Re: Trinityrnaseq status
I had to patch trinity fot gcc5, did you test with this version? I have provided patch to upstream, and can give it to you if necessary Le sam. 22 août 2015 02:57, Michael Crusoe michael.cru...@gmail.com a écrit : Hello again Olivier, Thank you for asking for an update on the trinityrnaseq related packages: trinityrnaseq: waiting on libjung-free-java, rsem, express, and jaligner. Otherwise all the tests run successfully for me. libjung-free-java package: in NEW queue courtesy Olivier https://ftp-master.debian.org/new/libjung-free-java_2.0.1-1.html rsem: waiting for r-bioc-ebseq; needs manpages, patch descriptions, add new patches to add hardening flags r-bioc-ebseq: ready for sponsoring now that r-cran-blockmodeling is in the archive express: now renamed to `berkeley-express` as 'bio-express' and 'seq-express' have other significant Google hits. Needs a patch to add hardening flags. jaligner: in NEW queue: https://ftp-master.debian.org/new/jaligner_1.0-1.html === Any and all assistance you and the group can provide for the above would be greatly appreciated! On Thu, Aug 20, 2015 at 11:32 PM olivier sallou osal...@debian.org wrote: Hi Michael, I was about to package trinityrnaseq when I found your ITP to package it. What is the status of the package? Thanks Olivier -- Michael R. Crusoe: Programmer Bioinformatician cru...@ucdavis.edu The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
Re: Help needed to update to latest fastqc
As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Olivier Le lun. 4 mai 2015 à 09:04, Olivier Sallou olivier.sal...@irisa.fr a écrit : Forwarded Message Subject: Help needed to update to latest fastqc Resent-Date: Sun, 3 May 2015 06:54:37 + (UTC) Resent-From: debian-med@lists.debian.org Date: Sun, 3 May 2015 08:54:22 +0200 From: Andreas Tille andr...@an3as.eu andr...@an3as.eu To: Debian Med Project List debian-med@lists.debian.org debian-med@lists.debian.org Hi, I tried to upgrade to the latest fasqc version. When doing so I decided to move from SVN to Git: Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git Upstream needs a new Build-Depends libjhdf5-java which I added. However, I was not able to fix the build. When trying I considered switching from the Makefile based build to ant (which sounds natural) Unfortunately I did not succeeded in adapting build.xml. Any help would be appreciated 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/20150503065422.gh5...@an3as.eu
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 07/08/15 10:24, Fabian Klötzl wrote: Hi, I will be on a week-long vacation, starting tomorrow. Please, feel free to continue committing so we can release an improved package, soon. On 06.08.2015 20:01, Andreas Tille wrote: On Thu, Aug 06, 2015 at 05:43:47PM +0200, Tomasz Buchert wrote: I'll also mention that theere are actually 2 different tarballs with 2.0.1: the one the package is based on (from googlecode) and the one that I used in my parallel packaging (from github). The latter has autoconf files removed for example and so is much smaller. I permitted myself to update debian/watch file, with filenamemangle option which renames the file to something with libdivsufsort prefix. In any case pleas point d/watch to github! Googlecode is dead and no watch file should point to this. d/watch looks correct now. Cheers, Fabian Hi Fabian, I hope you had great vacations. I've pushed another change to libdivsufsort which, to my knowledge, is The Right Thing To Do. I still needed to apply a custom patch for include directory because header files are generated on-the-fly, but other than that it seems fine. I propose to ask upstream to use them. Please review, Tomasz signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi, Am 22.08.2015 um 12:28 schrieb Tomasz Buchert: I've pushed another change to libdivsufsort which, to my knowledge, is The Right Thing To Do. I still needed to apply a custom patch for include directory because header files are generated on-the-fly, but other than