python-pysam (Was: Bug#787981: Status of python-pbcore)
Hi, On Wed, Jun 24, 2015 at 09:11:49PM -0700, Afif Elghraoui wrote: This package does not yet have python3 support. That can be added, but the tests must be run to make sure the porting is successful. As python-pbcore has a run-time dependency on a version of python-pysam not yet in unstable, running the test suite using the official Debian packages is not yet possible. Python-pysam was rejected by ftpmaster[1]. I wanted to fix this but it seems the Git repository is not complete. Changelog says UNRELEASED but the tag debian/0.8.3-1 is set. Could anybody commit the latest state (I have no access to the latest upload) and remove the tag. Preferably the missing license will be added as well and I'll upload as soon as this has happened (or I could also care for the license if something might remain unclear). Kind regards Andreas. [1] https://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-June/032600.html -- 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/20150625063740.ga28...@an3as.eu
Re: python-pysam
Le Wed, Jun 24, 2015 at 11:54:16PM -0700, Afif Elghraoui a écrit : On الأربعاء 24 حزيران 2015 23:37, Andreas Tille wrote: Python-pysam was rejected by ftpmaster[1]. I wanted to fix this but it seems the Git repository is not complete. Changelog says UNRELEASED but the tag debian/0.8.3-1 is set. I saw the email on the commit list that Charles updated the changelog to say unstable [1] when he uploaded. I don't see this in the repository now, though. In any case, I was working on this package a little earlier after hearing about rejection (but starting from the same state that you see). I excluded the whole htslib directory using Files-Excluded in debian/copyright since it's unnecessary anyway. Could anybody commit the latest state (I have no access to the latest upload) and remove the tag. Preferably the missing license will be added as well and I'll upload as soon as this has happened (or I could also care for the license if something might remain unclear). Should I push what I have so far? ..or was I not supposed to make commits on top of that ambiguous state? Hi all, I pushed the missing commit; sorry. The tag is accurate. I think that it is a good idea to remove the convenience copy of the htslib altogether. Have a nice day, -- Charles -- 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/20150625070808.ga9...@falafel.plessy.net
Re: python-pysam
Hi, Andreas, On الأربعاء 24 حزيران 2015 23:37, Andreas Tille wrote: Hi, On Wed, Jun 24, 2015 at 09:11:49PM -0700, Afif Elghraoui wrote: Python-pysam was rejected by ftpmaster[1]. I wanted to fix this but it seems the Git repository is not complete. Changelog says UNRELEASED but the tag debian/0.8.3-1 is set. I saw the email on the commit list that Charles updated the changelog to say unstable [1] when he uploaded. I don't see this in the repository now, though. In any case, I was working on this package a little earlier after hearing about rejection (but starting from the same state that you see). I excluded the whole htslib directory using Files-Excluded in debian/copyright since it's unnecessary anyway. Could anybody commit the latest state (I have no access to the latest upload) and remove the tag. Preferably the missing license will be added as well and I'll upload as soon as this has happened (or I could also care for the license if something might remain unclear). Should I push what I have so far? ..or was I not supposed to make commits on top of that ambiguous state? regards Afif 1. http://lists.alioth.debian.org/pipermail/debian-med-commit/2015-June/032396.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- 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/558ba598.6080...@ghraoui.name
Re: python-pysam
Hello, On الخميس 25 حزيران 2015 00:08, Charles Plessy wrote: Le Wed, Jun 24, 2015 at 11:54:16PM -0700, Afif Elghraoui a écrit : Should I push what I have so far? ..or was I not supposed to make commits on top of that ambiguous state? Hi all, I pushed the missing commit; sorry. The tag is accurate. Thanks I think that it is a good idea to remove the convenience copy of the htslib altogether. While revising the package, I noticed a couple of issues with the autopkgtest. I just pushed my current progress after merging in Charles' commit, but the package is not ready yet. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- 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/558babf4.4010...@ghraoui.name
Re: Help needed to update to latest fastqc
Hi Olivier, any news about this hdf5lib packaging? Kind regards Andreas. On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: On 05/04/2015 10:52 PM, Andreas Tille wrote: Hi Olivier, On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote: File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports HDFS5Factory from ch.systemsx.cisd.hdf5 but jhdf5.jar only contains files like: ncsa/hdf/hdf5lib/... and no HDF5Factory this jhdf5 is not the correctl lib (or an other one is needed). I guess its this one: https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html seems that original code source is the same (https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/) (/ncsa/...) but that /ch/... has not been included for a reason In addition, in debian/patches/build.xml is missing commons-math3.jar to be added in pathelement for classpath. for duplicate classes, I don't yet, but hdf5 first need to be resolved. If I do not hear from you I'll try the URL above tomorrow (if nobody else might beat me which would for sure welcome as always). Kind regards Andreas. -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- 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/55487063.1090...@irisa.fr -- 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/20150625073719.gc28...@an3as.eu
Re: python-pysam
Hi, Andreas, Please excuse the top-posting reply format from my phone...I don't know if I'll get to my development machine today. There are two issues. One is that I think there are other files missing a copyright declaration besides htslib. This must be checked before any upload so we don't get it rejected again. The other thing is that the python3 teats are failing due to some apparent 2-3 incompatibility in the test runner script. I couldn't properly test the python2 package due to some misconfiguration of adt, so I don't know how that fares. If you consider this polishing, then maybe we can leave this off for after the ftpmaster's review. regards Afif بتاريخ ٢٥/٠٦/٢٠١٥ ١:٥٠ ص، جاء من Andreas Tille andr...@an3as.eu: Hi Afif, On Thu, Jun 25, 2015 at 12:49:26AM -0700, Afif Elghraoui wrote: Just let me know if you are ready and I'll upload as soon as possible. Ok. Just to let you know, the next chance I will have to work on this likely won't be until this weekend. After pulling your last commits and fixing a minor lintian issue in d/watch from my point of view the package builds nicely without lintian issues and the problem claimed by ftpmaster is solved. So from my point of view the package looks ready. I have no idea what you intended to do on the package but may be it is sensible to upload it now since it might need another 1-3 days to be processed. If some polishing is left this can be done with an upload that makes it to unstable straigth. If there are some known issues I could also upload to experimental. What do your think? Yes, I had done so. I only forgot to push all branches. It should be in the repository now. ACK. 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/20150625085044.gd28...@an3as.eu
