Re: python-pysam version lagging
Hello, On الإثنين 8 حزيران 2015 09:38, Andreas Tille wrote: Hi, In any case, I bumped the upstream version and made some changes to the packaging. I'm having some trouble with pbuilder/cowbuilder building this, though. It does not install the build-depends in time, so building for me fails during the initial "clean" step: I: pybuild base:170: python3.4 setup.py clean Traceback (most recent call last): File "setup.py", line 246, in from setuptools import Extension, setup ImportError: No module named 'setuptools' The clean target is executed on your local machine and not inside the pbuilder chroot. Oh, I didn't expect that. Thanks for that information; it works now. So please do apt-get install python3-setuptools and the problem should vanish. If I can get past this problem, I can test it out and finish up the python-pysam changes. It might be ready now if someone can verify that the build works and lintian is ok. I hope Charles can answer this one. I was able to build it and clean it up a little more, but the package still has some lint: W: python-pysam source: dep5-copyright-license-name-not-unique (paragraph at line 40) I'm actually not sure what to do about this one. I: ...hardening-no-fortify-functions... I think these are false positives since the CPPFLAGS for fortification look like they're correctly set as I watch the package build. I: ...spelling-error-in-binary... This is maybe not worth fixing. I: python-pysam-tests: package-contains-timestamped-gzip usr/share/doc/python-pysam/tests/pysam_data/ex1.sam.gz I'm not sure what to do about this, either. Does it really affect ReproducibleBuilds if it's an upstream-provided compressed file? Please let me know what I can do to move this along. 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/557697f7.4090...@ghraoui.name
Re: python-pysam version lagging
Le Tue, Jun 09, 2015 at 12:38:31AM -0700, Afif Elghraoui a écrit : > > I was able to build it and clean it up a little more, but the package still > has some lint: Hi Afif, thanks a lot for all this work. > W: python-pysam source: dep5-copyright-license-name-not-unique (paragraph at > line 40) > > I'm actually not sure what to do about this one. Try public-domain instead of PublicDomain. "public-domain" is a special case in the machine-readable specification, so if the Lintian warning stays, I would consider it a false positive. https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ > I: ...hardening-no-fortify-functions... > > I think these are false positives since the CPPFLAGS for fortification look > like they're correctly set as I watch the package build. I have seen such apparent false positives in other packages. If you have time, maybe it is worth asking for comments on the debian-mentors mailing list ? > I: ...spelling-error-in-binary... > > This is maybe not worth fixing. Maybe the easiest way to get rid of it is a pull request to upstream on GitHub ? > I: python-pysam-tests: package-contains-timestamped-gzip > usr/share/doc/python-pysam/tests/pysam_data/ex1.sam.gz > > I'm not sure what to do about this, either. Does it really affect > ReproducibleBuilds if it's an upstream-provided compressed file? This is a false positive: there is a timestamp, but it will not change unless Upstream updates the file, hence the build of a given Debian package for Pysam is reproductible for that file. Please let us know when you need an upload. 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-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150609081450.gc16...@falafel.plessy.net
Re: python-pysam version lagging
Hi guys, just a few additional comments 2015-06-09 9:14 GMT+01:00 Charles Plessy : > Le Tue, Jun 09, 2015 at 12:38:31AM -0700, Afif Elghraoui a écrit : > > > > I was able to build it and clean it up a little more, but the package > still > > has some lint: > > Hi Afif, thanks a lot for all this work. > > > W: python-pysam source: dep5-copyright-license-name-not-unique > (paragraph at > > line 40) > > > > I'm actually not sure what to do about this one. > > Try public-domain instead of PublicDomain. "public-domain" is a special > case > in the machine-readable specification, so if the Lintian warning stays, I > would > consider it a false positive. > > https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ > > This is one of these weird lintian warnings that popped up recently. Seems that you can no longer define a License twice in d/copyright. I believe bug reports have been sent about the rationales behind this. > I: ...hardening-no-fortify-functions... > > > > I think these are false positives since the CPPFLAGS for fortification > look > > like they're correctly set as I watch the package build. > > I have seen such apparent false positives in other packages. If you have > time, > maybe it is worth asking for comments on the debian-mentors mailing list ? > +1 > > I: ...spelling-error-in-binary... > > > > This is maybe not worth fixing. > > Maybe the easiest way to get rid of it is a pull request to upstream on > GitHub ? > > Happened to me a few times, each time I ended up sending a patch upstream. It's up to you to decide whether you want to carry on a patch downstream just to fix such an inoffensive bug. I personally did not care to do so. Best regards, Ghislain
[fis-gtm] FW: GT.M V6.2-002 available
