python-cobra new release ready for upload
Hi, Andreas, Thanks for all your past uploads you did for me. I'm happy to see that python-cobra has been accepted to unstable, but a new release has come out while it was in the new queue. I've updated the package and pushed. Would you please be able to review and upload again? Many 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/559f49e4.6090...@ghraoui.name
Re: Problem creating R module in hyphy
Hi Sergei, another reply in a couple of hours - thanks for beeing that responsive. :-) On Thu, Jul 09, 2015 at 09:48:22AM -0700, Sergei L Kosakovsky Pond wrote: > I am copying our lead software engineer on this message so that he can help > you out. > We have moved the build system to CMAKE several years ago; please ensure you > are using > the latest release from github.com/veg/hyphy I confirm that I'm talking about the latest release (version 2.2.4). The R module build is not affected by the cmake build system and requires an additional script. > If you come across any issues in the build process, please report them on the > project page > (github.com/veg/hyphy), so there’s a record of their existence, and > references to patches. I'd happily open an issue un github - may be I'm waiting for a comment from Simon to make it more qualified. > As far as I recall, we don’t require .so files for standard binaries. I can confirm that the executables run fine and the library does not belong to the default build. However, if I build it than it is just created and not used by the executables - so what is the purpose of the library? > I’ve also copied my colleague Simon Frost, who has motivated the development > of the R > library. Thanks for forwarding Andreas. > > > > Hi Andreas. Thanks for your interest in adding HyPhy to your list. I’m > > copying Sergei Kosakovsky Pond, my collaborator who leads the HyPhy > > implementation work. He should be able to answer your questions. > > > > Best wishes- > > Spencer > > > > On Jul 9, 2015, at 7:34 AM, Andreas Tille wrote: > > > >> Hi Spencer, > >> > >> I'm writing you on behalf of the Debian Med team which has the objective > >> to package all relevant software for medicine and biology for the > >> official Debian distribution. Since we received a request to package > >> your program hyphy I have put it on our todo list[1]. I hope you are > >> the correct contact person. > >> > >> I managed to build packages for hyphygtk and hyphympi. Since the test > >> suite ran successfully I think these are OK and for the moment serve the > >> need of the user asking for it. However, I have some more questions: > >> > >> What is the role of the dynamic library libhyphy_mp.so if I provide the > >> LIB option to cmake? Usually in Debian it is good practice to do > >> dynamic linking if possible but it seems the library exists simply for > >> its own and the executables are statically linked. Could you please > >> clarify this? > >> > >> I also tried to provide the python and R modules as well. Following > >> src/lib/README I was calling > >> > >> sh build.sh LIBRARY R > >> > >> I noticed that this script requires Bash. If you want to run it using > >> any POSIX shell (Debian is using Dash that is more simple an thus starts > >> faster with a smaller memory footprint) please replase all "==" by "=". > >> While this is no real problem in this case the script does not run since > >> it seems to target at directory names of probably former versions of > >> hyphy > >> > >> > >> ... > >> +---+ > >> |Building a multi-threaded HYPHY library version| > >> +---+ > >> COMPILER=g++, gcc > >> COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive > >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../Core > >> > >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../NewerFunctionality > >> > >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../../SQLite/trunk > >> -D SQLITE_PTR_SIZE=sizeof(long) -D __UNIX__ -D__HYPHY_NO_CURL__ -D > >> __MP__ -D __MP2__ -D __HEADLESS__ -fPIC > >> -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/Link > >> -I > >> /home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../Source > >> build.sh: line 109: cd: ../Source: No such file or directory > >> Building *cpp > >> g++: error: *cpp: No such file or directory > >> g++: fatal error: no input files > >> compilation terminated. > >> > >> > >> This is caused by by the following chunks in the script that lead to > >> probably outdated directories: > >> > >> > >> compileAll ../Source cpp ../Library > >> compileAll ../GUI preferences.cpp ../Library > >> compileAll ../Source/SQLite c ../../Library > >> > >> > >> Since I do not like to wild guess I wonder whether you would be able to > >> fix this script to enable R support for hyphy. > >> > >> The Python modules seem to be fine so far - I need to run the test suite > >> on the final package, thought. I'll report in case of further problems > >> in a separate mail. > >> > >> Kind regards and thanks for providing hyphy as free software > >> > >> Andreas. > >> > >> [1] http://blend
Re: Help needed to try to fix activiz.net
Hi Steve, It doesn't work on Debian. I'm just trying to make it work. But activiz.net seems to have been updated to work with vtk6.1 : http://public.kitware.com/gitweb?p=activizdotnet.git 2015-07-09 17:40 GMT+02:00 Steve M. Robbins : > On July 9, 2015 03:50:58 PM Corentin Desfarges wrote: > > Thank you ! > > > > I'm faced a new problem : activiz is now working with libvtk6 [1], > > How did you manage that? I looked a couple months ago and the released, > free > ActiViz only built with VTK 5.8, not even with 5.10 let alone 6. > > -Steve >
Re: Help needed to try to fix activiz.net
On July 9, 2015 03:50:58 PM Corentin Desfarges wrote: > Thank you ! > > I'm faced a new problem : activiz is now working with libvtk6 [1], How did you manage that? I looked a couple months ago and the released, free ActiViz only built with VTK 5.8, not even with 5.10 let alone 6. -Steve signature.asc Description: This is a digitally signed message part.
