Re: Any volunteer to take some simple R packages as packaging training?
Hi Johannes, On Thu, Oct 22, 2015 at 02:25:10AM +0200, Johannes Schaffrath wrote: > Hi Andreas, > > I'm really sorry that I have lost track of this task, but I still want to > finish it. I have an alioth account and I'm reading the maintainers guide > since September. I'm planning to upload the packages within the next two > weeks. Cool. Feel free to ask here in case of any issues Andreas. > > Mit freundlichem Gruß > Johannes Schaffrath > > On 10/18/2015 09:19 AM, Andreas Tille wrote: > >Hi, > > > >I'm going through old mails in my mailbox and I'm wondering whether > >somebody wants to work on these very simple targets. There was some > >response from Johannes Schaffrath a year ago but no further action. > > > >These could be nice projects for Mentoring of the Month and I think > >the packages are simple enough to take way less than one month. > > > >Kind regards > > > > Andreas. > > > >On Thu, Sep 11, 2014 at 01:49:49PM +0200, Andreas Tille wrote: > >>Hi, > >> > >>according to > >> > >> > >> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-ebimage/trunk/debian/changelog?revision=17994&view=markup > >> > >>we need to package > >> > >> r-cran-tiff: http://cran.r-project.org/web/packages/tiff/index.html > >> r-cran-jpeg: http://cran.r-project.org/web/packages/jpeg/index.html > >> r-cran-png: http://cran.r-project.org/web/packages/png/index.html > >> > >>to get r-bioc-ebimage packaged. Usually R packages are quite simple and > >>thus a good learning example. I do not want to spoil the fun of some > >>newcomer and do it myself - so any takers for these? Any help in case > >>of trouble is granted for sure. > >> > >>Kind regards > >> > >>Andreas. > >> > >>-- > >>http://fam-tille.de > >> > >> > >>-- > >>To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org > >>with a subject of "unsubscribe". Trouble? Contact > >>listmas...@lists.debian.org > >>Archive: https://lists.debian.org/2014094949.gt19...@an3as.eu > >> > >> > > -- http://fam-tille.de
Re: Any volunteer to take some simple R packages as packaging training?
Hi Andreas, I'm really sorry that I have lost track of this task, but I still want to finish it. I have an alioth account and I'm reading the maintainers guide since September. I'm planning to upload the packages within the next two weeks. Mit freundlichem Gruß Johannes Schaffrath On 10/18/2015 09:19 AM, Andreas Tille wrote: Hi, I'm going through old mails in my mailbox and I'm wondering whether somebody wants to work on these very simple targets. There was some response from Johannes Schaffrath a year ago but no further action. These could be nice projects for Mentoring of the Month and I think the packages are simple enough to take way less than one month. Kind regards Andreas. On Thu, Sep 11, 2014 at 01:49:49PM +0200, Andreas Tille wrote: Hi, according to http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-ebimage/trunk/debian/changelog?revision=17994&view=markup we need to package r-cran-tiff: http://cran.r-project.org/web/packages/tiff/index.html r-cran-jpeg: http://cran.r-project.org/web/packages/jpeg/index.html r-cran-png: http://cran.r-project.org/web/packages/png/index.html to get r-bioc-ebimage packaged. Usually R packages are quite simple and thus a good learning example. I do not want to spoil the fun of some newcomer and do it myself - so any takers for these? Any help in case of trouble is granted for sure. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/2014094949.gt19...@an3as.eu
Bug#778578: marked as done (ITP: rsem -- RNA-Seq by Expectation-Maximization)