[sorry for the top post, Outlook doesn't do proper quoting] Hi Andreas, I uploaded the latest version of GT.M that we released yesterday. I tagged the version as unstable. Let me know if that was the correct thing to do. As always, thanks for help. Amul From: Bhaskar, KS Sent: Monday, June 08, 2015 1:48 PM To: Omar Shboul; Khamis Siksek; Ahmad Sharaf; Mohammed Sharaf; Murat Khemesh; Wasim Naffar Cc: FIS MLN GG GT.M Support Subject: GT.M V6.2-002 available V6.2-002 brings a number of modest enhancements to GT.M. Improving performance: * By reducing the number of dirty global buffers to be flushed in anticipation of an impending epoch, epoch tapers aim to ameliorate spikes in response time that can occur at epochs. * $ORDER(gvn,-1) - "reverse dollar order" - of global variables is faster. * Under conditions of high contention, processes holding locks exit faster, processes acquire database critical sections more efficiently when the mutex queue slots are all used, and lock acquisition is more efficient with substantially reduced impact on database throughput. * Code size reduction that also improves performance. Enhancements include: * Intrinsic special variables: $ZUT provides a universal (across systems and across time zones) time stamp, and $ZHOROLOG extends $HOROLOG with additional pieces that provide microsecond resolution and time zone information. * TLS for SOCKET devices benefits from enhancements to WRITE /TLS and $ZSOCKET(). * The environment variable gtm_autorelink_ctlmax provides a control to set the number of unique routine names in relink conrol files. VIEW "POOLLIMIT" functionality introduced as field test grade functionality in the production release V6.2-001 is considered production grade functionality in V6.2-002. As always, the release bring numerous smaller enhancements, including to the $ZQGBLMOD() function, better handling of split $PRINCIPAL, more helpful TPRESTART messages, and more. Robustness is improved, especially in the triggers, and security has been tightened by dropping support for dubious edge cases . These changes are described in the Release Notes (http://tinco.pair.com/bhaskar/gtm/doc/articles/GTM_V6.2-002_Release_Notes.html). Please do upgrade to V6.2-002, and tell us how it works for you. Thank you for using GT.M. Regards -- Bhaskar -- GT.M - Rock solid. Lightning fast. Secure. Pick any three. _ The information contained in this message is proprietary and/or confidential. If you are not the intended recipient, please: (i) delete the message and all copies; (ii) do not disclose, distribute or use the message in any manner; and (iii) notify the sender immediately. In addition, please be aware that any message addressed to our domain is subject to archiving and review by persons other than the intended recipient. Thank you.
Re: [fis-gtm] FW: GT.M V6.2-002 available
Hi Amul, On Tue, Jun 09, 2015 at 01:19:46PM +, Shah, Amul wrote: > I uploaded the latest version of GT.M that we released yesterday. Thanks for your work on this. > I tagged the version as unstable. Let me know if that was the correct thing > to do. Perfect. Unfortunately I'm on vacation behind a quite slow connection and thus can not upload any larger package. If somebody else might take this one it would be nice - otherwise please wait until end of June. 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/20150609143610.gp27...@an3as.eu
Bug#788224: ITP: python-cobra -- constraint-based modeling of biological networks
Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team X-Debbugs-Cc: debian-de...@lists.debian.org, aebra...@ucsd.edu * Package name: python-cobra Version : 0.3.2 Upstream Author : Ali Ebrahim * URL : http://opencobra.github.io/cobrapy/ * License : GPL3+ Programming Lang: Python Description : constraint-based modeling of biological networks COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accommodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux balance analysis, flux variability analysis, and gene deletion analyses. This packaging will be maintained by the Debian Med team at Vcs-Git: git://anonscm.debian.org/debian-med/python-cobra.git Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-cobra.git -- 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/5576fc25.4090...@ghraoui.name
Re: [fis-gtm] FW: GT.M V6.2-002 available
Hi Andreas, On 06/09/15 10:36, Andreas Tille wrote: Hi Amul, On Tue, Jun 09, 2015 at 01:19:46PM +, Shah, Amul wrote: I uploaded the latest version of GT.M that we released yesterday. Thanks for your work on this. I tagged the version as unstable. Let me know if that was the correct thing to do. Perfect. Unfortunately I'm on vacation behind a quite slow connection and thus can not upload any larger package. If somebody else might take this one it would be nice - otherwise please wait until end of June. Thanks for your work on this [amul:2] Thank you for responding while on vacation! I'm fine with waiting if no one can do the upload. Amul _ The information contained in this message is proprietary and/or confidential. If you are not the intended recipient, please: (i) delete the message and all copies; (ii) do not disclose, distribute or use the message in any manner; and (iii) notify the sender immediately. In addition, please be aware that any message addressed to our domain is subject to archiving and review by persons other than the intended recipient. Thank you. -- 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/55772fa1.3030...@fisglobal.com
