scitech May 2012

scitech@lists.fedoraproject.org

4 participants
7 discussions

Re: [Scitech] Package ode for Octave
by antonio montagnani 20 May '12

20 May '12

Il 20/05/2012 07:54, antonio montagnani ha scritto: > Il 19/05/2012 23:11, antonio montagnani ha scritto: >> Where can I find the odepkg rpm for Octave. Any idea?? >> >> Tnx > > Just for clarification: > > 1) this package is a package for solving ordinary differential equations > and more. > > 2) can't be installed from user inside octave by command pkg install > > 3) it is already available at leat for Debian/Ubuntu > if i try to install by hand I get: [PkgManager::packageChangeInstallState] Item clicked [PkgManager::downloadAndInstall()] 1 packages changed. 1 to install. 0 to remove. [OctaveBind::readyStdErr()] configure: error: in `/tmp/oct-IZFS19/odepkg-0.6.10/src': [OctaveBind::readyStdErr()] configure: error: C compiler cannot create executables See `config.log' for more details. [OctaveBind::readyStdErr()] the configure script returned the following error: checking for gcc... gcc checking whether the C compiler works... no [OctaveBind::readyStdErr()] error: called from `pkg>configure_make' in file /usr/share/octave/3.6.1/m/pkg/pkg.m near line 1372, column 9 error: called from: error: /usr/share/octave/3.6.1/m/pkg/pkg.m at line 826, column 5 [OctaveBind::readyStdErr()] error: /usr/share/octave/3.6.1/m/pkg/pkg.m at line 383, column 9 [OctaveBind::finished()] Octave process has finished -- Antonio Montagnani Fedora 17 Beta Acer 5670 ________________________ http://www.campingmonterosa.com

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Odepkg for Octave
by antonio montagnani 20 May '12

20 May '12

I dion't find Odepkg rpm for Octave: any help?? -- Antonio Montagnani Fedora 17 Beta Acer 5670 ________________________ http://www.campingmonterosa.com

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Fedora sagemath 5.0.rc0 - work in progress
by Paulo César Pereira de Andrade 13 May '12

13 May '12

I think I am close to have the first binaries. You can look at a full build log at http://kenobi.mandriva.com/~pcpa/sagemath.log.gz The initial sagemath.spec does not build documentation, but shortly should do so, as building documentation is also a way to check it is working. The current build fails like this: + '[' '%{buildarch}' = noarch ']' + QA_CHECK_RPATHS=1 + case "${QA_CHECK_RPATHS:-}" in + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/check-buildroot Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/matrix/matrix_mpolynomial_dense.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/singular/ring.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/singular/polynomial.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/singular/function.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/singular/singular.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/singular/option.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/singular/groebner_strategy.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/libs/lcalc/lcalc_Lfunction.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/rings/fraction_field_FpT.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/rings/polynomial/multi_polynomial_ideal_libsingular.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/rings/polynomial/polynomial_zmod_flint.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/rings/polynomial/plural.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/rings/polynomial/multi_polynomial_libsingular.so matches Binary file /home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64/usr/lib64/python2.7/site-packages/sage/rings/polynomial/polynomial_rational_flint.so matches Found '/home/pcpa/rpmbuild/BUILDROOT/sagemath-5.0.rc0-1.fc16.x86_64' in installed files; aborting error: Bad exit status from /var/tmp/rpm-tmp.14lRTk (%install) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.14lRTk (%install) I think it may be caused because I had a $HOME/.rpmmacros that had: %_enable_debug_packages %{nil} %debug_package %{nil} I will remove it and rebuild/reinstall singular, local and flint, and retry... But there are some optional components missing, that at first I just commented out, most notably should be http://www.coin-or.org/ that I do not know if is packaged with another name in fedora... Thanks, Paulo

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Experiment with sagemath and Polybori needs to be built
by Paulo César Pereira de Andrade 09 May '12

09 May '12

Polybori needs to be built. In Fedora 16, essentially, this is required to build with current cudd-devel polybori-0.8.1/libpolybori/include/polybori/ring/CCuddInterface.h --- polybori-0.8.1/libpolybori/include/polybori/ring/CCuddInterface.h.orig 2012-04-24 23:17:47.328677842 -0300 +++ polybori-0.8.1/libpolybori/include/polybori/ring/CCuddInterface.h 2012-04-24 23:17:53.406678079 -0300 @@ -54,8 +54,6 @@ inline const char* error_text(PBORI_PREF return("Invalid argument."); case CUDD_INTERNAL_ERROR: return("Internal error."); - case CUDD_TIMEOUT_EXPIRED: - return("Timed out."); case CUDD_NO_ERROR: return("No error. (Should not reach here!)"); } too bad cudd.h version identifier is only a string #define CUDD_VERSION "2.4.2" so, probably need to write a check in polybori-0.8.1/SConstruct It is also required a patch similar to this one to be able to build sagemath with it: http://svn.mandriva.com/viewvc/packages/cooker/polybori/current/SPECS/polyb… [...] I am still too noob with fedora, so, I could not finish the build, because, while I know how to git clone a fedora package, do not know how to fetch sources. For example, I see easily how to clone http://pkgs.fedoraproject.org/gitweb/?p=polybori.git but failed to finish build (did download upstream tarball) due to missing + tar xJf /home/pcpa/rpmbuild/SOURCES/polybori-logos.tar.xz -C /home/pcpa/rpmbuild/BUILDROOT/polybori-0.8.1-2.fc16.x86_64/usr/share/icons/hicolor tar (child): /home/pcpa/rpmbuild/SOURCES/polybori-logos.tar.xz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now and my guess to what to do failed also :-) Need to read more wiki pages and check fedpkg options for a readonly checkout, and if it can also be used to fetch sources. $ fedpkg clone polybori Cloning into 'polybori'... The authenticity of host 'pkgs.fedoraproject.org (209.132.181.4)' can't be established. RSA key fingerprint is fe:2e:6a:86:f3:41:e7:03:95:ea:9c:7f:75:9c:ce:9d. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'pkgs.fedoraproject.org,209.132.181.4' (RSA) to the list of known hosts. Permission denied (publickey). fatal: The remote end hung up unexpectedly Could not execute clone: Command '['git', 'clone', 'ssh://pcpa@pkgs.fedoraproject.org/polybori']' returned non-zero exit status 128 but as stated above, it would still fail to build sagemath anyway: Traceback (most recent call last): File "./setup.py", line 18, in <module> from module_list import ext_modules File "/home/pcpa/rpmbuild/BUILD/sage-4.8/spkg/build/sage-4.8/module_list.py", line 80, in <module> for line in open(SAGE_LOCAL + "/share/polybori/flags.conf"): IOError: [Errno 2] No such file or directory: '/home/pcpa/rpmbuild/BUILDROOT/sagemath-4.8-0.1.x86_64/usr/share/sagemath/local/share/polybori/flags.conf' [...] Just so that it should be easy to reproduce what I did tonight in a quick check of "how deep the water is", and initial adaptation of my Mandriva sagemath spec, I will attach the spec and patches. So far, mpir is not packaged in Mandriva, and besides sagemath, I also patched Macaulay2 to not hardcode mpir dependency also, and use gmp5. The patch to use unpatched ntl should have a nasty side effect in the notebook because it will miss the error message, if in the terminal, it will print the error message to stderr anyway before calling abort. But really, it should have been sagemath to convince upstream NTL for the need of a more complete api. Thanks, Paulo