Re: Help needed to try to fix activiz.net
Hi Corentin, On Thu, Jul 09, 2015 at 05:00:16PM +0200, Corentin Desfarges wrote: > It is complicated to give you a precise estimation, We do not need a precise but a sensible estimation in terms of - its current work in progress - it was regarded but is complicated - no work was done regarding vtk6 > because I'm currently > starting an other project, and I don't have all the arguments needed for > taking decisions about who works on fw4spl for Debian-Med, nor when. But > Debian-Med is always an important project for the IRCAD, and I suppose that > one or more people will work on fw4spl "for Debian". And personnaly, I > DON'T leave out the project. :-) > By the way, you have to know that fw4spl has several branches [1] > (==versions) > - 0.9.2 > - 0.10.0 > - 0.10.1 > - 0.10.2 > ... > > And some of them use vtk6. But the packaging of a different version sounds > to me be a big work. So why not packaging only one branch but pick one that supports vtk6? > I'm discussing of the VTK problem with my colleagues, and I tell you as > soon as I get more information about the packaging of the new version of > fw4spl. This is perfectly in line with what I imagined as "estimation". > Thank you for your very helpful support You are welcome 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/20150709150433.gb31...@an3as.eu
Re: Help needed to try to fix activiz.net
It is complicated to give you a precise estimation, because I'm currently starting an other project, and I don't have all the arguments needed for taking decisions about who works on fw4spl for Debian-Med, nor when. But Debian-Med is always an important project for the IRCAD, and I suppose that one or more people will work on fw4spl "for Debian". And personnaly, I DON'T leave out the project. By the way, you have to know that fw4spl has several branches [1] (==versions) - 0.9.2 - 0.10.0 - 0.10.1 - 0.10.2 ... And some of them use vtk6. But the packaging of a different version sounds to me be a big work. I'm discussing of the VTK problem with my colleagues, and I tell you as soon as I get more information about the packaging of the new version of fw4spl. Thank you for your very helpful support Best regards, Corentin [1] https://github.com/fw4spl-org/fw4spl 2015-07-09 16:18 GMT+02:00 Andreas Tille : > Hi Corentin, > > On Thu, Jul 09, 2015 at 03:50:58PM +0200, Corentin Desfarges wrote: > > I'm faced a new problem : activiz is now working with libvtk6 [1], and > > fw4spl with libvtk5. But, these packages are NOT compatible. > > So in the case where I fix activiz (by using libvtk6), fw4spl will not > > build with libvtk5 anymore, and this is currently not possible... > > Hmmm, that's a schame. Could you find any estimation when fw4spl might > be compatible with vtk6. I have heard rumors that vtk maintainers feel > overworked with maintaining two versions and it would be a good idea to > work straight to vtk6 compatibility. > > 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/20150709141858.gc29...@an3as.eu > >
Re: Help needed to try to fix activiz.net
Hi Corentin, On Thu, Jul 09, 2015 at 03:50:58PM +0200, Corentin Desfarges wrote: > I'm faced a new problem : activiz is now working with libvtk6 [1], and > fw4spl with libvtk5. But, these packages are NOT compatible. > So in the case where I fix activiz (by using libvtk6), fw4spl will not > build with libvtk5 anymore, and this is currently not possible... Hmmm, that's a schame. Could you find any estimation when fw4spl might be compatible with vtk6. I have heard rumors that vtk maintainers feel overworked with maintaining two versions and it would be a good idea to work straight to vtk6 compatibility. 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/20150709141858.gc29...@an3as.eu
Re: Help needed to try to fix activiz.net
Thank you ! I'm faced a new problem : activiz is now working with libvtk6 [1], and fw4spl with libvtk5. But, these packages are NOT compatible. So in the case where I fix activiz (by using libvtk6), fw4spl will not build with libvtk5 anymore, and this is currently not possible... 