Bug#788283: jessie-pu: package r-cran-rcurl/1.95-4.3-1+deb8u1
Package: release.debian.org Severity: normal Tags: jessie User: release.debian@packages.debian.org Usertags: pu Dear Stable release team, the r-cran-rcurl package provides curl functionalities for the R statistical environment. In Jessie (version 1.95-4.3-1), we built it against libcurl4-nss-dev, but this creates errors that prevent R users to download and install other R packages from GitHub (https://bugs.debian.org/786473). I wouldn't be surprised if there would be other problems not yet reported. In Unstable and Testing, we solved this in version 1.95-4.3-2 by building the package against libcurl4-openssl-dev. In the following proposed update (1.95-4.3-1+deb8u1), we do the same, but the package was built against Jessie. diff -Nru r-cran-rcurl-1.95-4.3/debian/changelog r-cran-rcurl-1.95-4.3/debian/changelog --- r-cran-rcurl-1.95-4.3/debian/changelog 2014-09-17 20:10:59.0 +0900 +++ r-cran-rcurl-1.95-4.3/debian/changelog 2015-06-09 21:54:48.0 +0900 @@ -1,3 +1,10 @@ +r-cran-rcurl (1.95-4.3-1+deb8u1) jessie; urgency=medium + + * Team upload. + * Build-Depend on libcurl4-openssl-dev only (Closes: #786473). + + -- Charles Plessy Tue, 09 Jun 2015 21:54:38 +0900 + r-cran-rcurl (1.95-4.3-1) unstable; urgency=medium * New upstream version diff -Nru r-cran-rcurl-1.95-4.3/debian/control r-cran-rcurl-1.95-4.3/debian/control --- r-cran-rcurl-1.95-4.3/debian/control2014-09-17 19:36:29.0 +0900 +++ r-cran-rcurl-1.95-4.3/debian/control2015-05-31 09:15:18.0 +0900 @@ -9,7 +9,7 @@ cdbs, r-base-dev, r-cran-bitops, - libcurl4-nss-dev | libcurl-dev + libcurl4-openssl-dev Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-rcurl/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-rcurl/trunk/ Have a nice day, Charles -- Charles Plessy Debian Med packaging team 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: https://lists.debian.org/20150609215824.20002.44701.reportbug@aqwa.igloo
Re: python-pysam version lagging
Hi, could you please check th eopen bugs of python-pysam whether the patch for #753490 applies to the new version and even more importantly if the new vesion closes the serious bug #763218. If this is the case a soon upload would be great. 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/20150610055958.ga15...@an3as.eu
Re: python-pysam version lagging
Hello, Thanks, both of you, for the comments. On الثلاثاء 9 حزيران 2015 06:09, Ghislain Vaillant wrote: Hi guys, just a few additional comments 2015-06-09 9:14 GMT+01:00 Charles Plessy mailto:ple...@debian.org>>: Hi Afif, thanks a lot for all this work. No problem. > W: python-pysam source: dep5-copyright-license-name-not-unique (paragraph at > line 40) > > I'm actually not sure what to do about this one. Try public-domain instead of PublicDomain. "public-domain" is a special case in the machine-readable specification, so if the Lintian warning stays, I would consider it a false positive. https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ This is one of these weird lintian warnings that popped up recently. Seems that you can no longer define a License twice in d/copyright. I believe bug reports have been sent about the rationales behind this. Done. > I: ...hardening-no-fortify-functions... > > I think these are false positives since the CPPFLAGS for fortification look > like they're correctly set as I watch the package build. I have seen such apparent false positives in other packages. If you have time, maybe it is worth asking for comments on the debian-mentors mailing list ? +1 I encountered this before on the first package I ever made. The problem there turned out to do be that the upstream build system did not make use of CPPFLAGS. The warning went away for that package when I appended the CPPFLAGS to CFLAGS. I didn't get to this yet, but I'll have a look if I get a chance. > I: ...spelling-error-in-binary... > > This is maybe not worth fixing. Maybe the easiest way to get rid of it is a pull request to upstream on GitHub ? Happened to me a few times, each time I ended up sending a patch upstream. It's up to you to decide whether you want to carry on a patch downstream just to fix such an inoffensive bug. I personally did not care to do so. Done [1]. Regards Afif 1. https://github.com/pysam-developers/pysam/pull/122 -- 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/5577dc29.2050...@ghraoui.name
Re: python-pysam version lagging
Hi, Andreas, On الثلاثاء 9 حزيران 2015 22:59, Andreas Tille wrote: Hi, could you please check th eopen bugs of python-pysam whether the patch for #753490 applies to the new version ok, I will take a look. and even more importantly if the new vesion closes the serious bug #763218. If this is the case a soon upload would be great. From the release notes to version 0.8.2 [1]: "Pysam now wraps htslib 1.2.1 and samtools version 1.2" samtools in unstable is version 1.1. I marked this version as closing this bug, but we should get to updating the samtools package as well, especially in case the 1.1/1.2 discrepancy introduces a similar problem. Thanks for pointing this out. Regards Afif 1. https://github.com/pysam-developers/pysam/releases -- 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/5577dd09.4000...@ghraoui.name
