Owner: Gianfranco Costamagna costamagnagianfra...@yahoo.it * Package name : amap Version : 5.4 Upstream Author : Van Hauser v...@thc.org * URL : http://www.thc.org/thc-amap/ * License : GPL-2+ Programming Lang: C Description : Next-generation scanning tool for pentesters Dear Gianfranco, note that there is already a program called ‘amap’ in Debian, to align nucleic acid sequences. It is distributed by the package ‘amap-align’. Have a nice week-end, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140705104535.ge11...@falafel.plessy.net
Bug#753704: ITP: amap -- Next-generation scanning tool for pentesters
Le Sat, Jul 05, 2014 at 11:56:28AM +0100, Gianfranco Costamagna a écrit : I looked before at amap-align, but the package provided by your one is only amap-align, there is no amap installable, hence I don't think there will be a clash for the packages, right? The ‘amap-align’ package version 2.2-4 install the file ‘amap’ in ‘/usr/bin’, this is why I am worried about clashes. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140705110329.gf11...@falafel.plessy.net
Bug#753704: ITP: amap -- Next-generation scanning tool for pentesters
Il Sabato 5 Luglio 2014 13:03, Charles Plessy ple...@debian.org ha scritto: The ‘amap-align’ package version 2.2-4 install the file ‘amap’ in ‘/usr/bin’, this is why I am worried about clashes. Le Sat, Jul 05, 2014 at 12:11:37PM +0100, Gianfranco Costamagna a écrit : According to both popcons, and according to the fact that both of them are really niche packages and in really different environments (one for penetration testing and the other for med science) how do you feel about making them non-coinstallable? This violates the Policy's section 10.1, but it is still my favorite solution for the reason that you explained above. Please ping me if your package has been accepted in unstable and installs a ‘amap’ file in ‘/usr/bin’. I will then upload an update of ‘amap-align’ that conflictson ‘amap’. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140705120145.gh11...@falafel.plessy.net
Bug#731599: ITP: r-cran-locfit -- GNU R local regression, likelihood and density estimation
Le Sat, Dec 07, 2013 at 02:38:04PM +0100, Andreas Tille a écrit : Package: wnpp Severity: wishlist Owner: Andreas Tille ti...@debian.org * Package name: r-cran-locfit Version : 1.5-9.1 Upstream Author : Catherine Loader * URL : http://cran.r-project.org/web/packages/locfit * License : GPL Programming Lang: R Description : GNU R local regression, likelihood and density estimation This package provides a set of functions to support local regression, likelihood and density estimation. It is helpful for running the test suites of several GNU R related packages in Debian. Hi Andreas, locfit rings a bell. The cufflinks package also contains files from locfit with the same copyright holders, and there the license has non-free clauses. So either there are good news that somebody from the R community managed to get locfit relicensed (which would mean that we can move cufflinks to main), or maybe there are bad news that locfit's README file in the R package was wrongly removed, and the package is actually non-free... http://ftp-master.metadata.debian.org/changelogs/non-free/c/cufflinks/cufflinks_2.1.1-4_copyright Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131207225337.gd5...@falafel.plessy.net
Bug#729483: Copyright review for the package vokoscreen 1.8.1-1.
user debian-le...@lists.debian.org usertags 729483 one-copyright-review thanks Dear Joao, In the hope of speeding up and strenghtening the processing of the NEW queue I had a look at your package vokoscreen 1.8.1-1. The rationale is explained in the proposal in the following wiki page. http://wiki.debian.org/CopyrightReview I have not found explicit copyright or licence statement that would be missing from your debian/copyright file, with perhaps the exception of this public domain dedication in libqxt/qxtglobal.h. / ** This file is derived from code bearing the following notice: ** The sole author of this file, Adam Higerd, has explicitly disclaimed all ** copyright interest and protection for the content within. This file has ** been placed in the public domain according to United States copyright ** statute and case law. In jurisdictions where this public domain dedication ** is not legally recognized, anyone who receives a copy of this file is ** permitted to use, modify, duplicate, and redistribute this file, in whole ** or in part, with no restrictions or conditions. In these jurisdictions, ** this file shall be copyright (C) 2006-2008 by Adam Higerd. / You might consider adding it to your Debian copyright file. Have a nice Sunday, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131117111521.ga30...@falafel.plessy.net
Bug#729282: ITP: htslib -- C library for high-throughput sequencing data formats
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Hello everybody,
I intend to package the HTSlib, that some existing packages (samtools,
tabix) will need later.
Cheers,
-- Charles Plessy, Tsurumi, Kanagawa, Japan
Package name: htslib
Version : 0.2
Upstream Author : See below
URL : https://github.com/samtools/htslib/tree/develop
License : Mostly MIT, see below
Programming Lang: C
Description : C library for high-throughput sequencing data formats
Package: libhts0
Architecture: any
Multi-Arch: same
Depends: ${shlibs:Depends},
${misc:Depends}
Description: C library for high-throughput sequencing data formats
HTSlib is a unified C library for accessing common file formats, such as SAM
(Sequence Alignment/Map) and VCF (Variant Call Format), used for nucleic acid
sequence data obtained by high-throughput sequencing.
.
HTSlib implements a generalized BAM (binary SAM) index. The HTSlib file
reader first looks for the new index and then for the old if the new index is
absent.
.
HTSlib is still experimental. It has not been tested on large-scale real
data. Some
useful APIs are missing.
Package: libhts-dev
Architecture: any
Multi-Arch: same
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends}
Description: Development files for the HTSlib
HTSlib is a unified C library for accessing common file formats, such as SAM
(Sequence Alignment/Map) and VCF (Variant Call Format), used for nucleic acid
sequence data obtained by high-throughput sequencing.
.
This package contains development files: headers, static library, manual pages,
etc.
Package: htslib-test
Architecture: all
Depends: ${misc:Depends}
Description: Test data for HTSlib
HTSlib is a unified C library for accessing common file formats, such as SAM
(Sequence Alignment/Map) and VCF (Variant Call Format), used for nucleic acid
sequence data obtained by high-throughput sequencing.
.
This package contains test files and scripts for the HTSlib.
Files: *
Copyright: (C) 2012-2013 Genome Research Ltd.
(c) 2008 Broad Institute / Massachusetts Institute of Technology
The Wellcome Trust Sanger Institute
(c) 2008, 2009, 2011 by Attractive Chaos attrac...@live.co.uk
License: MIT
Files: cram/*
Copyright: (c) 2012-2013 Genome Research Ltd.
(c) 1995-1996 MEDICAL RESEARCH COUNCIL
License: Various_BSD-3-Clause
Files: cram/md5.?
Copyright: No copyright is claimed
License: solar-MD5
This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
MD5 Message-Digest Algorithm (RFC 1321).
.
Homepage:
http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
.
Author:
Alexander Peslyak, better known as Solar Designer solar at openwall.com
.
This software was written by Alexander Peslyak in 2001. No copyright is
claimed, and the software is hereby placed in the public domain.
In case this attempt to disclaim copyright and place the software in the
public domain is deemed null and void, then the software is
Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
general public under the following terms:
.
Redistribution and use in source and binary forms, with or without
modification, are permitted.
.
There's ABSOLUTELY NO WARRANTY, express or implied.
Files: htslib/razf.?
Copyright: 2008, Jue Ruan ruan...@gmail.com, Heng Li l...@sanger.ac.uk
License: BSD-2-clause~with-minor-differences-in-the-disclaimer
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Bug#681335: Review of the copyright file for libmath-int64-perl 0.30-1.
user debian-le...@lists.debian.org usertags 681335 one-copyright-review thanks Dear Perl packagers, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page. http://wiki.debian.org/CopyrightReview I only found a minor error (strtoint.h - strtoint64.h), that I corrected in the package's git repository. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131026071105.gf17...@falafel.plessy.net
Bug#725205: Copyright review for the packages libpath-isdev-perl, libpath-finddev-perl and libfile-sharedir-projectdistdir-perl.
user debian-le...@lists.debian.org usertags 725205 one-copyright-review usertags 725204 one-copyright-review usertags 725135 one-copyright-review thanks Dear Perl maintainers, In the hope of speeding up and strenghtening the processing of NEW I had a look at your packages libpath-isdev-perl, libpath-finddev-perl and libfile-sharedir-projectdistdir-perl. The rationale is explained in the proposal in the following wiki page. http://wiki.debian.org/CopyrightReview I have not found explicit copyright or licence statement that would be missing from your debian/copyright file. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131026071526.gg17...@falafel.plessy.net
Bug#726262: O: python-m2crypto -- a crypto and SSL toolkit for Python
Le Thu, Oct 24, 2013 at 01:38:42AM +0300, Andrii Senkovych a écrit : Sorry, I've found the library is going to be orphaned just now (just read debian-devel wnpp digest). I have also found that subject is a dependency for salt-common which is under team maintainership I'm a member of. I'm going to ask if it's better to support via DPMT or move under maintainership of pkg-salt-team since latter primarily uses git. Also asking Salt team if it's ok for me to maintain this library under team Maintainership if such decision is made. Hi Andrii, thanks a lot for proposing your help, and sorry that I forgot to CC the reverse-dependent packages ! Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131023225206.gc28...@falafel.plessy.net
Bug#726262: O: python-m2crypto -- a crypto and SSL toolkit for Python
Package: wnpp Severity: normal Subject: O: python-m2crypto -- a crypto and SSL toolkit for Python Le Mon, Sep 23, 2013 at 12:44:56PM +0900, Charles Plessy a écrit : m2crypto currently has 5 bugs of severity Important, which I am not able to solve. I was wondering if Dima was planning to solve them or is the Python modules team would be interested in taking care of m2crypto together with Dima. The source package is currenlty maintained in Git with patches commited direclty to the master branch. Since this is definitely not (yet ?) a standard way, please let me know if you would like me to convert it to a more classical packaging style. Le Sat, Oct 05, 2013 at 08:46:18AM +0900, Charles Plessy a écrit : Dima, I think that I will orphan the package if you do not answer. Anyway, it is easy to be reverted. In case I orphan the package, would the Python modules team interested in adopting it ? Since nobody answered to my emails, I orphan this package. -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131013232514.ga25...@falafel.plessy.net
Bug#692872: Review of the copyright file for owncloud-client 1.3.0+dfsg-1.
user debian-le...@lists.debian.org usertag 692872 one-copyright-review thanks Dear owncloud-client maintainers, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package (from the Git repository). The rationale is explained in the proposal in the following wiki page. http://wiki.debian.org/CopyrightReview I have not found explicit copyright or licence statement that would be missing from your debian/copyright file. However, I looked at the contents of the resources directory, and it appears that some images are missing their source, as they were made as a vector graphics with Inkscape. See for instance dialog-ok.png. $ exiftool resources/dialog-ok.png ExifTool Version Number : 9.13 File Name : dialog-ok.png Directory : resources File Size : 1948 bytes File Modification Date/Time : 2013:08:03 19:10:13+09:00 File Access Date/Time : 2013:08:03 19:11:13+09:00 File Inode Change Date/Time : 2013:08:03 19:10:13+09:00 File Permissions: rw-r--r-- File Type : PNG MIME Type : image/png Image Width : 48 Image Height: 48 Bit Depth : 8 Color Type : RGB with Alpha Compression : Deflate/Inflate Filter : Adaptive Interlace : Noninterlaced Significant Bits: 8 8 8 8 Pixels Per Unit X : 1329 Pixels Per Unit Y : 1329 Pixel Units : Meters Software: www.inkscape.org Image Size : 48x48 In my understanding, it would be necessary to include their sources in your package to strictly conform with the DFSG. However, I am not sure if this is strictly enforced or not. Have a nice week-end, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130803113528.gf17...@falafel.plessy.net
Bug#710786: Review of the copyright file for ruby-fakeweb 1.3.0debian-1
user debian-le...@lists.debian.org usertags 710786 one-copyright-review thanks Dear Joseph, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page. http://wiki.debian.org/CopyrightReview I have not found explicit copyright or licence statement that would be missing from your debian/copyright file. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130803114501.gg17...@falafel.plessy.net
Bug#700860: About your ITP on r-cran-scales.