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gf2x package ready for review
by Jerry James 04 May '12

04 May '12

I put together a gf2x package. It is ready for review: https://bugzilla.redhat.com/show_bug.cgi?id=819099 The gf2x library can be used by NTL to speed up some operations. Paulo noted recently that sage needs the combination of the two. As always, I am happy to swap reviews. -- Jerry James http://www.jamezone.org/

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Sagemath needs a newer pari
by Paulo César Pereira de Andrade 01 May '12

01 May '12

I still did not learn all about procedures to get packages updated in Fedora, so, I am asking for yet another "informal" review: Spec URL: http://kenobi.mandriva.com/~pcpa/pari.spec SRPM URL: http://kenobi.mandriva.com/~pcpa/pari-2.5.1-1.fc16.src.rpm As expected, pari update causes several other packages to be rebuilt. Most notably is that in this update, libpari-gmp.so.2 major is bumped to libpari-gmp.so.3. With this pari, for sagemath build, it needs to rebuild at least the previous lcalc package I asked for a review, and then actually apply the lcalc patch, and from the installed build requires, needs do also rebuild eclib. Thanks, Paulo

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sagemath needs a lcalc package
by Paulo César Pereira de Andrade 01 May '12

01 May '12

Hi, Not making an "official" package review request, but please review: Spec URL: http://kenobi.mandriva.com/~pcpa/lcalc.spec SRPM URL: http://kenobi.mandriva.com/~pcpa/lcalc-1.23-1.fc16.src.rpm It is not an official request because I just commented patch0 that is required to build with pari 2.5.0, but fedora 16 has pari 2.3.5, and this is another showstopper, as sagemath absolutely needs pari 2.5.0. For the record, here is where sagemath build fails now: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/home/pcpa/rpmbuild/BUILDROOT/sagemath-4.8-0.1.x86_64/usr/share/sagemath/local/include -Ic_lib/include -I/home/pcpa/rpmbuild/BUILDROOT/sagemath-4.8-0.1.x86_64/usr/share/sagemath/devel/sage/sage/ext -I/usr/include/python2.7 -c sage/libs/pari/gen.c -o build/temp.linux-x86_64-2.7/sage/libs/pari/gen.o -w sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_82Ser': sage/libs/pari/gen.c:12377:293: error: too many arguments to function 'gtoser' /usr/include/pari/paridecl.h:1144:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_226bnfisnorm': sage/libs/pari/gen.c:26636:284: error: too few arguments to function 'bnfisnorm' /usr/include/pari/paridecl.h:844:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_248idealmul': sage/libs/pari/gen.c:29034:288: error: too few arguments to function 'idealmulred' /usr/include/pari/paridecl.h:637:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_283quadhilbert': sage/libs/pari/gen.c:32540:237: error: too few arguments to function 'quadhilbert' /usr/include/pari/paridecl.h:780:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_329qflll': sage/libs/pari/gen.c:36863:281: error: too few arguments to function 'qflll0' /usr/include/pari/paridecl.h:716:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_330qflllgram': sage/libs/pari/gen.c:36969:285: error: too few arguments to function 'qflllgram0' /usr/include/pari/paridecl.h:717:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_361type': sage/libs/pari/gen.c:39917:31: error: 't_FFELT' undeclared (first use in this function) sage/libs/pari/gen.c:39917:31: note: each undeclared identifier is reported only once for each function it appears in sage/libs/pari/gen.c:40173:31: error: 't_CLOSURE' undeclared (first use in this function) sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_363algdep': sage/libs/pari/gen.c:40419:281: error: too few arguments to function 'algdep' /usr/include/pari/paridecl.h:687:5: note: declared here sage/libs/pari/gen.c: In function '__pyx_pf_4sage_4libs_4pari_3gen_3gen_365lindep': sage/libs/pari/gen.c:40582:282: error: too few arguments to function 'lindep0' /usr/include/pari/paridecl.h:694:5: note: declared here error: command 'gcc' failed with exit status 1 Paulo

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scitech May 2012