scitech September 2012

scitech@lists.fedoraproject.org

2 participants
4 discussions

sagemath x86_64 f17 repository
by Paulo César Pereira de Andrade 10 Nov '12

10 Nov '12

Rdieter suggested me to make an experimental repository for early adopters, so, my first fedora repository has been created :-) To enable it, run something like: # su # cd /etc/yum.repos.d # wget http://fedorapeople.org/~pcpa/sagemath/sagemath-f17.repo and then: # yum install sagemath There is no guarantee that nothing will break in dependencies. It should install cleanly in a fedora 17 using the kde "scientific" iso image. You can look at the contents of the repository at: http://fedorapeople.org/~pcpa/sagemath/f17/x86_64/ Note that it will update pari, libmpc, maxima, givaro, numpy, etc what may cause issues with updates of other packages later. Please report any issues. But remember this is the first prototype/package for fedora. I will later make a repository for f18, that should have very few dependencies as most are already in f18. Thanks, Paulo PS: If you are on it, please also, if you have any comments about my experimental/prototype packages at: http://fedorapeople.org/~pcpa/coinor/ I would like any feedback

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Re: [Scitech] [Coin-discuss] Some problems on experimental coin-or fedora package
by Paulo César Pereira de Andrade 25 Sep '12

25 Sep '12

2012/9/23 Ted Ralphs <ted(a)lehigh.edu>: > Hi Paulo, Hi Ted, > Thanks very much for your e-mail. I am switching the conversation over the > CoinBinary project mailing list (I just realized that the project's XML page > says that the mailing list for the project is coin-discuss---I will update > that). One of the goals of the CoinBinary project (and of the creation of > the CoinALl package) since the beginning has been to make it possible to put > together packages for Linux distributions (as well as installers for other > platforms). We have made a lot of changes to the build system in recent > years to support this eventual goal, but have lacked the manpower to follow > through in doing the packaging. I'll try to answer some of your questions > below, but we will probably have to have a bit of back and forth to work > everything out. I was looking a bit more around, and learning of previous efforts, and I believe the package split layout on https://projects.coin-or.org/svn/CoinBinary/rpm/releases/1.2.0/Coin.spec should be good enough, just that instead of using the CoinAll tarball, use the tarball specific for every project. I will try to learn a bit more from https://projects.coin-or.org/CoinBinary/wiki/CoinDeb and https://projects.coin-or.org/CoinBinary/wiki/BuildingCoinRpms > On Sun, Sep 23, 2012 at 5:50 PM, Paulo César Pereira de Andrade > <paulo.cesar.pereira.de.andrade(a)gmail.com> wrote: >> >> Hi, >> >> I made an experimental coin-or package, at first from the CoinAll >> tarball, >> any feedback is welcome, e.g. if it is really desirable to make a package >> for >> every sub project, for easier updates, etc (I am more friendly to CoinAll >> because it is supposed to be tested that all bits work together). > > > > The purpose of CoinAll was exactly this. For reasons we can discuss in more > detail, I think it is best to have a separate package for each project > (CoinUtils, Clp, Cbc, etc.). We have made a number of design choices with > the build system to support this. There should be a reason fro CoinDeb using "coinor" instead of "coin-or" prefix to package names, so I think I should also use "coinor". I think logically, every pkgconfig file should be in a specic package. The experimental monolithic package I made has these: $ rpm -ql coin-or-devel | egrep '\.pc$' /usr/lib64/pkgconfig/alps.pc /usr/lib64/pkgconfig/bcp.pc /usr/lib64/pkgconfig/bcps.pc /usr/lib64/pkgconfig/blis.pc /usr/lib64/pkgconfig/bonmin.pc /usr/lib64/pkgconfig/cbc.pc /usr/lib64/pkgconfig/cgl.pc /usr/lib64/pkgconfig/clp.pc /usr/lib64/pkgconfig/coindatamiplib3.pc /usr/lib64/pkgconfig/coindatanetlib.pc /usr/lib64/pkgconfig/coindatasample.pc /usr/lib64/pkgconfig/coinmp.pc /usr/lib64/pkgconfig/coinutils.pc /usr/lib64/pkgconfig/couenne.pc /usr/lib64/pkgconfig/cppad.pc /usr/lib64/pkgconfig/dip.pc /usr/lib64/pkgconfig/dylp.pc /usr/lib64/pkgconfig/flopcpp.pc /usr/lib64/pkgconfig/ipopt.pc /usr/lib64/pkgconfig/os.pc /usr/lib64/pkgconfig/osi-cbc.pc /usr/lib64/pkgconfig/osi-clp.pc /usr/lib64/pkgconfig/osi-dylp.pc /usr/lib64/pkgconfig/osi-sym.pc /usr/lib64/pkgconfig/osi-unittests.pc /usr/lib64/pkgconfig/osi-vol.pc /usr/lib64/pkgconfig/osi.pc /usr/lib64/pkgconfig/symphony-app.pc /usr/lib64/pkgconfig/symphony.pc /usr/lib64/pkgconfig/vol.pc >> Running fedora-review on the package I see these fatal errors: >> >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/miplib3/AUTHORS >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/miplib3/LICENSE >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Netlib/README >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Sample/AUTHORS >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Sample/LICENSE >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Netlib/LICENSE >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/miplib3/README >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Sample/README >> coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Netlib/AUTHORS >> >> Maybe those were supposed to be symbolic links? > > > The data projects are strange beasts---they consist of data files that are > part of widely distributed test sets. The origin of many of the files is > difficult to ascertain, so creating AUTHORS, README, and even LICENSE files > is difficult. We have had on our long-term TODO list to come up with a > solution for this, but in any case, they are not necessary for anything else > to work---they are mainly there for unit testing. We made them separate > projects to keep them isolated (to keep the provenance of other projects > cleaner) and to make it possible to choose whether to install them more > easily. Ok. Splitting in multiple sub packages should make it easier to handle this, otherwise, based on your comments, I would have just not installed them on a final package :-) >> The warnings from fedora-review are issues that I can easily handle, >> for example, \r\n line endings on some files, sources with executable bit >> set, etc. These may be of special interest: >> >> coin-or.x86_64: W: no-manual-page-for-binary cbc >> coin-or.x86_64: W: no-manual-page-for-binary blis >> coin-or.x86_64: W: no-manual-page-for-binary symphony >> coin-or.x86_64: W: no-manual-page-for-binary clp >> coin-or.x86_64: W: no-manual-page-for-binary OSSolverService >> >> help2man is not of much use for these, but it should be easy to create >> simple manpages based on documentation. > > > Yes, this should be asy to do. > >> >> Another issue, I see that the COIN-OR-1.6.2-linux-x86_64-gcc4.4.5.tar.gz >> tarball does not distribute the AUTHORS, README and LICENSE files, >> but does distribute several pdf files. I do not see a make target to >> create >> those, but I may be missing something trivial. > > > You are correct that there is no target to create the PDF files that are > part of these, but we could create a target for that pretty easily. I'm not > sure what you mean about the tarball not distributing AUTHORS, README, etc. I mean't: $ tar ztvf COIN-OR-1.6.2-linux-x86_64-gcc4.4.5.tar.gz|egrep '(README|LICENSE|AUTHORS)' -rwxr-xr-x ted/ted 94 2012-02-22 14:23 COIN-OR/examples/branchCutPriceAUTHORS -rwxr-xr-x ted/ted 11611 2012-02-22 14:23 COIN-OR/examples/branchCutPriceLICENSE that is, comparing contents of the generated package (from make install) and contents of the binary distribution. > Those should be installed for each project in the /share/doc directory. I will try to rework it a bit to install in the usual rpm documentation directory /usr/share/doc/%{name}-%{version} >> The initial package is at: >> Spec: http://fedorapeople.org/~pcpa/coin-or.spec >> SRPM: http://fedorapeople.org/~pcpa/coin-or-1.6.0-1.fc19.src.rpm > > > Keep us posted and we'll be happy to help in whatever way we can. Ok. I will try to come with a more detailed packaging plan and/or prototype in the next few days. > Ted > -- > Dr. Ted Ralphs > Associate Professor, Lehigh University > (610) 628-1280 > ted 'at' lehigh 'dot' edu > coral.ie.lehigh.edu/~ted Thanks, Paulo