Le Sun, Jun 09, 2013 at 12:51:58PM +0200, Benjamin Eikel a écrit : yes, I am fine with it. As Ivo already mentioned, he already did some work and uploaded some of his packages. If I can help somehow, please contact me. My goal is just to have an up to date version of ggplot2 in Debian. Hi Benjamin, I went ahead and uploaded r-cran-munsell with you as the Uploader. This is needed before uploading r-cran-scales. Do you intend to take care of further updates ? Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130610050515.gb17...@falafel.plessy.net
Bug#700860: About your ITP on r-cran-scales.
Dear Benjamin, I am contacting you about work on a r-cran-scales. Are you still interested in it ? If yes, please contact us on the Debian Med mailing list, so that we can coordinate an upload. As you know, we need it to update ggplot2. Have a nice Sunday, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130609010439.ga26...@falafel.plessy.net
Bug#705653: ITP: numatop -- display Linux processes on a NUMA system
Le Thu, Apr 18, 2013 at 03:10:37AM +, Anibal Monsalve Salazar a écrit : Package: wnpp Severity: wishlist X-Debbugs-CC: debian-de...@lists.debian.org * Package name: numatop Version : 1.0 Upstream Author : Jin Yao * URL : https://01.org/numatop * License : See below Description : display Linux processes on a NUMA system Description NumaTOP is an observation tool for runtime memory locality characterization and analysis of processes and threads running on a NUMA system. It helps the user characterize the NUMA behavior of processes and threads and identify where the NUMA-related performance bottlenecks reside. Hi Anibal, how is it going ? It has been years since you sponsored my packages, let me thank you again :) For that ITP, I would like to suggest to expand the NUMA acronym somewhere in the long description. Have a nice week-end, Charles -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130420004014.gc15...@falafel.plessy.net
Bug#705085: ITP: pear-aws-channel -- PEAR channel definition file for aws
Le Tue, Apr 09, 2013 at 09:49:25PM -0400, David Prévot a écrit : Package: wnpp Severity: wishlist Owner: David Prévot taf...@debian.org Control: block 705070 by -1 * Package name: pear-aws-channel Version : 0~20130409 * URL : http://pear.amazonwebservices.com/ * License : public-domain Programming Lang: XML Description : PEAR channel definition file for aws This is the PEAR channel registry entry for aws. PEAR is a framework and distribution system for reusable PHP components. A PEAR channel is a website that provides package for download and a few extra meta-information for files. Hi David, can you update the description to mention that AWS means Amazon Web Services ? Thanks, and bonne journée ! -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130410015554.gb28...@falafel.plessy.net
Bug#704760: ITP: python-pecan -- WSGI object-dispatching web framework
Le Fri, Apr 05, 2013 at 11:19:35PM +0800, Thomas Goirand a écrit : Package: wnpp Severity: wishlist Owner: Thomas Goirand z...@debian.org * Package name: python-pecan Version : 0.2.1 Upstream Author : Jonathan LaCour jonat...@dreamhost.com * URL : https://github.com/dreamhost/pecan * License : BSD Programming Lang: Python Description : WSGI object-dispatching web framework The Pecan Python module is a WSGI object-dispatching web framework designed to be lean and fast with few dependencies. Pecan comes bundled with a lightweight WSGI development server based on Python's wsgiref.simpleserver. Pecan applications also come with an interactive Python shell which can be used to execute expressions in an environment very similar to the one your application runs in (using the pecan shell command). Bonjour Thomas, maybe you could detail in the long description what WSGI means ? Bon week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130406001243.gb22...@falafel.plessy.net
Bug#700506: ITP: trinity -- A Linux System call fuzz tester
Le Thu, Feb 14, 2013 at 02:39:59PM -0300, gustavo panizzo gfa a écrit : On 02/14/2013 01:32 PM, Salvo Tomaselli wrote: On Wednesday 13 February 2013 17.46.19 gustavo panizzo wrote: Package: wnpp Severity: wishlist Owner: gustavo panizzo g...@zumbi.com.ar * Package name: trinity Version : 1.1 Upstream Author : Dave Jones da...@redhat.com * URL : http://codemonkey.org.uk/projects/trinity * License : GPLv2 Programming Lang: C Description : A Linux System call fuzz tester At 1st I thought it was about the desktop environment http://www.trinitydesktop.org/ Maybe it should be called something different? trinity desktop (which is not shipped within debian) does not ship any binary named that way (AFAIK) and their packages have the kde- preffix Dear Gustavo, there is also http://trinityrnaseq.sourceforge.net/, althouth I can not say if it will be packaged for Debian or not in the future. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130214235210.ga18...@falafel.plessy.net
Bug#700506: ITP: trinity -- A Linux System call fuzz tester
Le Thu, Feb 14, 2013 at 10:00:33PM -0300, gustavo panizzo gfa a écrit : On 02/14/2013 08:52 PM, Charles Plessy wrote: there is also http://trinityrnaseq.sourceforge.net/, althouth I can not i would call it trinity-rnaseq or trinity-rna Definitely, but please consider whether it would make sense to call your package trinity-fuzz or something else. If the software you package is not of broad use, then Trinity is likely to become the name of other works. If they are more popular, then it may be that renaming packages will be necessary (think about the renaming of git to gnuit for instance). You can pre-emptively avoid that problem by not calling your package trinity. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130215011641.gb29...@falafel.plessy.net
Bug#693094: RFH: cloud-init -- configuration and customization of cloud instances
Le Thu, Nov 15, 2012 at 05:34:50PM +0100, Ghe Rivero a écrit : I think I can help you with this package. In which state is the package? I see an upload to experimental almost half a year ago but nothing else. Hi Ghe, I uploaded to experimental because on one hand I could not test the package, but on the other hand, I wanted to be able to use Debian's bugtracker and PTS, and have more visibility to attract co-maintainers. Now that Wheezy is frozen, and now that there are more eyes looking at the package (see the debian-cloud mailing list), it would make sense to upload the latest upstream release (0.7.1) to unstable. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121116010242.ga28...@falafel.plessy.net
Bug#693094: RFH: cloud-init -- configuration and customization of cloud instances
Package: wnpp Severity: normal I request assistance with maintaining the cloud-init package. The package description is: System to handle early initialization of a cloud instance. Cloud-init can for example set a default locale and a host name, generate SSH private host keys, add SSH keys to a user's .ssh/authorized_keys so they can log in, and set up ephemeral mount points. . Cloud-init's behavior can be configured via user-data, given by the user at instance launch time. Cloud-init is a complex system written in Python, and I do not have much experience in both. I would like cloud-init to be maintained by a team of skilled developers who are also experienced users. See http://lists.debian.org/debian-cloud/2012/11/msg3.html for a longer call for help. The source package is currently hosted by the Python Applications team, but can be moved if need is. Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121113000457.12415.16691.reportbug@aqwa.igloo
Bug#681640: O: mime-support -- MIME files 'mime.types' 'mailcap', and support programs
Package: wnpp Severity: normal Following the Brian's message on debian-devel@l.d.o, I orphan mime-support. http://lists.debian.org/CAJHDDhFGG=5K1tY=qo3sbu1bhrsnt0uvd7enmfhqce6e2-s...@mail.gmail.com -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120715001051.4953.51953.reportbug@aqwa.igloo
Bug#679547: ITP: ben -- toolbox for Debian maintainers
Le Fri, Jun 29, 2012 at 07:21:21PM +0200, Mehdi Dogguy a écrit : This is a collection of useful tools that Debian maintainers can use to make their packaging work easier. They all work with regular Debian package list files, and should be useful for Debian derivatives as well. This package ships a single executable, ben, with the following subcommands: Hi, this looks very interesting, but I worry about future name conflicts with the following scenario: - More than one project is likely to be intested for taking /usr/bin/ben as a program name. - Since Debian's ben is Debian-specific, it will not be noticed by projects aiming at a wider audience. - If such a project comes to existence and becomes popular, we will have another name conflict à la node.js. An alterative scenario is that another project of narrow audience picks ben, which will cause a conflict of lesser importance as it will be solved on the usual first-arrived-first-served basis. But the key point is that if we do not aim at hundred thousands users for a tool, I think that we should avoid three-letter names. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120630010312.ga29...@falafel.plessy.net
Bug#672503: Review of the copyright file for ruby-classifier_1.3.3-1_amd64.changes.
user debian-le...@lists.debian.org usertags 672503 one-copyright-review thanks Dear Youhei, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package (from the Git repository). The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I found that while you indicate LGPL-2.0+ as a license, the upstream sources distribute the LGPL-2.1, and indicate this file in the README for reference. Perhaps you can clarify with the authors what is their intention: LGPL-2.0+ ? LGPL-2.1 ? LGPL-2.1+ ? Also, the file lib/classifier.rb seems to be licensed under both the MIT and LGPL terms. Lastly, more of a detail, it lools like lib/classifier/extensions/vector.rb is copyrighted by Ernest Ellingson. I also looked at the other ruby package you uploaded alonside with ruby-classifyer, and did not find anything to report about them. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/2012062704.gd32...@falafel.plessy.net
Bug#678608: ITP: wsdl2c
forcemerge 678608 678159 thanks Le Sun, Jun 24, 2012 at 05:27:14PM +, Bart Martens a écrit : There was already ITP 678159. I'm not sure about next steps, because your package is already in NEW. Maybe Brian Thomason wants to co-maintain ? Hi Bart, I missed Brian's ITP. But in the package I uploaded to NEW, he is the lead uploader anyway :) Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120625010754.ga25...@falafel.plessy.net
Bug#678608: ITP: wsdl2c -- stripped down axis2 source bundle suitable for running WSDL2C
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Hello everybody,
in order to get the cloud platform Eucalyptus in Debian, we need some
Java libraries. The following source package brings them all at once.
We recognise that it is not ideal, but it is the only way to not
postpone the upload of eucalyptus ad æternam. We are committed to
support this package for the whole support time of Wheezy. We hope
that by the next stable release, it will have been properly broken
down in simpler packages.