that it seems fine. Patch looks ok to me, but I am not an expert on these things. I propose to ask upstream to use them. Definitely, once we have the patches ready, they should be bundled in a pull request. Then we should notify upstream via mail, because they don't seem to be an active GitHub user. With respect to bug #794729. I guess that is fixed now and can be closed. But since libdivsufsort-dev now depends on libdivsufsort3 should we also add the 3 to the -dev package: libdivsufsort3-dev? What is the usual debian way to handle that? Best, Fabian -BEGIN PGP SIGNATURE- Version: GnuPG v2 iQIcBAEBCAAGBQJV2FwWAAoJEA/ahZpWA3bBSDUQAJ/MAoaJGuoMUam/N811oiGY gI2pSPC6+ryMmwRpZI655iVsn3Vo4et23p/V45DfOshgfuaVdn29iWuDEplw23TC khef43sgdZzdJZc+NWlMws86o41ADWKyGWN5TWeOGI8tpy2Ermxus4INYu7SxQmb PnmtCYHLhT56MCjVMGFYZPunsFA7nLVmiTquuTU5WsNZLMa8c54DcqyeeSuT6PL3 zwpVzOr9P0+kch748/ZMRYQYgqN5EDJuG8lqFk7VuyfYUfCMY368kF5C34wiwZvQ ZwXYCY+OdKbPL4Jy3pNki1+Ic6fOCWTFPz9alIwMrhk9wLh+gaPKTdK8de7YPxYR Qoyueo8Qy2yQUr7nXf95Ie12HfHNckaWYt/TlbymzXm2aUD3QhOAt3WQ4tREYGUf UOWIVMedh65E0qJGL3FSwewVX+QyGJZSCglOXT534XAfHvenS6cPPFluXc9iWWuD mpX2rN2m6yDY3XwuzP6T0+c13HU0gpCMV5zYWBpTUEQpd6LlyVaenPiu+t1S1CqN TK6cLUS4tTLodFbZtktITrTENnNMdgll+hGkX2CjGpDGTVYyuADtKwe4AM0Bzv9i WpvOUz5Mc3ZU9pNjv311j4sLliLKYqRs2vneUk86O0rmpYq5Egm/NTwLt1ldlgUz 9T9lduRraFzP6Z/O1Mnd =FZdA -END PGP SIGNATURE-
Cc'ing list: Bug#796487: Acknowledgement (ITP: repeatmasker-recon -- indentification of repeat families from biological sequences)
-- Forwarded message - From: Debian Bug Tracking System ow...@bugs.debian.org Date: sam. 22 août 2015 à 08:39 Subject: Bug#796487: Acknowledgement (ITP: repeatmasker-recon -- indentification of repeat families from biological sequences) To: Olivier Sallou osal...@debian.org Thank you for filing a new Bug report with Debian. This is an automatically generated reply to let you know your message has been received. Your message is being forwarded to the package maintainers and other interested parties for their attention; they will reply in due course. As you requested using X-Debbugs-CC, your message was also forwarded to debian-de...@lists.debian.org (after having been given a Bug report number, if it did not have one). Your message has been sent to the package maintainer(s): w...@debian.org If you wish to submit further information on this problem, please send it to 796...@bugs.debian.org. Please do not send mail to ow...@bugs.debian.org unless you wish to report a problem with the Bug-tracking system. -- 796487: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=796487 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 22/08/15 13:25, Fabian Klötzl wrote: Hi, Am 22.08.2015 um 12:28 schrieb Tomasz Buchert: I've pushed another change to libdivsufsort which, to my knowledge, is The Right Thing To Do. I still needed to apply a custom patch for include directory because header files are generated on-the-fly, but other than that it seems fine. Patch looks ok to me, but I am not an expert on these things. Hi, I did it according to the bug I mentioned. It is supposed to work even when cross-compiling, but I didn't check it. I propose to ask upstream to use them. Definitely, once we have the patches ready, they should be bundled in a pull request. Then we should notify upstream via mail, because they don't seem to be an active GitHub user. With respect to bug #794729. I guess that is fixed now and can be closed. But since libdivsufsort-dev now depends on libdivsufsort3 should we also add the 3 to the -dev package: libdivsufsort3-dev? What is the usual debian way to handle that? The usual way is to have libdivsufsort-dev. Wrt the bug: as the dependency is now explicit, you can close in the next release. More genrally, you need to format the changelog with a nice summary of all changes. Best, Fabian Cheers, Tomasz signature.asc Description: Digital signature
Re: Help needed to update to latest fastqc
