April 2012 - scitech - Fedora Mailing-Lists

Experiment with sagemath and Polybori needs to be built

by Paulo César Pereira de Andrade

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/pol... [...] 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

11 years, 6 months

2
28
0 / 0

Sagemath needs a newer pari

by Paulo César Pereira de Andrade

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

11 years, 7 months

2
4
0 / 0

sagemath needs a lcalc package

by Paulo César Pereira de Andrade

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

11 years, 7 months

2
3
0 / 0

sagemath needs singular packaged

by Paulo César Pereira de Andrade

I see there is a libfac-devel package that attempts to provide partially some of the features required. To start, after building pari 2.5.1, rebuilding lcalc with the pari patch applied, and rebuilding eclib (that AFAIK could use the latest upstream, not just use the sagemath spkg), the build failure now is: [...] g++ -pthread -shared build/temp.linux-x86_64-2.7/sage/libs/ppl.o build/temp.linux-x86_64-2.7/sage/libs/ppl_shim.o -Lc_lib -L/home/pcpa/rpmbuild/BUILDROOT/sagemath-4.8-0.1.x86_64/usr/share/sagemath/local/lib -L/usr/lib64 -lcsage -lppl -lgmpxx -lgmp -lm -lstdc++ -lntl -lpython2.7 -o build/lib.linux-x86_64-2.7/sage/libs/ppl.so 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/ratpoints.c -o build/temp.linux-x86_64-2.7/sage/libs/ratpoints.o -w sage/libs/ratpoints.c:244:23: fatal error: ratpoints.h: No such file or directory compilation terminated. error: command 'gcc' failed with exit status 1 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/singular -I/home/pcpa/rpmbuild/BUILDROOT/sagemath-4.8-0.1.x86_64/usr/share/sagemath/local/include/factory -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/singular/singular.cpp -o build/temp.linux-x86_64-2.7/sage/libs/singular/singular.o -w sage/libs/singular/singular.cpp:241:29: fatal error: factory/factory.h: No such file or directory compilation terminated. [...] It is building in parallel, so, nice to know about the ratpoints failure also. ratpoints I believe could just adapt the Mandriva package I made long ago: http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/ratpoints/curr... but singular is a beast :-) At first I would suggest also using my package from Mandriva, but since a lot of packages are being reviewed, it should be worth to give a try at using the actual latest upstream release. But beware now I am getting at one of the most critical packages to build sagemath using system wide packages... and ending with a funcional sagemath, not just getting coredumps and memory corruption :-) The Mandriva package can be viewed at: http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/singular/curre... What I would change first is to install binaries in libexecdir and no longer build a static library package. Thanks, Paulo

11 years, 7 months

1
0
0 / 0

Self introduction and sponsorship request

by Paulo César Pereira de Andrade

Hi, I made a first contribution package for xedit, that happens to be the text editor I use for most tasks :-) see https://bugzilla.redhat.com/show_bug.cgi?id=815624 I would like to contribute to SciTech SIG. I notice there is https://fedoraproject.org/wiki/SIGs/SciTech/SAGE, and actually, I have packaged sagemath in Mandriva, and kept the package functional and updated to latest upstream for around 3 years. Sagemath itself depends on roughly 300 different upstream packages, and other packages I would like to contribute at some point is salome, that I also packaged in Mandriva, http://www.salome-platform.org/. Currently it is not functional in Mandriva cooker but should be in released versions, I got a hacked workaround described at https://qa.mandriva.com/show_bug.cgi?id=65396 Other large "scientific" system I package is texlive, that I made several perl and sh scripts that allows translating texlive package management control files, etc to rpm specs, so that can keep up to date with latest TeX Live. This is a very large set of packages, due to matching 1 to 1 with texlive, e.g.: $ urpmq -a texlive- | sort -u | wc -l 2376 There is already such a texlive packaging schema for fedora described at http://fedoraproject.org/wiki/Features/TeXLive so I should at least be able to help a bit :-) I understand that there is plenty of bureaucracy to get packages in the distro, and do not expect them to be "core" packages, but expect them to be unsupported, contrib packages. Most important packages I maintain in Mandriva should be gcc, glibc, valgrind and java-1.*.0-openjdk. Note that I am a Mandriva employee and my major interest is to become more aware of how Fedora works, so, I want to contribute like I did with several other projects in the past, that is, after work at home and/or weekends. Thanks, Paulo

11 years, 7 months

3
3
0 / 0

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

scitech April 2012