Have a nice day,
-- Charles, for the Debian Eucalyptus Maintainers team.
wsdl2c (0.1-1) unstable; urgency=low
Source: wsdl2c
Section: java
Priority: extra
Maintainer: Debian Eucalyptus Maintainers
pkg-eucalyptus-maintain...@lists.alioth.debian.org
DM-Upload-Allowed: yes
Uploaders: Brian Thomason brian.thoma...@eucalyptus.com
Build-Depends: debhelper (= 7),
cdbs,
ant,
default-jdk,
libbackport-util-concurrent-java,
libcommons-cli-java,
libcommons-fileupload-java,
libcommons-httpclient-java,
libcommons-logging-java,
libgeronimo-jms-1.1-spec-java,
libgnumail-java,
libhttpcore-java,
libjaxen-java,
libwsdl4j-java
Standards-Version: 3.9.3
Homepage: https://github.com/a13m/wsdl2c
Package: libwsdl2c-java
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: stripped down axis2 source bundle suitable for running WSDL2C
This is an amalgam of code from several java projects which are required to use
WSDL2C from the Apache Axis 2 project. The goal is to have code which can be
built from source without the chain of dependencies needed to build each of
these projects in their entirety.
.
The code in this project coms from the following sources:
.
http://svn.apache.org/repos/asf/axis/axis2/java/core/tags/v1.4.1
http://svn.apache.org/repos/asf/webservices/commons/tags/axiom/1.2.12
http://svn.apache.org/repos/asf/webservices/commons/tags/neethi/neethi-3.0.1
http://svn.apache.org/repos/asf/webservices/commons/tags/XmlSchema/1.4.2
http://svn.apache.org/repos/asf/webservices/woden/tags/1.0M9
https://svn.java.net/svn/jsr311~svn/tags/jsr311-api-1.1.1
svn://svn.annogen.codehaus.org/annogen/scm [1]
.
At this point, none of the sources have been modified. Note that the jsr311
code (i.e., the files under javax/ws/rs) is provided under the CDDL, while all
other code uses the Apache Software License, version 2.0.
.
Notes: [1] could not access this link, and pulled the code out of a jpackage
RPM, but theoretically the code still lives in this repo.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: wsdl2c
Source: https://github.com/a13m/wsdl2c
Files: src/org/*
Copyright: The Apache Software Foundation
License: Apache-2.0
Files: src/org/apache/axis2/wsdl/codegen/schema/soap-enc.xsd
Copyright: 2001 Martin Gudgin, Developmentor.
2001 W3C (Massachusetts Institute of Technology, Institut National de
Recherche en Informatique et en Automatique, Keio University)
The Apache Software Foundation
License: Apache-2.0 and W3C
Files: src/org/codehaus/jam/JInvokable.java
src/org/codehaus/jam/provider/JamServiceContext.java
src/org/codehaus/jam/mutable/MInvokable.java
Copyright: © 2003 The Apache Software Foundation
© 2003 BEA Systems
License: Apache-1.1+BEA
Files: src/javax/*
Copyright: Sun Microsystems Inc.
License: CDDL-1.0
Files: debian/*
Copyright: 2012 Eucalyptus Systems, Inc.
License: GPL-2+
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Bug#677289: ITP: libnetty3.1-java -- Java NIO client/server socket framework
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org * Package name: libnetty3.1-java Version : 3.1.0.CR1 Upstream Author : Red Hat Middleware LLC, and individual contributors * URL : http://www.jboss.org/netty * License : LGPL-2.1+ Programming Lang: Java Description : Java NIO client/server socket framework Description: Java NIO client/server socket framework Netty is a Java NIO client/server framework which enables quick and easy development of network applications such as protocol servers and clients. It greatly simplifies and streamlines network programming such as TCP and UDP socket server. Debian has Netty 3.2, but unfortunately it is significantly different from Netty 3.1, which we need for Eucalyptus, an open-source cloud system that implements the industry-standard Amazon Web Services (AWS) cloud APIs. See http://wiki.debian.org/pkg-eucalyptus for more details about our packaging progresses. -- Charles Plessy Debian pkg-eucalyptus-maintainers team http://wiki.debian.org/pkg-eucalyptus Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120612230831..50386.reportbug@aqwa.igloo
Bug#672104: ITP: pv-grub-menu.lst
Le Fri, May 11, 2012 at 04:17:39PM +0100, Ian Campbell a écrit : Can I just check I understand the motivation for this script properly. There are two ways of setting up the disk for a VM. The first is the whole disk scheme. In this configuration the VM configuration contains the entire xvda which contains a partition table in the usual way. In this configuration either grub-legacy or grub-pc can be installed and grub-install /dev/xvda does the right thing including setting up the MBR. This is useful because you can flip quite easily from PV to HVM just by changing the VM config and rebooting. (This is the setup I generally use myself, so I'm mostly familiar with it) The second scheme is the split partitions scheme. In this configuration the VM config contains xvda1 and xvda2 etc which appear to the guest OS as partitions but critically there is no overall xvda and therefore no partition table. This means that grub-install cannot work. This is the configuration which EC2 etc use and therefore this update-grub variant is necessary. Is that right? Exactly. When installing Debian on a EC2 volume with Debian Installer, the partition is a whole disk, completely usable by grub. But that means that when the newly prepared Debian system is booted, it is a root partition, which is split partitions in the Amazon cloud and grub hooks will fail when installing a new kernel (I did not have time to triplecheck). Perhaps that could be solved by making the hooks checking for the availability of a MBR before running grub, but the grub packages are quite critical, and I am not sure how this additional complexity would be welcome. In addition there is a second problem. Pv-grub needs a menu.lst file that is made by GRUB 1. But Debian's GRUB 1 package is in maintainance-only mode, I do not know what are the plans to remove it eventually, but once GRUB 2 can replace it in all cases, this may happen. So it is probably better to have a menu.lst-builder script for pv-grub maintained somewhere else. The pkg-xen project on Alioth is a good idea indeed. Or maybe pv-grub could be extended to parse menu.cfg files ? But I do not know how long it would take for this new function to propagate to Amazon. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120524000807.gc15...@falafel.plessy.net
Bug#673182: ITP: pscan -- finds overrepresented transcription factor binding sites
Le Wed, May 16, 2012 at 07:48:46PM +0200, Steffen Moeller a écrit : Package: wnpp Severity: wishlist Owner: Steffen Moeller steffen_moel...@gmx.de * Package name: pscan Version : 1.2.1 * URL : http://159.149.109.9/pscan/ * License : unclear Programming Lang: C++ Description : finds overrepresented transcription factor binding sites This packages takes a motif database of transcription factor binding sites (TFBS) and expects a list of genes that are found co-regulated. It then points to those TFBS that seem statistically most unlikely to be observed by chance. Hello everybody, we have a problem... EMBOSS also distributes a program called pscan, as well as the pscan package itself (Format string security checker for C files). Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- 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/20120516215729.gb17...@falafel.plessy.net -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120516215729.gb17...@falafel.plessy.net
Bug#672375: ITP: cloud-init
Package: wnpp
Hello everybody,
I was reminded to send an ITP for cloud-init, so that the progress in packaging
can be followed. Here are prospective control and copyright files.
I tried to rework the description using
https://help.ubuntu.com/community/CloudInit.
Your comments, proofreading, etc. are very welcome.
Cheers,
-- Charles
Source: cloud-init
Section: admin
Priority: optional
Maintainer: Python Applications Packaging Team
python-apps-t...@lists.alioth.debian.org
Uploaders: Charles Plessy ple...@debian.org
Build-Depends: cdbs (= 0.4.90~),
debhelper (= 9),
po-debconf,
pyflakes,
pylint,
python (= 2.6.6-3~),
python-nose,
python-mocker,
Standards-Version: 3.9.3
Homepage: https://launchpad.net/cloud-init
Vcs-Svn: svn://svn.debian.org/python-apps/packages/cloud-init/trunk/
Vcs-Browser: http://svn.debian.org/websvn/python-apps/packages/cloud-init/trunk/
Package: cloud-init
Architecture: all
Depends: cloud-utils,
ifupdown (= 0.6.10ubuntu5),
procps,
python,
python-cheetah,
python-configobj,
python-oauth,
python-software-properties,
python-yaml,
${misc:Depends},
${python:Depends}
Description: configuration and customization of cloud instances
System to handle early initialization of a cloud instance. Cloud-init can for
example set a default locale and a host name, generate SSH private host keys,
add SSH keys to a user's .ssh/authorized_keys so they can log in, and set up
ephemeral mount points.
.
Cloud-init's behavior can be configured via user-data, given by the user at
instance launch time.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source:
https://launchpad.net/cloud-init/trunk/0.6.3/+download/cloud-init-0.6.3.tar.gz
Files: *
Copyright: © 2009-2012, Canonical Ltd.
© 2012 Hewlett-Packard Development Company, L.P.
© 2012 Cosmin Luta
License: GPL-3
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License version 3, as
published by the Free Software Foundation.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/.
.
The complete text of the GPL version 3 can be seen in
/usr/share/common-licenses/GPL-3.