Hi, On Sat, Aug 22, 2015 at 08:27:39AM +, olivier sallou wrote: As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Since I personally have bo proper test case I'd vote for starting to upload the first link in the chain of dependencies. There might be pretty much time to fix things while its hanging in the new queue (hopefully less time). Thanks for your work on this Andreas. -- http://fam-tille.de
Re: Trinityrnaseq status
Hi, On Sat, Aug 22, 2015 at 12:57:20AM +, Michael Crusoe wrote: trinityrnaseq: waiting on libjung-free-java, rsem, express, and jaligner. Otherwise all the tests run successfully for me. I really hope that jaligner will make it soon - no idea why several packages later in the queue made it way faster. libjung-free-java package: in NEW queue courtesy Olivier https://ftp-master.debian.org/new/libjung-free-java_2.0.1-1.html rsem: waiting for r-bioc-ebseq; needs manpages, patch descriptions, add new patches to add hardening flags r-bioc-ebseq: ready for sponsoring now that r-cran-blockmodeling is in the archive Uploaded. express: now renamed to `berkeley-express` as 'bio-express' and 'seq-express' have other significant Google hits. Needs a patch to add hardening flags. s/express/berkeley-express/ in tasks file. jaligner: in NEW queue: https://ftp-master.debian.org/new/jaligner_1.0-1.html Keep on crossing fingers that this will make it soon. Any and all assistance you and the group can provide for the above would be greatly appreciated! Please be more verbose if you see tasks I could do to support this. Kind regards Andreas. -- http://fam-tille.de
Re: Help needed to update to latest fastqc
On 08/22/2015 03:35 PM, Andreas Tille wrote: Hi, On Sat, Aug 22, 2015 at 08:27:39AM +, olivier sallou wrote: As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to be fine, you may want to build/install them locally to test your fastqc update ? As it makes use of the libraries, it would also be a good additional test for those libs before uploading them Since I personally have bo proper test case I'd vote for starting to upload the first link in the chain of dependencies. There might be pretty much time to fix things while its hanging in the new queue (hopefully less time). ok, I have uploaded libsis-base-java (the first one in chain) Thanks for your work on this Andreas. -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Re: vtk6 transition
Hello Anton, On 22.08.2015 22:00, Anton Gladky wrote: thanks a lot for an interest to help with vtk6-transition! Just FYI I have prepared a new upload for vtk6, great! but due to the current conflicts in build-depends I cannot upload it. Hopefully GCC-5 will over soon. I think it should be possible to upload to experimental by preparing with the experimental libgdal-dev package. Doing so would have the advantage that the new vtk6(v5) packages could already be processed by ftp-master and for the later re-upload to sid we wouldn't have to wait for it to pass through the NEW pipeline again. Well, i'm still only DM, so this is up to you ;) Best Gert
Re: vtk6 transition
Hi Gert, thanks a lot for an interest to help with vtk6-transition! Just FYI I have prepared a new upload for vtk6, but due to the current conflicts in build-depends I cannot upload it. Hopefully GCC-5 will over soon. Same here, nice to associate email with a real person! Best regards Anton 2015-08-21 22:02 GMT+02:00 Gert Wollny gw.foss...@gmail.com: Hi, it seems that the vtk6 transition can now be properly prepared. I found out that the latest version of libgdal-dev available from 'experimental' is what we actually need. I'd promise to work on this, but for the next two weeks I'm mostly off-line. After this I'll happily step up, also to add and test all the patches that are available for vtk6. It was nice meeting some of you in person :) Best wishes, Gert
Re: Trinityrnaseq status