Re: python-pysam
Hi, Andreas, On الخميس 25 حزيران 2015 09:50, Afif Elghraoui wrote: Hi, Andreas, Please excuse the top-posting reply format from my phone...I don't know if I'll get to my development machine today. There are two issues. One is that I think there are other files missing a copyright declaration besides htslib. This must be checked before any upload so we don't get it rejected again. The other thing is that the python3 teats are failing due to some apparent 2-3 incompatibility in the test runner script. I couldn't properly test the python2 package due to some misconfiguration of adt, so I don't know how that fares. If you consider this polishing, then maybe we can leave this off for after the ftpmaster's review. regards Afif بتاريخ ٢٥/٠٦/٢٠١٥ ١:٥٠ ص، جاء من Andreas Tille andr...@an3as.eu: Just let me know if you are ready and I'll upload as soon as possible. Ok. Just to let you know, the next chance I will have to work on this likely won't be until this weekend. I ended up getting a chance today. I heavily modified the copyright file and I think it is ready enough to go back to the ftpmaster for review. Please upload to unstable or experimental at your discretion based on the potential problem I mentioned before about getting the tests to run. After pulling your last commits and fixing a minor lintian issue in d/watch from my point of view the package builds nicely without lintian issues and the problem claimed by ftpmaster is solved. So from my point of view the package looks ready. I have no idea what you intended to do on the package but may be it is sensible to upload it now since it might need another 1-3 days to be processed. If some polishing is left this can be done with an upload that makes it to unstable straigth. If there are some known issues I could also upload to experimental. Regards Afif -- 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/558cd107.40...@ghraoui.name
Re: Packaging HTQC for Debian - one test failure
Hi, On Thu, Jun 25, 2015 at 01:09:33PM +0800, Xi Yang wrote: Hi: From a packagers point of view it makes sense to use the same name as the download archive. If you might continue to maintain htqc1 and htqc2 our automatic sentinel that tracks download locations will have touble to realise new versions of htqc (version 1) since the htqc2 download tarballs seem to be higher. Would it help if I put HTQC 1 and 2 in separate directories in sourceforge download site? This would enable the version tracking mechanism to work properly. I'll put this on my todo list. In any case you could help me to write a proper description that explains the differences to the users. The current packaging (under the name htqc - I did not yet updated to htqc2) contains the description you see here: Is it possible to use the same description for HTQC 1 and 2? Because the changes are subtle, and the major change is about programming API and program functionality separation. Sure that is possible but descriptions are way to transport a message to your users to give them a helping hand to decide what program to use. In this sense I do not consider identical descriptions as the best idea. Since you did not suggested any change to the description here https://anonscm.debian.org/cgit/debian-med/htqc.git/tree/debian/control I assume you are happy with it, right? 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/20150625060118.ga26...@an3as.eu
Re: python-pysam
Hi, On Thu, Jun 25, 2015 at 12:21:24AM -0700, Afif Elghraoui wrote: I pushed the missing commit; sorry. The tag is accurate. Thanks I think that it is a good idea to remove the convenience copy of the htslib altogether. While revising the package, I noticed a couple of issues with the autopkgtest. I just pushed my current progress after merging in Charles' commit, but the package is not ready yet. Just let me know if you are ready and I'll upload as soon as possible. BTW, while changelog refers to version 0.8.3+ds1 there is no according information for this in the pristine-tar branch. Please make sure you import this changed tarball and commit this branch. Thanks for your work on this 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/20150625073414.gb28...@an3as.eu
Re: python-pysam
On الخميس 25 حزيران 2015 00:34, Andreas Tille wrote: While revising the package, I noticed a couple of issues with the autopkgtest. I just pushed my current progress after merging in Charles' commit, but the package is not ready yet. Just let me know if you are ready and I'll upload as soon as possible. Ok. Just to let you know, the next chance I will have to work on this likely won't be until this weekend. BTW, while changelog refers to version 0.8.3+ds1 there is no according information for this in the pristine-tar branch. Please make sure you import this changed tarball and commit this branch. Yes, I had done so. I only forgot to push all branches. It should be in the repository now. Thanks for your work on this No problem. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -- 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/558bb286.2000...@ghraoui.name
Re: python-pysam
Hi Afif, On Thu, Jun 25, 2015 at 12:49:26AM -0700, Afif Elghraoui wrote: Just let me know if you are ready and I'll upload as soon as possible. Ok. Just to let you know, the next chance I will have to work on this likely won't be until this weekend. After pulling your last commits and fixing a minor lintian issue in d/watch from my point of view the package builds nicely without lintian issues and the problem claimed by ftpmaster is solved. So from my point of view the package looks ready. I have no idea what you intended to do on the package but may be it is sensible to upload it now since it might need another 1-3 days to be processed. If some polishing is left this can be done with an upload that makes it to unstable straigth. If there are some known issues I could also upload to experimental. What do your think? Yes, I had done so. I only forgot to push all branches. It should be in the repository now. ACK. 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/20150625085044.gd28...@an3as.eu