--
Charles Plessy
Tsurumi, Kanagawa, Japan
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Archive: http://lists.debian.org/20120510133051.ga2...@merveille.plessy.net
Bug#672104: ITP: pv-grub-menu.lst
Le Thu, May 10, 2012 at 02:41:23PM +0100, Ian Campbell a écrit : I've not looked at the tool yet, but I wonder if this might be something which could be usefully maintained as part of the upstream Xen project (of which I'm one maintainer) alongside pygrub. Or is the tool mostly about the Debian integration rather than the generation of a compatible menu.lst? What do you think? Hello, that would be great if this facility could be shared in Xen, as it would benefit more users than just in Debian. Currently it looks like the whole scripts are debian-specific. I have pushed them in a Git repository on Alioth so that you can browse them. http://git.debian.org/?p=collab-maint/pv-grub-menu.lst.git;a=tree;f=debian Among them, update-grub-legacy-ec2 is the one that creates menu.lst. The others are Debian-specific hooks for package installation and automatic refreshing when a new kernel is installed. update-grub-legacy-ec2 is derived from update-grub scripts that are also Debian-specific. But if they could be replaced by something more generic, that would be great. I guess the next step is to look at how Fedora does... 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120510234216.ga11...@falafel.plessy.net
Bug#666229: Adding CA certficates outside of ca-certificates (see ITP #666229)
Le Mon, Apr 16, 2012 at 03:44:51PM +0200, Dennis van Dok a écrit : There seems to be no real way to include extra ca-certificates-* packages at the moment. I've tried to conform as much as possible to the structure of the ca-certificates package, and the way I've packaged it right now is that the administrator has the choice to include individual certificates from IGTF in /etc/ssl upon reconfiguring ca-certficates. http://mentors.debian.net/package/igtf-policy-bundle Dear Dennis and everyboyd, perhaps a broader package would be useful ? I am still looking for a sane place for the Amazon EC2 public certificate, see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=573857 I also welcome comments. Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120417074649.ga26...@falafel.plessy.net
Bug#668556: ITP: dparser -- a scannerless GLR parser generator
Le Thu, Apr 12, 2012 at 10:00:52PM +0200, Markus Wanner a écrit : * Package name: dparser Description : a scannerless GLR parser generator DParser is a scannerless GLR parser generator based on the Tomita algorithm. It is self-hosted and very easy to use. Grammars are written in a natural style of EBNF and regular expressions and support both speculative and final actions. There's an archived RPF for dparser: #248589 Dear Markus, I would like to suggest to explicit the GLR, RPF, and perhaps EBNF acronyms in the long description. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120414033700.gd4...@falafel.plessy.net
Bug#659863: ITP: vegan -- Community Ecology Package for R
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. Stevens, Helene Wagner URL : http://vegan.r-forge.r-project.org/ License : GPL-2 Programming Lang: R, C, FORTRAN Description : Community Ecology Package for R Ordination methods, diversity analysis and other functions for community and vegetation ecologists. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120214110229.3139.65451.reportbug@localhost.localdomain
Bug#659863: ITP: vegan -- Community Ecology Package for R
Le Tue, Feb 14, 2012 at 01:04:22PM +0100, Andreas Tille a écrit : Hi Charles, the description is a bit sparse for the package itself as for the task where I would like to include it. Could you please try to be a bit more verbose for the general Debian user audience? How about this ? R package for community ecologists. It contains most multivariate analysis needed in analysing ecological communities, and tools for diversity analysis. Most diversity methods assume that data are counts of individuals. . These tools are sometimes used outside the field of ecology, for instance to study populations of white blood cells or RNA molecules. Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120214124612.ga13...@falafel.plessy.net
Bug#659863: ITP: vegan -- Community Ecology Package for R
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 for both the source and binary package names. Hi, I remember seeing a discussion somewhat recently; was it http://lists.debian.org/debian-devel/2011/11/msg00433.html or even more recent ? I must say that I am not particularly convinced, as I have seen R packages moving from Omegahat to CRAN, or from CRAN to Bioconductor, and renaming source packages is quite inconvenient. If there is a need to implement simple namespaces for our source packages, perhaps just r- would be enough ? But if we adopt a naming scheme, it would be great to record it somewhere. Unless I am the only one to not use r-cran- as a prefix, or unless we reach a conclusion, I would prefer keeping vegan as a source package name. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120214235741.gc30...@falafel.plessy.net
Bug#659863: Source package names for R libraries (and Perl, Python, Java, …).
Le Tue, Feb 14, 2012 at 04:23:40PM -0800, Don Armstrong a écrit : http://lists.debian.org/debian-perl/2008/08/msg00055.html http://lists.debian.org/debian-policy/2008/01/msg00019.html #505309 among others. For sure there are discussions, but what we need is a summarized conclusion. (The folowing is my opinion, not an attempt to conclude). To follow the naming scheme of the Perl team, I have renamed one of my binary packages ‘bioperl’ to ‘libbio-perl-perl’, but I doubt it would be helpful to have such a name as a source package. Similarly, for R libraries, it looks simplest to keep upstream's name. Then, arises the problem of conflicts between source package names. This is nothing specific to R or Perl libraries, and restricted naming schemes will not solve that problem entirely, although it helps to mitigate. Then, if one choses a Debian-specific name for an upstream work, it is advantageous to keep the same name for the source and binary package, and for R and Perl, there are conventions in place. But as I indicated, R's convention is not the same as Perl's since it indicates the repository for download in the name, which may change. Perl packages do not have CPAN in their name. An additional complication comes when a source package produces more than one binary package, for instance a R and a Perl library at the same time. The convention on the source package name is therefore at best a “should”. On top of this, the benefit of of having a policy on source package names will be limited as it is unlikely to rename the existing ones. My conclusion is that predictable binary package names are well followed and useful (for instance to avoid conflicts with third-party repositories like debian-cran), but I doubt about the benefits of a source package naming scheme. This said, it is also improductive to have some source packages follow a naming scheme, and some not. Let's try to agree on a brief policy on naming schemes. Perhaps Perl, Python and Java maintainers can comment on whether it would make sense to have a common one (drafted as a DEP ?). 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120215022215.ga30...@falafel.plessy.net
Bug#659689: ITP: permute -- R functions for generating restricted permutations of data
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 Programming Lang: R Description : R functions for generating restricted permutations of data Implements a set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples). 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeble or one of the restricted designs. The permute package is modelled after the permutation schemes of Canoco 3.1 by Cajo ter Braak. This R library is needed to package the “vegan” R library. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120213090248.16199.76320.reportbug@localhost.localdomain
Bug#657825: ITP: umegaya -- Umegaya is a MEtadata GAtherer using YAml
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 Description : Umegaya is a MEtadata GAtherer using YAml Hello everybody, I really liked one thing Raphaël wrote during his DPL campaign: “Use what we package and package what we use.” I therefore plan to package the scripts running upstream-metadata.debian.net. I hope that it will help to make the service more reliable, and help people to understand how it works. Have a nice Sunday, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120129080852.26829.43073.reportbug@aqwa.igloo
Bug#645289: O: soundconverter
Le Fri, Oct 14, 2011 at 11:31:15AM +0800, Jason Heeris a écrit : Subject: O: soundconverter -- GNOME application to convert audio files into other formats Package: wnpp Severity: normal I intend to orphan the soundconverter package. I'm not using or contributing to Debian any longer. There are RC bugs in this package that need to be fixed. Someone has expressed interest in taking over maintenance, so hopefully it won't be O'd for too long. Thanks again Jason for your work. Lars, I have sponsored soundconverter in the past but never used it. Will you adopt it, or how about trying to call for maintainers on debian-mentors ? Cheers, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20111016225914.gb20...@merveille.plessy.net
Bug#639535: ITP: libdebian-copyright-perl -- perl module to parse, merge and write Debian copyright files
Le Sat, Aug 27, 2011 at 10:08:55PM +0100, Nicholas Bamber a écrit : * Package name: libdebian-copyright-perl Version : 0.1 Upstream Author : Nicholas Bamber nicho...@periapt.co.uk * URL : http://search.cpan.org/dist/Debian-Copyright/ * License : GPL-2+ Programming Lang: Perl Description : perl module to parse, merge and write Debian copyright files Debian::Copyright can be used for the representation, manipulation and merging of Debian copyright files in an object-oriented way. It provides easy reading and writing of the debian/copyright file found in Debian source packages. Dear Nicholas, thanks for producing this parser. Perhaps the description could include the keywords “machine-readable” and “DEP 5” to make it easier to find. By the way, since the version of DEP 5 that is distributed in the debian-policy package uses 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110828051906.ge31...@merveille.plessy.net
Bug#638720: ITP: openerp6-server -- Enterprise Resource Management (server)
Le Sun, Aug 21, 2011 at 02:57:22PM +0200, W. Martin Borgert a écrit : OpenERP is a complete ERP and CRM. The main features are accounting (analytic and financial), stock management, sales and purchases management, tasks automation, marketing campaigns, help desk, POS, etc. Technical features include a distributed server, flexible workflows, an object database, a dynamic GUI, customizable reports, and NET-RPC and XML-RPC interfaces. Dear Martin, I think that it would help to understand that the package contains if the acronyms ERP, CRM, POS were expanded (and maybe also GUI and *-RPC). Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110822031030.gc9...@merveille.plessy.net
Bug#636181: ITP: libsnappy-java -- Snappy for Java, a fast compressor/decompresser
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: (lib)snappy-java Version : 1.0.3 Upstream Author : Taro L. Saito URL : http://code.google.com/p/snappy-java/ License : Apache Licence Version 2.0 Programming Lang: Java Description : Snappy for Java, a fast compressor/decompresser Java port of snappy, a fast compresser/decompresser, which is developed in C++ by Google. This package is needed to update picard-tools, a package for bioinformatics maintained by the Debian Med team. But since snappy-java is not restricted to use for life sciences, I will maintain it in the Debian Java Packaging project. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110801044218.21526.18347.reportbug@localhost.localdomain
Bug#632002: ITP: pvclust -- Hierarchical Clustering with P-Values via Multiscale Bootstrap
Le Wed, Jun 29, 2011 at 08:14:29AM +0200, Andreas Tille a écrit : for me this looks like a precondition for something else but not directly something for the tasks pages. If I'm wrong, could you insert it on the proper place? Hi Andreas, it is in our statistics task. We use it at work when comparing measurments of transcriptome expression. I will wait a day before uploading to give opportunity to others for feedback, so I thought there is no need to update the task by adding the ITP just for one day. Have a nice day, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110629062353.gc17...@merveille.plessy.net
Bug#632002: ITP: pvclust -- Hierarchical Clustering with P-Values via Multiscale Bootstrap
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: pvclust Version : 1.2-2 Upstream Author : Ryota Suzuki suz...@ef-prime.com, Hidetoshi Shimodaira sh...@is.titech.ac.jp URL : http://www.is.titech.ac.jp/~shimo/prog/pvclust/ License : GPL-2+ Programming Lang: R Description : Hierarchical Clustering with P-Values via Multiscale Bootstrap Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Uploaders: Charles Plessy ple...@debian.org DM-Upload-Allowed: yes Homepage: http://www.is.titech.ac.jp/~shimo/prog/pvclust/ Vcs-Git: git://git.debian.org/debian-med/pvclust.git Vcs-Browser: http://git.debian.org/?p=debian-med/pvclust.git Package: r-cran-pvclust Architecture: all Description: Hierarchical Clustering with P-Values via Multiscale Bootstrap pvclust is a package for assessing the uncertainty in hierarchical cluster analysis. It provides AU (approximately unbiased) p-values as well as BP (boostrap probability) values computed via multiscale bootstrap resampling. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110629040143.7328.77954.reportbug@localhost.localdomain