Your message dated Wed, 21 Oct 2015 11:00:18 + with message-id and subject line Bug#778578: fixed in rsem 1.2.22+dfsg-1 has caused the Debian Bug report #778578, regarding ITP: rsem -- RNA-Seq by Expectation-Maximization to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 778578: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778578 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- Package: wnpp Severity: wishlist Owner: Debian Med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: rsem Version : 1.2.19 Upstream Author : Bo Li * URL : http://deweylab.biostat.wisc.edu/rsem/ * License : GPL-3 Programming Lang: C++, Perl Description : RNA-Seq by Expectation-Maximization RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute’s Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator. RSEM is a popular bioinformatics program and a dependency of trinityrnaseq. It will be maintained by the Debian Med team. --- End Message --- --- Begin Message --- Source: rsem Source-Version: 1.2.22+dfsg-1 We believe that the bug you reported is fixed in the latest version of rsem, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 778...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe (supplier of updated rsem package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Format: 1.8 Date: Thu, 27 Aug 2015 13:17:53 -0400 Source: rsem Binary: rsem Architecture: source amd64 Version: 1.2.22+dfsg-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: rsem - RNA-Seq by Expectation-Maximization Closes: 778578 Changes: rsem (1.2.22+dfsg-1) unstable; urgency=low . * Initial release (Closes: #778578) Checksums-Sha1: cf4465ffd932acdc4af9afd8adebe557a59bd7b3 1974 rsem_1.2.22+dfsg-1.dsc 9b042597f22ca80c2cd65602ba3e3b187f978653 128327 rsem_1.2.22+dfsg.orig.tar.gz 18ea6b1a85218aab8ad5014c2b90f8fb384e77ba 5728 rsem_1.2.22+dfsg-1.debian.tar.xz aa6bcb9aadd1b6f8ebbb69838027f3653e50e4cc 475010 rsem_1.2.22+dfsg-1_amd64.deb Checksums-Sha256: f2ea8f62bec5be9022420e972af311a90f096dd9e25105b5c6bd0d761e27ff95 1974 rsem_1.2.22+dfsg-1.dsc 72259849fb3303fd9998a9496925a0d4c3cee7b9eb4d2b660d06e9de83ad3651 128327 rsem_1.2.22+dfsg.orig.tar.gz 4feac9bb70392014fc065f251434795a66e10a6ed3f13cbfdacf4be3f5fb560f 5728 rsem_1.2.22+dfsg-1.debian.tar.xz 8a5cae64ce9bef8aa8a02f7b6a84884fb9a46b031c410fa765a9a704b4792f42 475010 rsem_1.2.22+dfsg-1_amd64.deb Files: a232d21f01a1340dc2d92e6a22159280 1974 science optional rsem_1.2.22+dfsg-1.dsc acce30151308dfc3d234a29ead6c3ee1 128327 science optional rsem_1.2.22+dfsg.orig.tar.gz cee89ad822a9501d4cc9d7157d9e5148 5728 science optional rsem_1.2.22+dfsg-1.debian.tar.xz 7b8e85a28b4fedca403a2aac8a7ab369 475010 science optional rsem_1.2.22+dfsg-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1 iQIcBAEBCAAGBQJWJq2AAAoJEFeKBJTRxkbRbpwP/RBvB9H23Nuyoj+U36rlhcsK l7GTpo/ht8l8K2DdZFTa0L+kKGCze8AIYxCo1J74aSAPoZOLG98pu/bIQbopOj2o SvcrRspAz2MqGltuKqv1BIbyRaYtx4magxcJ9ZVB2yFRqBAN0mZRXznbU6VDgau9 SH
How to mention Debian-external support for applications?!?
Hello, we have quite some tools and packages for which there is support from upstream (there are these kind of infrastructure grants) or there are some external consultants whose time one can rent. >From our debian-med.alioth.debian.org home page we have a link to http://debian-med.alioth.debian.org/support.xml which lists EagleGenomics (some more come to mind by now, please raise your hands) and there is also http://debian-med.alioth.debian.org/organisations.xml that should possibly also be updated. Not even the folks behind Bio-Linux are appearing, which they definitely should. Are there any ideas popping up on how to give references to individual packages and respective support? Should this possibly be in the task pages? I am writing this in an attempt to gather ideas for a presentation of Debian Med on scientific conference. What should not happen is that a booth of ours attracts many people that are yet somewhat remote to our community, maybe those with a more biological background that are now forced into next-generation sequencing. The posters of the booth say that Debian is well-equipped and runs on all today's popular cloud infrastructures, but we then have nobody to take them along. Ideas? Many greetings Steffen