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Some problems on experimental coin-or fedora package
by Paulo César Pereira de Andrade 24 Sep '12

24 Sep '12

Hi, I made an experimental coin-or package, at first from the CoinAll tarball, any feedback is welcome, e.g. if it is really desirable to make a package for every sub project, for easier updates, etc (I am more friendly to CoinAll because it is supposed to be tested that all bits work together). Running fedora-review on the package I see these fatal errors: coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/miplib3/AUTHORS coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/miplib3/LICENSE coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Netlib/README coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Sample/AUTHORS coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Sample/LICENSE coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Netlib/LICENSE coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/miplib3/README coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Sample/README coin-or.x86_64: E: zero-length /usr/share/coin/doc/Data/Netlib/AUTHORS Maybe those were supposed to be symbolic links? The warnings from fedora-review are issues that I can easily handle, for example, \r\n line endings on some files, sources with executable bit set, etc. These may be of special interest: coin-or.x86_64: W: no-manual-page-for-binary cbc coin-or.x86_64: W: no-manual-page-for-binary blis coin-or.x86_64: W: no-manual-page-for-binary symphony coin-or.x86_64: W: no-manual-page-for-binary clp coin-or.x86_64: W: no-manual-page-for-binary OSSolverService help2man is not of much use for these, but it should be easy to create simple manpages based on documentation. Another issue, I see that the COIN-OR-1.6.2-linux-x86_64-gcc4.4.5.tar.gz tarball does not distribute the AUTHORS, README and LICENSE files, but does distribute several pdf files. I do not see a make target to create those, but I may be missing something trivial. The initial package is at: Spec: http://fedorapeople.org/~pcpa/coin-or.spec SRPM: http://fedorapeople.org/~pcpa/coin-or-1.6.0-1.fc19.src.rpm Thanks, Paulo

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Minor update to sagemath 5.2 rawhide work in progress package
by Paulo César Pereira de Andrade 18 Sep '12

18 Sep '12

Hi, I updated https://fedoraproject.org/wiki/SIGs/SciTech/SAGE to match the current state, and uploaded updated packages to http://fedorapeople.org/~pcpa/sagemath/ Actually, it was not the first time I had uploaded packages, but this time I made significant work: - Add sphinx workaround to have editable tutorial forms (#839321) - Make interactive 3d plots using jmol applet functional (#837166) - Use system genus2reduction - Add workaround to mp_set_memory_functions call from pari library If you have a rawhide x86_64 system, vm, etc, please give it a try. BTW, I also commented out gap-sonata requires, as it is not "really" required, and it appears it is another case of a package I had only in my system; Jerry may have any information about it :-) Also, it is very close to be able to make a formal review request, waiting for a response to my python-flask* review requests: https://bugzilla.redhat.com/show_bug.cgi?id=839097 https://bugzilla.redhat.com/show_bug.cgi?id=839071 https://bugzilla.redhat.com/show_bug.cgi?id=839098 There will be significant debug to be done, based on a full sage -testall output: http://fedorapeople.org/~pcpa/sagemath/test.log Thanks, Paulo

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scitech September 2012