Bug#629641: ITP: filo -- FILe and stream Operations
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: filo Version : 1.1.0 Upstream Author : Aaron Quinlan, University of Virginia; Assaf Gordon, Cold Spring Harbor Laboratories URL : https://github.com/arq5x/filo License : GPL-2.0 Programming Lang: C++ Description : FILe and stream Operations The following tools are available as part of the filo package: . groupBy is a useful tool that mimics the groupBy clause in database systems. . shuffle will randomize the order of lines in a file. In other words, if you have a sorted file, shuffle will undo the sort. . stats is a small utility for computing descriptive statistic on a given column of a tab-delimited file or stream. groupBy is a command that was formerly part of the BEDtools package for bioinformatics, very recently accepted in Debian, and that its users will probably miss if it is not available. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110608110234.25408.18819.reportbug@localhost.localdomain
Bug#629641: ITP: filo -- FILe and stream Operations
Le Wed, Jun 08, 2011 at 10:54:53PM +, The Fungi a écrit : On Wed, Jun 08, 2011 at 05:53:06PM +0600, Andrey Rahmatullin wrote: On Wed, Jun 08, 2011 at 08:02:34PM +0900, Charles Plessy wrote: shuffle will randomize the order of lines in a file. In other words, if you have a sorted file, shuffle will undo the sort. sort -R [...] Also worth noting is that /usr/bin/shuf in coreutils is traditionally used to this end as well. Thanks for your comments. I have presented Upstream the classical approaches of Debian with too generic command names (wrapper, renaming, /usr/lib/package), and asked him what shuffle does, that alternatives do not. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110609000814.ga22...@merveille.plessy.net
Bug#629597: ITP: bedtools -- suite of utilities for comparing genomic features
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: bedtools Version : 2.12.0 Upstream Author : Aaron Quinlan URL : http://code.google.com/p/bedtools/ License : GPL-2+ Programming Lang: C++ Description : suite of utilities for comparing genomic features The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together. BEDTools is very popular in its field and will be a nice addition to Debian. A package is almost ready at http://git.debian.org/?p=debian-med/bedtools.git 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110607233751.4153.68459.reportbug@chouca.igloo
Bug#628882: ITP: r-bioc-edger -- Empirical analysis of digital gene expression data in R
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: r-bioc-edger Version : 2.2.5 Upstream Author : Mark Robinson mrobin...@wehi.edu.au, Davis McCarthy dmccar...@wehi.edu.au, Gordon Smyth sm...@wehi.edu.au URL : http://www.bioconductor.org/packages/release/bioc/html/edgeR.html License : LGPL-2+ Programming Lang: R Description : Empirical analysis of digital gene expression data in R Bioconductor package for differential expression analysis of whole transcriptome sequencing (RNA-seq) and digital gene expression profiles with biological replication. It uses empirical Bayes estimation and exact tests based on the negative binomial distribution. It is also useful for differential signal analysis with other types of genome-scale count data. (I use it at work) -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110602054559.25674.38372.reportbug@localhost.localdomain
Bug#628548: ITP: r-bioc-limma -- linear models for microarray data
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: r-bioc-limma Version : 3.8.2 Upstream Author : Gordon Smyth sm...@wehi.edu.au URL : http://bioinf.wehi.edu.au/limma/ License : GPL, LGPL Programming Lang: R, C Description : linear models for microarray data A Bioconductor package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The package includes pre-processing capabilities for two-colour spotted arrays. The differential expression methods apply to all array platforms and treat Affymetrix, single channel and two channel experiments in a unified way. r-bioc-limma is needed to package edgeR (r-bioc-edger), which is quite popular for the analysis of high-throughput transcriptome sequencing experiments. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110530050649.16986.1568.reportbug@localhost.localdomain
Bug#627799: libbam-dev ships sam.h in /usr/include/samtools
Dear Alex, As the Perl transition is over, I have updated libbam to serve its headers in /usr/include/samtools, and libbio-samtools-perl to search for them there. You can go ahead with a similar change in cufflinks any time you like. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110525023515.ga21...@merveille.plessy.net
Bug#620018: Openstack Compute nova, Cactus release, Squeeze built available in our private repo
Le Sat, Apr 16, 2011 at 10:43:43AM +0800, Thomas Goirand a écrit : Again, if other DDs want to participate to this packaging effort, you'd be welcome. Especially, it seems that the current version of euca tools are broken (uec-publish-tarball got me stuck on my work for a week), and would need debugging. Hi Thomas, Debian's euca2ools package is definitely outdated. Is the problem with uec-publish-tarball fixed in upstream's version 1.3.1 ? I will be mostly unavailable for the next three weeks, with two business trips followed by vacations. So if you or anybody else would like to go ahead and update the package, you are most welcome ! I can add you to the pkg-eucalyptus group any time. Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110417050544.gf30...@merveille.plessy.net
Bug#622404: Review of the copyright file of duo-unix_1.5-1.dsc.
user debian-le...@lists.debian.org usertag 622404 one-copyright-review thanks Dear Kees, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I found that there are two missing copyright statements and one missing license statement: Files: autotools/stack-protector.m4 Copyright: 2007 Google Inc. License: Apache-2.0 Files: pam_duo/testpam.c Copyright: 2004 Darren Tucker dtucker at zip.com.au 2002 Networks Associates Technology, Inc. License: combined Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. . THE SOFTWARE IS PROVIDED AS IS AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. . . Based in part on OpenSSH's auth-pam.c which is under the following copyright: . Copyright (c) 2002 Networks Associates Technology, Inc. All rights reserved. . This software was developed for the FreeBSD Project by ThinkSec AS and NAI Labs, the Security Research Division of Network Associates, Inc. under DARPA/SPAWAR contract N66001-01-C-8035 (CBOSS), as part of the DARPA CHATS research program. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: pam_duo/pam_extra.c License: BSDorGPL Adapted from Linux-PAM . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, and the entire permission notice in its entirety, including the disclaimer of warranties. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. . ALTERNATIVELY, this product may be distributed under the terms of the GNU Public License, in which case the provisions of the GPL are required INSTEAD OF the above restrictions. (This clause is necessary due to a potential bad interaction between the GPL and the restrictions contained in a BSD-style copyright.) . THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http
Bug#622700: ITP: fastx-toolkit -- FASTQ/A short nucleotide reads pre-processing tools
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: fastx-toolkit Version : 0.0.13 Upstream Author : Assaf Gordon gor...@cshl.edu URL : http://hannonlab.cshl.edu/fastx_toolkit/ License : AGPL-3+, MIT Programming Lang: C Description : FASTQ/A short nucleotide reads pre-processing tools The FASTX-Toolkit is a collection of command line tools for preprocessing short nucleotide reads in FASTA and FASTQ formats, usually produced by Next-Generation sequencing machines. The main processing of such FASTA/FASTQ files is mapping (aligning) the sequences to reference genomes or other databases using specialized programs like BWA, Bowtie and many many others. However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome—manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110414003331.3299.5874.reportbug@chouca.igloo
Bug#595427: Review of the copyright file of winetricks_0.0~20110305+svn220-1.
user debian-le...@lists.debian.org usertag 595427 one-copyright-review thanks Dear Jaari and Tony, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I have two small comments about the debian/copyright file: 1) It does not validate with “config-edit -application dpkg-copyright -ui none”. (See http://ddumont.wordpress.com/2011/01/13/debian-copyright-dep5-parsereditorvalidatormigrator-is-released/ ) The reason is that it uses LGPL-2.0 and LGPL-2.0+, but gives the boilerplate for LGPL-2.0 only. 2) The LGPL-2.0 is actually the “Library” GPL, not the “Lesser” GPL: you are using the boilerplate from the LGPL-2.1. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110414004936.ge28...@merveille.plessy.net
Bug#618774: ITP: cctools -- cooperative computing tools
Le Fri, Mar 18, 2011 at 08:36:32AM -0400, Michael Hanke a écrit : Package: wnpp Severity: wishlist Owner: Michael Hanke m...@debian.org * Package name: cctools Version : 3.3.0 Upstream Author : Douglas Thain * URL : http://nd.edu/~ccl/software/ * License : GPL-2 Programming Lang: C, Python Description : cooperative computing tools Dear Michael and Luke, I just realised that both of you are preparing a package under the same name. Perhaps you need to discuss this before the first of you uploads. http://git.debian.org/?p=collab-maint/cctools.git http://git.debian.org/?p=pkg-exppsy/cctools.git 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110325023006.ga10...@merveille.plessy.net
Bug#607929: Review of the copyright file of dimbl_0.8-1.
user debian-le...@lists.debian.org usertag 607929 one-copyright-review thanks Dear Joost, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I found a possible omission in your debian/copyright file: the copyright holders and license of acinclude.m4 and m4/openmp.m4 are not the same as for the rest of the package. The other m4 files also have a different copyright homders and license, but it seems accepted to not list files that originate from the autoconf, automake or libtool packages (although it is of course fine to do so if you feel like). acinclude.m4 and m4/openmp.m4, on the other hand, are independant contributions. If you update your package, this will not change its seat number in the NEW queue, and it may save you some time, in case the package were rejected for the errors above. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110219075611.gb19...@merveille.plessy.net
Bug#429610: gbrowse: changing back from RFP to ITP
retitle 429610 ITP: gbrowse -- The Generic Genome Browser from GMOD owner 429610 ! thanks I am not working much on this package personally, but others do. They are of course welcome to take over the ITP. -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110220011223.ga17...@merveille.plessy.net
Bug#613517: Review of the copyright file of libsbsms_1.7.0-1.
user debian-le...@lists.debian.org usertag 613517 one-copyright-review thanks Dear Benjamin, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I found that the files m4/ac_c99_func_*.m4 were not documented in your copyright file. I attached a patch. If you update your package, this will not change its seat number in the NEW queue, and it may save you some time, in case the package were rejected for the error above. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan From 834882274f79a91a6e778dce2fd3ba80fb29 Mon Sep 17 00:00:00 2001 From: Charles Plessy ple...@debian.org Date: Sat, 19 Feb 2011 15:33:01 +0900 Subject: [PATCH] =?UTF-8?q?Document=20the=20license=20and=20copyright=20of=20=E2=80=98m4/ac=5Fc99=5Ffunc=5F*.m4=E2=80=99.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- debian/copyright |9 + 1 files changed, 9 insertions(+), 0 deletions(-) diff --git a/debian/copyright b/debian/copyright index a2c84d3..3fe39f1 100644 --- a/debian/copyright +++ b/debian/copyright @@ -18,6 +18,15 @@ Files: src/real.h Copyright: 2001-2003, Erik de Castro Lopo er...@mega-nerd.com License: GPL-2+ +Files: m4/ac_c99_func_*.m4 +Copyright: Erik de Castro Lopo erikd AT mega-nerd DOT com +License: other + Permission to use, copy, modify, distribute, and sell this file for any + purpose is hereby granted without fee, provided that the above copyright + and this permission notice appear in all copies. No representations are + made about the suitability of this software for any purpose. It is + provided as is without express or implied warranty. + Files: debian/* Copyright: 2011, Benjamin Drung bdr...@debian.org License: GPL-2+ -- 1.7.2.3
Bug#613486: ITP: libgtextutils -- Gordon Text_utils library
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Hello everybody,
I will package some bioinformatics tools called FASTX-Toolkit, and they
require a separate library, gtextutils, which is used only by them. But
since it is distributed as a separate tarball, the simplest is still
to distribte it as a separate package. Here are the control and copyright
files. I did not have much to say in the description…
Source: libgtextutils
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
DM-Upload-Allowed: yes
Uploaders: Charles Plessy ple...@debian.org
Build-Depends: debhelper (= 8), autotools-dev
Standards-Version: 3.9.1
Vcs-Browser: http://git.debian.org/?p=debian-med/libgtextutils.git
Vcs-Git: git://git.debian.org/git/debian-med/libgtextutils.git
Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
Package: libgtextutils-dev
Section: libdevel
Architecture: any
Depends: libgtextutils0 (= ${binary:Version}), ${misc:Depends}
Description: Gordon Text_utils library (development files)
Development files for the Gordon Text_utils (gtextutils) library.