On Sat, Aug 22, 2015 at 6:49 AM Andreas Tille andr...@an3as.eu wrote: Hi, On Sat, Aug 22, 2015 at 12:57:20AM +, Michael Crusoe wrote: trinityrnaseq: waiting on libjung-free-java, rsem, express, and jaligner. Otherwise all the tests run successfully for me. I really hope that jaligner will make it soon - no idea why several packages later in the queue made it way faster. On the upside it is now the second oldest package in queue so hopefully it will get some attention soon. libjung-free-java package: in NEW queue courtesy Olivier https://ftp-master.debian.org/new/libjung-free-java_2.0.1-1.html rsem: waiting for r-bioc-ebseq; needs manpages, patch descriptions, add new patches to add hardening flags r-bioc-ebseq: ready for sponsoring now that r-cran-blockmodeling is in the archive Uploaded. Thanks! Any and all assistance you and the group can provide for the above would be greatly appreciated! Please be more verbose if you see tasks I could do to support this. Do have experience in what incantations it takes to add the hardening build flags to recalcitrant packages? -- Michael R. Crusoe: Programmer Bioinformatician cru...@ucdavis.edu The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
Processed: block 395843 with 778489
Processing commands for cont...@bugs.debian.org: block 395843 with 778489 Bug #395843 [wnpp] RFP: wgs-assembler -- Whole-Genome Shotgun Assembler 395843 was blocked by: 793763 784863 395843 was blocking: 787977 Added blocking bug(s) of 395843: 778489 thanks Stopping processing here. Please contact me if you need assistance. -- 395843: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=395843 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Re: Trinityrnaseq status
On Fri, Aug 21, 2015 at 11:05 PM olivier sallou olivier.sal...@gmail.com wrote: I had to patch trinity fot gcc5, did you test with this version? I have provided patch to upstream, and can give it to you if necessary Yeah, I just ran into those problems. Feel free to send the patch to me or commit it directly. I'm sure upstream will appreciate them as well! Le sam. 22 août 2015 02:57, Michael Crusoe michael.cru...@gmail.com a écrit : Hello again Olivier, Thank you for asking for an update on the trinityrnaseq related packages: trinityrnaseq: waiting on libjung-free-java, rsem, express, and jaligner. Otherwise all the tests run successfully for me. libjung-free-java package: in NEW queue courtesy Olivier https://ftp-master.debian.org/new/libjung-free-java_2.0.1-1.html rsem: waiting for r-bioc-ebseq; needs manpages, patch descriptions, add new patches to add hardening flags r-bioc-ebseq: ready for sponsoring now that r-cran-blockmodeling is in the archive express: now renamed to `berkeley-express` as 'bio-express' and 'seq-express' have other significant Google hits. Needs a patch to add hardening flags. jaligner: in NEW queue: https://ftp-master.debian.org/new/jaligner_1.0-1.html === Any and all assistance you and the group can provide for the above would be greatly appreciated! On Thu, Aug 20, 2015 at 11:32 PM olivier sallou osal...@debian.org wrote: Hi Michael, I was about to package trinityrnaseq when I found your ITP to package it. What is the status of the package? Thanks Olivier -- Michael R. Crusoe: Programmer Bioinformatician cru...@ucdavis.edu The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe -- Michael R. Crusoe: Programmer Bioinformatician cru...@ucdavis.edu The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
How to edit the tasks list
On Thu, Aug 20, 2015 at 1:18 PM Andreas Tille andr...@an3as.eu wrote: This IMHO does not need any discussion. I simply changed the tasks files (which you could do as well). By following the directions in the policy I get ``` $ debcheckout -a debian-med declared svn repository at svn+ssh:// svn.debian.org/svn/blends/projects/med/trunk/debian-med/ svn co svn+ssh://svn.debian.org/svn/blends/projects/med/trunk/debian-med/ debian-med ... svn: E17: URL 'svn+ssh:// svn.debian.org/svn/blends/projects/med/trunk/debian-med' doesn't exist checkout failed (the command above returned a non-zero exit code) ``` What am I missing? :-) -- Michael R. Crusoe: Programmer Bioinformatician cru...@ucdavis.edu The lab for Data Intensive Biology; University of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