2015-07-08 18:54 GMT+02:00 Andreas Tille : > Hi Corentin, > > please be so kind and do not CC me (as per lists.debian.org policy). :-) > > On Wed, Jul 08, 2015 at 06:25:33PM +0200, Corentin Desfarges wrote: > > > Feel free to discuss everything that might be unclear on the usual > > > channels you learned to know at MoM. :-) I'd start by > > > > > >debian/get-orig-source > > > > So I have to extract manually the files next the folder debian, right ? > > I'm not sure what you mean - you need to create a recent upstream > tarball and import it via `gbp import-orig --pristine-tar`. The > get-orig-source script should create a proper tarball (since upstream > does not deliver any downloadable tarball). It might be a good idea > to ask upstream about this. > > > > after fixing the VERSION properly. > > > > Are you talking about the new vtk version (6.1) ? > > Please look into the debian/get-orig-source script to understand what > I mean by VERSION. :-) > > > I have a question ; How can I apply quilt patches on the files which have > > been updated in upstream ? > > You need to update these patches. If you are lucky > >quilt push > > just detects "fuzz" and is able to apply the patch. This can be fixed > using `quilt refresh`. In the less lucky case you need to do manual > intervention. There might be more clever approaches than I'm following. > I usually keep a backup of the patch file and than manually strip the > chunks that do not apply and use `quilt edit ...` to reapply the changes > that did not apply. > > > The numbers of the impacted lines are different, but the changes have > > nevertheless > > to be apply. > > This sounds like a > >quilt push >quilt refresh > > (==lucky) case. > > Hope this helps > > 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/20150708165403.gn13...@an3as.eu > >
Re: Seqan moved from svn to Git
On Thu, Jul 09, 2015 at 09:57:25PM +1000, Kevin Murray wrote: > I have a couple of large Debian Jessie machines, will give it a go there. I'll offer a $DRINK in case we might meet at some event (may be next years Debian Med sprint?) Thanks 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/20150709123818.gd23...@an3as.eu
Re: Seqan moved from svn to Git
Hi Andreas, I have a couple of large Debian Jessie machines, will give it a go there. Cheers, Kevin On 10:43 09/07, Andreas Tille wrote: > Hi Michael (and others who would like to help with seqan upgrade), > > as promised some time ago I now migrated seqan SVN repository to Git > with some loss of old tags and a bit broken Jessie branch - but I think > we should focus on the future and not on the past. When doing so I > spotted and fixed a git-svn issue I need to report and I do not want to > spent more time in old code history. > > It would be great if somebody with a powerfull machine could give it a > try (I hope next week I'll have access to a speedy Debian machine as > well). We should try to get version 2.0.0 out for experimental first > and try to rebuild seqan dependencies against this (which usually > creates trouble for all upgrades since consumers of seqan follow the > habit to use aged code copies and stick to these). > > Any help would be welcome > >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/20150709084324.gh1...@an3as.eu > --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A -- 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/20150709115725.ga2...@klaptop.kdmurray.id.au
Bug#788224: marked as done (ITP: python-cobra -- constraint-based modeling of biological networks)
Your message dated Thu, 09 Jul 2015 12:00:14 + with message-id and subject line Bug#788224: fixed in python-cobra 0.3.2-1 has caused the Debian Bug report #788224, regarding ITP: python-cobra -- constraint-based modeling of biological networks 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.) -- 788224: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=788224 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- 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 --- End Message --- --- Begin Message --- Source: python-cobra Source-Version: 0.3.2-1 We believe that the bug you reported is fixed in the latest version of python-cobra, 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 788...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Afif Elghraoui (supplier of updated python-cobra 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: Tue, 09 Jun 2015 06:20:48 -0700 Source: python-cobra Binary: python-cobra python3-cobra python-cobra-data Architecture: source all amd64 Version: 0.3.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Afif Elghraoui Description: python-cobra - constraint-based modeling of biological networks (Python 2) python-cobra-data - constraint-based modeling of biological networks (data) python3-cobra - constraint-based modeling of biological networks (Python 3) Closes: 788224 Changes: python-cobra (0.3.2-1) unstable; urgency=medium . * Initial release (Closes: #788224) * Add patches to improve Python3 compatibility * Specify copyright for the externally-contributed modules * Exclude cobra/test/data/update_pickles.py * Create package for data and documentation * Use packaged versions of javascript libraries where available Checksums-Sha1: 51a9d1d784b6b8ec5560de157e3e102e379af988 2237 python-cobra_0.3.2-1.dsc 52bf3368d3fa2d30d93f675bd71c82816a99351f 2666330 python-cobra_0.3.2.orig.tar.gz 618c5d134effb2a8ace4ada30560ced2ca7ae6f7 