Package: libgtextutils0
Section: libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Gordon Text_utils library
The Gordon Text_utils (gtextutils) library is a text utilities library used by
the FASTX-Toolkit, a suite of programs for biological sequence analysis.
Format: DEP-5
Source: http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.tar.bz2
Files: *
Copyright: © 2008,2009 Assaf Gordon (gor...@cshl.edu)
License: AGPLv3
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published
by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see http://www.gnu.org/licenses/
Files: src/gtextutils/natsort.h
Copyright: © 2000, 2004 by Martin Pool mbp sourcefrog net
© 2009 Assaf Gordon (gor...@cshl.edu)
License: AGPLv3 and zlib
Files: src/gtextutils/strnatcmp.c src/gtextutils/strnatcmp.h
Copyright: © 2000, 2004 by Martin Pool mbp sourcefrog net
License: zlib
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
.
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
.
1. The origin of this software must not be misrepresented; you must not
claim that you wrote the original software. If you use this software
in a product, an acknowledgment in the product documentation would be
appreciated but is not required.
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
Files: src/Makefile.am src/gtextutils/Makefile.am Makefile.am m4/Makefile.am
doc/Makefile.am tests/Makefile.am
Copyright: © 2008 Assaf Gordon gor...@cshl.edu
License:
This file is free software; as a special exception the author gives
unlimited permission to copy and/or distribute it, with or without
modifications, as long as this notice is preserved.
.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY, to the extent permitted by law; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Files: src/gtextutils/inbuf1.hpp src/gtextutils/outbuf3.hpp
Copyright: © 1999 Nicolai M. Josuttis
© 2009 Assaf Gordon (gor...@cshl.edu)
License: AGPLv3 and other
License: other
Permission to copy, use, modify, sell and distribute this software
is granted provided this copyright notice appears in all copies.
This software is provided as is without express or implied
warranty, and with no claim as to its suitability for any purpose.
License: AGPLv3
…
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Bug#611828: ITP: probalign -- multiple sequence alignment using partition function posterior probabilities
Le Fri, Feb 04, 2011 at 10:33:05AM +0100, Tanguy Ortolo a écrit : Le mercredi 02 février 2011, andr...@an3as.eu a écrit : Description : multiple sequence alignment using partition function posterior probabilities Is that about DNA sequences? I think this should be explicited in the description, with something like: detect multiple sequence alignment in DNA sequences Dear Tanguy, probalign can align DNA and protein sequences. It is a frequent request on this list to add more information in the synopsis so that readers can know what kind of sequence is aligned, without any other information like the long description, Debtags or the package's section. But we only have 80 characters to for the synopsis… Here are synopsis for other multiple sequence alignment programs: boxshade - Pretty-printing of multiple sequence alignments dialign-tx - Segment-based multiple sequence alignment dialign - Segment-based multiple sequence alignment kalign - Global and progressive multiple sequence alignment mafft - Multiple alignment program for amino acid or nucleotide sequences mummer - Efficient sequence alignment of full genomes muscle - Multiple alignment program of protein sequences poa - Partial Order Alignment for multiple sequence alignment probcons - PROBabilistic CONSistency-based multiple sequence alignment proda - multiple alignment of protein sequences sigma-align - Simple greedy multiple alignment of non-coding DNA sequences In general, we try to reproduce the upstream short description. This is the case for probalign. Unless this is causing significant confusion, like mislead users from other fields wasting their time installing bioinformatics package, I would recommend to keep the short description as it is. Have a nice week-end, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110205062729.gb20...@merveille.plessy.net
Bug#551338: Review of the copyright file of mediathekview_2.4.0-2.
Le Fri, Feb 04, 2011 at 03:00:26PM +0100, Christoph Martin a écrit : Am 04.02.2011 01:43, schrieb Charles Plessy: By the way, I think that in your changelog, the ITP bug number is wrong: 321720 instead of 551338. I can't see the problem. 551338 is RFP: zdfmediathk -- download/subscribe to streams (online in Mediathek) from public german TV stations (ARTE, ARD, ZDF, 3Sat, MDR, SF DRS) and 321720 is libgrypt11: cannot enable executable stack as shared object requires: Error 14 And 551338 is correctly in the changelog Good :) I only found mediathekview_2.4.0-1 on mentors.d.n, where this was not yet corrected. Have a nice week-end, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110205055936.ga20...@merveille.plessy.net
Bug#551338: Review of the copyright file of mediathekview_2.4.0-2.
user debian-le...@lists.debian.org usertag 551338 one-copyright-review thanks Dear Thomas, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I found two inconsistencies in your copyright file: - According to the file headers and its website, MediathekView is using the version 3 or superior of the GPL (not 2 or superior). - I found one copyright statement that is not reproduced: io/History.java is Copyright (C) 2010 by Andreas M. If you update your package, this will not change its seat number in the NEW queue, and it may save you some time, in case the package were rejected for the errors above. By the way, I think that in your changelog, the ITP bug number is wrong: 321720 instead of 551338. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110204004301.gd31...@merveille.plessy.net
Bug#610603: ITP: sra-sdk -- utilities for the NCBI Sequence Read Archive
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: sra-sdk Version : 2.0.0rc1 Upstream Author : National Center for Biotechnology Information (U. S. A.) URL : http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=showf=softwarem=softwares=software License : Public domain (U. S. A. governmental work) Programming Lang: C Description : utilities for the NCBI Sequence Read Archive Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq. It also includes sources to loader tools that are still under test. The intention is to give pre-release access to the reader code. . The textual dumpers sra-dump and vdb-dump are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE. . The help information will be improved in near future releases, and the tool options will become standardized across the set. We will also be providing documentation on our web site. . Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts. I will first upload to experimental until a final release is published. There will be 3 binary packages: sra-toolkit with the binaries, sra-toolkit-libs0 with the runtime libraries, and sra-toolkit-libs-dev for developers. I understand that having one package per library is ideal, but the number of different libaries is quite large: /usr/lib/libwkdb.so.1.1.2 /usr/lib/libkproc.so.1.0.0 /usr/lib/libsra-schema.so.1.0.0 /usr/lib/libvdb.so.2.0.4 /usr/lib/libkq.so.1.0.0 /usr/lib/libksrch.so.1.0.2 /usr/lib/libkfs.so.1.0.2 /usr/lib/libkdb.so.1.1.2 /usr/lib/libwvdb.so.2.0.4 /usr/lib/libksproc.so.1.0.0 /usr/lib/libkfg.so.1.0.0 /usr/lib/libkxml.so.1.0.2 /usr/lib/libwsradb.so.3.0.1 /usr/lib/libklib.so.1.1.0 /usr/lib/libsrareader.so.1.0.0 /usr/lib/libsradb.so.3.0.1 This said, if a more experienced developer would still recommend me to make one package per library, I will. I checked with upstream and these libraries are intended for public use (although given that they are recent, there is no known third-party using them yet). 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110120121543.11240.41916.report...@anx178.gsc.riken.jp
Bug#599727: Review of the copyright file of peg-solitaire_1.0.2-1.
user debian-le...@lists.debian.org usertag 599727 one-copyright-review thanks Dear Innocent, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I have not found explicit copyright or licence statement that would be missing from your debian/copyright file. However, I looked at the contents of the images directory, and it appears that most of them are missing their source, as they were made as a vector graphics with Inkscape. See for instance edit-redo.png $ exiftool edit-redo.png ExifTool Version Number : 8.15 File Name : edit-redo.png Directory : . File Size : 1019 bytes File Modification Date/Time : 2011:01:21 09:17:40+09:00 File Permissions: rw-rw-r-- File Type : PNG MIME Type : image/png Image Width : 22 Image Height: 22 Bit Depth : 8 Color Type : RGB with Alpha Compression : Deflate/Inflate Filter : Adaptive Interlace : Noninterlaced Significant Bits: 8 8 8 8 Software: www.inkscape.org Image Size : 22x22 In my personal opinion, it would be necessary to include their sources in your package to strictly conform with the DFSG. If you picked these icons from a collection, you need in addition to credit their author and check that their license is compatible with the GPLv3, and of course document this in debian/copyright. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110121004551.gd6...@merveille.plessy.net
Bug#606446: ITP: tabix -- generic indexer for TAB-delimited genome position files
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: tabix Version : 0.2.3 Upstream Author : Heng Li l...@live.co.uk URL : http://samtools.sourceforge.net/tabix.shtml License : MIT/X Programming Lang: C, plus some Java, python and Perl bindings Description : generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosme), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. A draft package is available here: Vcs-Git: git://git.debian.org/debian-med/tabix.git Vcs-Browser: http://git.debian.org/?p=debian-med/tabix.git;a=summary I update the draft from time to time when I use it at work, and will eventually upload it ‘when it is ready’. Do not hesitate to express your interest in it, and I will fast-track it. Have a nice day, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20101209102827.10301.53358.report...@anx178.gsc.riken.jp
Bug#585999: Review of the copyright file for okasha_0.1.0-1.dsc.
user debian-le...@lists.debian.org usertags 585999 one-copyright-review thanks Dear Ahmed, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview I found the two following problems: 1) files/okasha-docbook.css is not documented in your copyright file (Copyright 2003 Tammy Fox, Garrett LeSage, and Red Hat, Inc. Copyright 2005 Tommy Reynolds tommy.reyno...@megacoder.com License: GPL ) 2a) files/jquery.min.js is not the “preferrable form for modification”. However, since your package is non-free, this is not a blocking problem. 2b) files/jquery.min.js can be considered as an “embedded code copy”. It causes the following maintainance problem: in case a bug is found in this library, all the packages that would use a copy of this file would have to be modified in order to correct the bug. The solution is to depend on libjs-jquery and use /usr/share/javascript/jquery/jquery.min.js from there. In addition, I see that you chose the GPLv3+ for your packaging work; I do not recommend it, since it is not compatible with “Waqf”: It may cause headaches if you would like to forward patches or files (manpages, …), that would be GPLv3+ unless stated otherwise. Have a nice week-end, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100710150336.ga2...@merveille.plessy.net
Bug#585999: Review of the copyright file for okasha_0.1.0-1.dsc.
Hi again, sorry for not realising that you were alredy doing the right thing with jquery.min.js; I made too hasty conclusion from the absence of patch in the source package… Here are answers to your other questions. Le Sat, Jul 10, 2010 at 06:25:28PM +0300, أحمد المحمودي a écrit : On Sun, Jul 11, 2010 at 12:03:36AM +0900, Charles Plessy wrote: 1) files/okasha-docbook.css is not documented in your copyright file (Copyright 2003 Tammy Fox, Garrett LeSage, and Red Hat, Inc. Copyright 2005 Tommy Reynolds tommy.reyno...@megacoder.com License: GPL ) Thanks for spotting that. I wonder though, how you spotted it, licensecheck only checked the python source files. I often use ‘grep -ri copyright .’ and pipe the result in a couple of ‘grep -v’ commands if there is a frequent motif that I would like to remove from the output after I made sure that it corresponds to already documented files. 2a) files/jquery.min.js is not the “preferrable form for modification”. However, since your package is non-free, this is not a blocking problem. I don't understand this part. In order to save some bandwith, the size of this javascript file is reduced by removing whitespace and comments, and shortening variable names. This results in a file that is not the “preferrable form for modification”, since new versions are made by working on the original large size version, and reducing it again. It is a similar situation as having a source file and a binary file, and therefore in Debian (not non-free), in my understanding, it is not allowed to keep such a file in the source package if its source is not in as well. In addition, I see that you chose the GPLv3+ for your packaging work; I do not recommend it, since it is not compatible with “Waqf”: It may cause headaches if you would like to forward patches or files (manpages, …), that would be GPLv3+ unless stated otherwise. Yes, this issue was raised by Jakub Wilk (who sponsored the package), and since I do not have any patches, I don't see a problem. Anyways, in case there are patches, I think I can put them under Waqf. (or GPL3+ or Waqf ?) In that case, my personal choice is to provide the packaging work under terms that allow relicensing (like the BOLA license for instance). But “GPLv3+ or Waqf” is also a good solution. 1) files/okasha-docbook.css is not documented in your copyright file (Copyright 2003 Tammy Fox, Garrett LeSage, and Red Hat, Inc. Copyright 2005 Tommy Reynolds tommy.reyno...@megacoder.com License: GPL ) ---end quoted text--- GPL = GPL-1 or what ? Although the authors probably intended GPLv2 or superior, we can not tell for them. Therefore I would pick GPLv1+ (“any version of the GPL”). Fortunately, the full-text copy of this license is making its way in /usr/share/common-licenses. Have a nice Sunday, -- Charles -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100711002846.ga30...@merveille.plessy.net
Bug#583217: Review of the copyright file for libconfig-mvp-reader-ini-perl.
user debian-le...@lists.debian.org usertags 583217 one-copyright-review thanks Dear Ansgar and Gregor, In the hope of speeding up and strenghtening the processing of NEW I had a look at your package. The rationale is explained in the proposal in the following wiki page: http://wiki.debian.org/CopyrightReview Fortunately, I have not found any problem with your copyright file :) 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100526235405.gf16...@kunpuu.plessy.org
Bug#435915: mira: changing back from RFP to ITP
retitle 435915 ITP: mira -- Whole Genome Shotgun and EST Sequence Assembler owner 435915 ! thanks There is a wrapper for mira in EMBASSY; it would be nice to have it available, for a full EMBOSS support. I do not have time right now but am still considering packaging mira. Of course, anybody is welcome to help or take over. -- Charles Plessy Debian Med packaging team Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100525141358.gb8...@kunpuu.plessy.org
Bug#429610: gbrowse: changing back from RFP to ITP
retitle 429610 ITP: gbrowse -- The Generic Genome Browser from GMOD owner 429610 ! thanks I am still interested to package Gbrowse. Help is of course much welcome, since it is a complex program. Most dependancies are packaged now, and the last difficulty to solve is to install it in a LSB-compliant way. Please do not hesitate to express your interest in this package in order to make me work harder on it ! -- Charles Plessy Debian Med packaging team Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100525042644.gc6...@kunpuu.plessy.org
Bug#580277: GMAP -- Align mRNA and EST sequences to a genome
Le Tue, May 04, 2010 at 06:30:26PM -0700, Shaun Jackman a écrit : I've packaged GMAP: Align mRNA and EST sequences to a genome GMAP: Genomic Mapping and Alignment Program GSNAP: Genomic Short-read Nucleotide Alignment Program The ITP is here: http://bugs.debian.org/580277 The git repository is here: git://git.debian.org/git/debian-med/gmap.git http://git.debian.org/?p=debian-med/gmap.git Dear Shaun, thank you very much for helping us to stay up to date in the field of next-generation sequencing. Just out of curiosity, will you use the package yourself, or did you prepare it for a friend or a colleague? I had a look at your package and have the following comments: - It is non-free: ‘Distribution of this Package as part of a commercial software product requires prior arrangement with the Developers.’ I updated debian/control accordingly. Since this license is not compatible with the GPL, I recommend that you chose another license for your packaging work, in order to avoid headaches in the future. - We will have to be careful when doing modifications. ‘Distribution of a modified version of this Package requires prior arrangement with the Developers.’ I am not sure of what it means for the manpages you wrote. If you have written them using the output of the programs as a template, they are a derivative of them, and the above may mean that we need agreement of the upstream developpers before redistributing them. But anyway, manpages are better to be forwarded upstream. Have you contacted them? - Location of the databases. I have seen ‘-DGMAPDB=\/usr/share/gmap\’ in the build logs. Does that mean that the users will have to install their databases there, or is there a way to override this path? In general, I think Debian users expect /usr/share to be completely under the control of the packaging system. Perhaps another path would be better? - How to cite gmap. I am preparing a system to transfer bibliographic information from the packages VCS to the Ultimate Debian Database, so that sites like our web sentinel can easily include this information. It is not finished yet, but you can find more information here: http://wiki.debian.org/UpstreamMetadata - Package description. How about this one: Description: spliced and SNP-tolerant alignment programs for mRNA and short reads This package contains the GMAP and GSMAP programs to align biological sequences, and additional utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning cDNAs (complementary DNA) to reference genomes. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single and paired-end sequence reads as short as 14 nt and of arbitrarily long length. It can do de novo discovery of splice sites (including interchromosomal splicing) or use a datbase of known splice sites. It also tolerates known single nucleotide polymorphisms (SNPs) and can align bisulfite-treated DNA. Maybe it would be good to propose to the authors to proofread this description, so that we are sure that I did not under- or over-estimate the possibilities of their programs. Have a nice day, -- Charles Plessy Debian Med packaging team Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100505040120.gd22...@kunpuu.plessy.org
Bug#545717: Bug#574569: ITP: clamz -- A command-line program to download MP3's from Amazon
merge 545717 574569 thanks Le Thu, Mar 18, 2010 at 10:29:04PM -0500, Chris Silva a écrit : Package: wnpp Severity: wishlist Owner: Chris Silva rac...@makeworld.com * Package name: clamz Version : 0.2 Upstream Author : Benjamin Moody floppusmaxi...@users.sf.net * URL : http://code.google.com/p/clamz/ * License : GPL-3 Programming Lang: C Description : A command-line program to download MP3's from Amazon Hello Chris, there is already an ITP filled for clamz, http://bugs.debian.org/545717. Please have a look at it: your help is welcome, but there are issues about which section clamz should go in. Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100319115448.gc10...@kunpuu.plessy.org
Bug#557199: [Debian-med-packaging] r-cran-epir_0.9-22-1_amd64.changes REJECTED
Le Thu, Jan 28, 2010 at 09:12:35AM +0100, Andreas Tille a écrit : Perhaps we should extract the information given in #557199 and put this into a template for future R packages, perhaps inside the r-base-dev documentation. What do you think? Hi all, I have just copied some information from http://bugs.debian.org/557199 to http://wiki.debian.org/ACCEPT-FAQ. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#561177: RFS: cobertura
Le Mon, Feb 01, 2010 at 09:15:54PM -0430, Miguel Landaeta a écrit : Upstream clarify this in her website (http://cobertura.sourceforge.net/license.html ): Because ant tasks are loaded directly into the runtime of ant, and the GPL is incompatable with all versions of the Apache Software License, ant tasks can not be licensed under the GPL. Dear Miguel, this information is outdated as the GPL version 3 is compatible with the Apache License version 2.0, see: http://www.apache.org/licenses/GPL-compatibility.html Have a nice day, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#566364: RFH: doc-central
Le Sat, Jan 23, 2010 at 12:00:25PM +0100, Stefano Zacchiroli a écrit : I find this request of yours unsubstantiated. The RC bug has a patch pending and is pretty easy to fix. I might eventually NMU it to fix that, even though I'm not willing to maintain the package right now. Beside that bug, the package works quite well, has a respectable number of popcon user (as you observe); I, for instance, am a daily user of it. So, exactly *why* you want this package to be removed, considering that there are way more bad packages in the archive (and almost completely unused) that would deserve removal first? I am also a happy user of doc-central and I am not saying that it should be removed by all means. However, if it is de facto abandonned, the Project should seek for a long term solution since it is a native package (i.e. it has not upstream apart from Debian itself.) This package was NMUed in Lenny and needs to be NMUed for Squeeze. If we do not want to rely on somebody to NMU it in Squeeze+1, I think it needs to be maintained or removed. I would be most happy if it would be maintained, therefore I have CCed the person who seems to care most for this package. If you NMU this package, may I suggest to orphan it and put it in collab-maint? I offer to do the work if you like the idea (svn or git, just let me know). Cheers, -- Charles Plessy Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#566364: RFH: doc-central
Package: wnpp Severity: normal Dear Robert and everybody, The native package doc-central looks abandonned by its listed maintainer, Guilherme de S. Pastore (gpastore), whose last upload was four years ago. It currently has 298 popcon users, and has been updated two times in NMU by Robert Luberda, who kept the package alive for the Lenny release. doc-central has one release-critical bug, making it unfit for the release. Are there volunteers to adopt it? Robert? The QA team? Otherwise, despite it is useful, it is maybe time to give up and remove it from our archive... Only two packages recommend doc-central, libsuitesparse-doc and gnumed-client. I have filed bugs on them to loosen the dependancy to suggest or drop it, since these package do not particuarly need doc-central and it is already suggested by the doc-base package. Have a nice day, -- Charles Plessy, Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557199: Is tabular data in binary format acceptable for Debian ?