7264 python-cobra_0.3.2-1.debian.tar.xz 7f92962f565e6b178b403ace1435e65ffb899f4d 1539312 python-cobra-data_0.3.2-1_all.deb a8c9dedab61b782c769b8d12498ef68dd35bffbb 155306 python-cobra_0.3.2-1_amd64.deb 2eeffcc6042db5cf8cdb4d9513a5648e28958169 141188 python3-cobra_0.3.2-1_amd64.deb Checksums-Sha256: 9628f32588cb8d5a46ab12252a3782383e504bc0d5d14ad3629a430e0dd146de 2237 python-cobra_0.3.2-1.dsc e3657f5c51aecbf2c88de633f2731e8d00dd08b787d6fe3d02a85d4d1a838cd2 2666330 python-cobra_0.3.2.orig.tar.gz 40029f025b2ac82fa1c3d4c8fde741c8850e39aca0382463428f8ecac61c4c54 7264 python-cobra_0.3.2-1.debian.tar.xz e2a93bc38124d9b780a13862fbed7183aab7a5e875413489a4440df4e888d31f 1539312 python-cobra-data_0.3.2-1_all.deb 30cb7e7e65077aa349bea25bd009524ca47ebe32411ba4f104cb172383194f6a 155306 python-cobra_0.3.2-1_amd64.deb 3eddd6f3ddefe4a9e8c2e32a19ab2763b054edffb996db828873e1374e51fef5 141188 python3-cobra_0.3.2-1_amd64.deb Files: 72c2092e2608c955f5f3072f8db6af85 2237 python optional python-cobra_0.3.2-1.dsc a264850241c44e20030415c253fab6c4 2666330 python optional
Problem creating R module in hyphy
Hi Spencer, I'm writing you on behalf of the Debian Med team which has the objective to package all relevant software for medicine and biology for the official Debian distribution. Since we received a request to package your program hyphy I have put it on our todo list[1]. I hope you are the correct contact person. I managed to build packages for hyphygtk and hyphympi. Since the test suite ran successfully I think these are OK and for the moment serve the need of the user asking for it. However, I have some more questions: What is the role of the dynamic library libhyphy_mp.so if I provide the LIB option to cmake? Usually in Debian it is good practice to do dynamic linking if possible but it seems the library exists simply for its own and the executables are statically linked. Could you please clarify this? I also tried to provide the python and R modules as well. Following src/lib/README I was calling sh build.sh LIBRARY R I noticed that this script requires Bash. If you want to run it using any POSIX shell (Debian is using Dash that is more simple an thus starts faster with a smaller memory footprint) please replase all "==" by "=". While this is no real problem in this case the script does not run since it seems to target at directory names of probably former versions of hyphy ... +---+ |Building a multi-threaded HYPHY library version| +---+ COMPILER=g++, gcc COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../Core -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../NewerFunctionality -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../../SQLite/trunk -D SQLITE_PTR_SIZE=sizeof(long) -D __UNIX__ -D__HYPHY_NO_CURL__ -D __MP__ -D __MP2__ -D __HEADLESS__ -fPIC -I/home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/Link -I /home/andreas/debian-maintain/alioth/debian-med_git/build-area/hyphy-2.2.4+dfsg/src/lib/../Source build.sh: line 109: cd: ../Source: No such file or directory Building *cpp g++: error: *cpp: No such file or directory g++: fatal error: no input files compilation terminated. This is caused by by the following chunks in the script that lead to probably outdated directories: compileAll ../Source cpp ../Library compileAll ../GUI preferences.cpp ../Library compileAll ../Source/SQLite c ../../Library Since I do not like to wild guess I wonder whether you would be able to fix this script to enable R support for hyphy. The Python modules seem to be fine so far - I need to run the test suite on the final package, thought. I'll report in case of further problems in a separate mail. Kind regards and thanks for providing hyphy as free software Andreas. [1] http://blends.debian.org/med/tasks/bio#hyphy -- 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/20150709113428.ga23...@an3as.eu
Seqan moved from svn to Git
Hi Michael (and others who would like to help with seqan upgrade), as promised some time ago I now migrated seqan SVN repository to Git with some loss of old tags and a bit broken Jessie branch - but I think we should focus on the future and not on the past. When doing so I spotted and fixed a git-svn issue I need to report and I do not want to spent more time in old code history. It would be great if somebody with a powerfull machine could give it a try (I hope next week I'll have access to a speedy Debian machine as well). We should try to get version 2.0.0 out for experimental first and try to rebuild seqan dependencies against this (which usually creates trouble for all upgrades since consumers of seqan follow the habit to use aged code copies and stick to these). Any help would be welcome 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/20150709084324.gh1...@an3as.eu