Dear all, I would like to ask on this list a question I asked to the FTP team last December, and for which I have not received answer yet. Is tabular data in a binary format that can be read, written, modified and exported using free software acceptable for Debian, or shall we contact the upstream author to check if he used an intermediate format (be it text, or binary like .odt or .xls) and require the addition of this file to the source, or shall we provide a text export? I ask because it was one of the reasons for rejecting the r-cran-epir package. * Also the data/*.Rdata files appear to be binary. I don't know enough about them to make an iformed decision on if those can be built from source or if they are in their native format. These files are tables stored as binary R objects. Using the GNU R program, one can load, modify, display and save them, and export them to common formats such as CSV. I tried to clarify the situation with the FTP team, but no answer seems to come since my last email, on the 8th of January. http://bugs.debian.org/557199 I therefore submit the question to everybody's sagacity on Debian's main discussion place. An important part of the problem is that other r-cran-* packages have similar files, since they play a role in the documentation, as example data, and also in regression tests. I am currently holding my work on the r-cran-* packages on which I am uploader. My personnal policy is to not upload anything if I am not sure it would not be accepted as a new package. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557199: [Debian-med-packaging] r-cran-epir_0.9-19-1_i386.changes REJECTED
Le Thu, Jan 07, 2010 at 09:51:05PM +0100, Joerg Jaspert a écrit : more than ASCII format, what we need is the preferred form for making modifications. Binary format by itself is not a problem since there is no loss of information between both formats. I am not against including a text dump of the R object, but I would like to make clear that if this becomes a requirement for R packages to enter in Debian, then many packages from the gnu-r section are probably RC-buggy… I would like to know your conclusion on *Rdata files. They are example data files for the documentation and the regression tests. Many r-cran-* packages contain them. My personal opinion is that since they can be read, written, modified, and exported with R, they are a ‘preferential form’ for modification. I am currently holding my work on the r-cran-* packages I co-maintain until I get your answer. How are they usually modified? The format in which that happens is what we need (together with the ability to do that within Debian). Hi Joerg, While each of them is different, I think I can say that they are usually not modified. Their value is to stay the same for years, so that examples derived from them are reproductible. Here are a couple of examples from the core R package: The data give the speed of cars and the distances taken to stop. Note that the data were recorded in the 1920s. This data set provides information on the fate of passengers on the fatal maiden voyage of the ocean liner ‘Titanic’, summarized according to economic status (class), sex, age and survival. The ‘Indometh’ data frame has 66 rows and 3 columns of data on the pharmacokinetics of indomethicin. The (approximately) quarterly approval rating for the President of the United states from the first quarter of 1945 to the last quarter of 1974. Interestingly, the datasets shipped in the core R source package are not in binary format, but in R code format, for instance: cars - data.frame( speed = c(4, 4, 7, 7, 8, 9, 10, 10, 10, 11, 11, 12, 12, 12, 12, 13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 16, 16, 17, 17, 17, 18, 18, 18, 18, 19, 19, 19, 20, 20, 20, 20, 20, 22, 23, 24, 24, 24, 24, 25), dist = c(2, 10, 4, 22, 16, 10, 18, 26, 34, 17, 28, 14, 20, 24, 28, 26, 34, 34, 46, 26, 36, 60, 80, 20, 26, 54, 32, 40, 32, 40, 50, 42, 56, 76, 84, 36, 46, 68, 32, 48, 52, 56, 64, 66, 54, 70, 92, 93, 120, 85)) presidents - structure(c(NA, 87, 82, 75, 63, 50, 43, 32, 35, 60, 54, 55, 36, 39, NA, NA, 69, 57, 57, 51, 45, 37, 46, 39, 36, 24, 32, 23, 25, 32, NA, 32, 59, 74, 75, 60, 71, 61, 71, 57, 71, 68, 79, 73, 76, 71, 67, 75, 79, 62, 63, 57, 60, 49, 48, 52, 57, 62, 61, 66, 71, 62, 61, 57, 72, 83, 71, 78, 79, 71, 62, 74, 76, 64, 62, 57, 80, 73, 69, 69, 71, 64, 69, 62, 63, 46, 56, 44, 44, 52, 38, 46, 36, 49, 35, 44, 59, 65, 65, 56, 66, 53, 61, 52, 51, 48, 54, 49, 49, 61, NA, NA, 68, 44, 40, 27, 28, 25, 24, 24), .Tsp = c(1945, 1974.75, 4), class = ts) The example above is interesting because there are missing values (NA). Dealing with missing value is a delicate issue in statistics, and correcting the above table to fill the missing value would make it lose its interest as an example of a time serie with missing values. The Rdata files are examples of real data, not scientific references meant to be corrected or extended. My opinion is therefore that the binary format offers the same freedoms as the R code format, or as a CSV table, an Excel table, an Openoffice table, etc. What the author used to produce the R objects is of little relevance as it is more a disposable intermediate than a source that should stay available for helping people to modify. Note that there is no evidence that all Rdata files come from R code as above. My wild guess is that many have been imported as a CSV table at some point. To be carricatural, I would say that the Rdata format is not less obscure as a .csv.gz format. Both need an command line to be transformed to csv format. I hope I have not been confusing. If you would like external opinion, I suggest to contact to our Debian expert Dirk Eddelbuettel (e...@debian.org). His work on and with R is reckognised internationally. Have a nice day and thanks for the fast answer, I really appreciate it. -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557199: [Debian-med-packaging] r-cran-epir_0.9-19-1_i386.changes REJECTED
Le Wed, Dec 16, 2009 at 12:05:45AM +0900, Charles Plessy a écrit : Dear Andreas and FTP team, more than ASCII format, what we need is the preferred form for making modifications. Binary format by itself is not a problem since there is no loss of information between both formats. I am not against including a text dump of the R object, but I would like to make clear that if this becomes a requirement for R packages to enter in Debian, then many packages from the gnu-r section are probably RC-buggy… Dear FTP team, I would like to know your conclusion on *Rdata files. They are example data files for the documentation and the regression tests. Many r-cran-* packages contain them. My personal opinion is that since they can be read, written, modified, and exported with R, they are a ‘preferential form’ for modification. I am currently holding my work on the r-cran-* packages I co-maintain until I get your answer. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#560744: O: xview -- XView UI toolkit library and client programs
Le Fri, Dec 11, 2009 at 10:35:09PM +0100, Martin Buck a écrit : I'm orphaning the XView package, containing the XView UI toolkit libraries Reverse dependencies from other source packages are: treetool Dear Martin an potential adopters, treetool has been removed from Debian since Lenny. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557199: [Debian-med-packaging] r-cran-epir_0.9-19-1_i386.changes REJECTED
Le Fri, Dec 11, 2009 at 07:29:48PM +, Barry deFreese a écrit : I am rejecting r-cran-epir for the following reasons: * Upstream tarball does not include full copy of GPLv2 license and none of the headers explicitly indicate a license. * doc/epiR.pdf has not corresponding source files to recreate it at build time. * Also the data/*.Rdata files appear to be binary. I don't know enough about them to make an iformed decision on if those can be built from source or if they are in their native format. Dear Barry, FTP team, and Debian Med team, doc/epiR.pdf can be generated by the command ’R CMD Rd2pdf r-cran-epir-0.9-22’. I also looked at the .Rdata files. These are data files in binary format for testing or example purposes. Each of these datasets are described in the accompaning documentation, that is reproduced in the PDF file. For instance, the source of epi.epidural.RData stems from the two following academic articles: * Deeks JJ, Altman DG, Bradburn MJ (2001). Statistical methods for examining heterogeneity and combining results from several studies in meta-analysis. In: Egger M, Davey Smith G, Altman * D (eds). Systematic Review in Health Care Meta-Analysis in Context. British Medical Journal, London, pp. 291 - 299. The epi.*.RData files can be loaded, manipulated and saved using /usr/bin/R. I believe that this makes them a preferred form of modification for R users. For the missing COPYING file, while I am very confident that there is no doubt this package is licensed under the GPL version 2, I note that most other R packages do indeed have a COPYING or a LICENSE file, and that therefore it would be worthwile asking a clarification to the authors. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557882: ITP: libextutils-manifest-perl -- utilities to write and check a MANIFEST file
Le Thu, Nov 26, 2009 at 12:12:35PM +0100, Xavier Oswald a écrit : On 19:54 Thu 26 Nov , Charles Plessy wrote: I just injected libextutils-manifest-perl in your SVN repository. Given the concerns I expressed above, I would like to see a green light before uploading to NEW… Seems well done, but I think you forgot the debian/* copyright holder in debian/copyright Le Thu, Nov 26, 2009 at 01:17:49PM +0200, Niko Tyni a écrit : On Wed, Nov 25, 2009 at 09:18:50AM +0900, Charles Plessy wrote: I intend to package the ExtUtils::Manifest Perl module. It is already packaged in the perl-modules packages, but in Lenny the provided version is too low to allow backports of one package of mine that would be fine otherwise. Have you checked if your package actually needs something from the newer ExtUtils::Manifest? It could be just a spurious dependency. Dear Xavier and Niko, thanks for your answers. The latest version of the BioPerl package really needs ExtUtils::Manifest; that was discussed on the upstream mailing list a couple of times. But actually ExtUtils::Manifest contains only one .pm file. As an ugly workaround, maybe I could try to add it to the bioperl backport source package and work out debian/rules so that it is recognised by Perl at build time in its path to search for packages. That would save the perl-modules package Provides, Replaces and Conflicts fields from getting one additional entry, and make one less package to manage in Squeeze, since as you noted well, it looks like its only use for the moment would be to help the backport of Bioperl. I will follow your recommendation on this issue. As for the debian/* copyright entry, I tend to omit it when I do not have the feeling that my contribution is complex enough to be coyrightable, but for the sake of consistency in the pkg-perl repository, I will add it if this package is not cancelled. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557882: ITP: libextutils-manifest-perl -- utilities to write and check a MANIFEST file
Le Wed, Nov 25, 2009 at 09:18:50AM +0900, Charles Plessy a écrit : I intend to package the ExtUtils::Manifest Perl module. It is already packaged in the perl-modules packages, but in Lenny the provided version is too low to allow backports of one package of mine that would be fine otherwise. My purpose is therefore to prepare a libextutils-manifest-perl package similar in design to libmodule-build-perl, which is also dually present in Debian, and then to submit a backport to backports.org after the package migrated in Testing. Please let me know if this would create problems or if more coordination is required with the perl-modules package. Hello Perl team I just injected libextutils-manifest-perl in your SVN repository. Given the concerns I expressed above, I would like to see a green light before uploading to NEW… 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#557882: ITP: libextutils-manifest-perl -- utilities to write and check a MANIFEST file
Package: wnpp Severity: wishlist Owner: Charles Plessy ple...@debian.org Package name: libextutils-manifest-perl Version : 1.57 Upstream Author : Andreas Koenig andreas.koe...@anima.de URL : http://search.cpan.org/~rkobes/ExtUtils-Manifest-1.57/ License : Perl Programming Lang: Perl Description : utilities to write and check a MANIFEST file Dear Perl team and Debian developers, I intend to package the ExtUtils::Manifest Perl module. It is already packaged in the perl-modules packages, but in Lenny the provided version is too low to allow backports of one package of mine that would be fine otherwise. My purpose is therefore to prepare a libextutils-manifest-perl package similar in design to libmodule-build-perl, which is also dually present in Debian, and then to submit a backport to backports.org after the package migrated in Testing. Please let me know if this would create problems or if more coordination is required with the perl-modules package. Here is a tentative description: ExtUtils::Manifest is a Perl module that provides a number of utilities to write and check a MANIFEST file. At present the list includes mkmanifest, manicheck, filecheck, fullcheck, skipcheck, manifind, maniread, manicopy, and maniadd. 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#550542: ITP: jhdf -- Java HDF5 Object Package
Le Sun, Oct 11, 2009 at 12:08:35AM +0200, Sylvestre Ledru a écrit : 4. All publications or advertising materials mentioning features or use of this software must acknowledge that it was developed by the National Center for Supercomputing Applications at the University of Illinois, and credit the Contributors. Hi Sylvestre, note the potential danger of infringement of this clause, for instance if one makes flyers for Debian Science live CDs that mention capacity to work with the HDF5 format. In the past, I managed to convince academic upstream authors of a program I package to remove a similar clause, by referring to the following essay on the FSF website: http://www.fsf.org/licensing/essays/bsd.html. Maybe you can give it a try? 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-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
