Upgrade bliss package to 0.73 with Debian patches; install header files in location expected by polymake #20901

mkoeppe · 2016-06-28T23:54:15Z

New upstream archive: http://www.tcs.hut.fi/Software/bliss/bliss-0.73.zip (we have 0.72)

Upstream bliss does not have a proper build system (in particular no 'make install').
"spkg-install" installs header files with generic names such as "graph.hh" flat into $SAGE_LOCAL/include/

Debian has https://packages.debian.org/sid/math/bliss
which autotoolizes the package and adjust the include file location.
This matches where Polymake (#20892) expects the header files.

On https://github.com/mkoeppe/bliss in branch sage_package I have applied the Debian patches and a few more patches for Sage. The spkg-src script clones from there and builds a distribution. The result is available here:

tarball: https://github.com/mkoeppe/bliss/releases/download/sage_package%2F0.73%2Bdebian-1%2Bsage-2016-08-02/bliss-0.73.debian-1.sage-2016-08-02.tar.gz (rename to bliss-0.73+debian-1+sage-2016-08-02.tar.gz)

Upstream: Reported upstream. No feedback yet.

CC: @sagetrac-azi @jdemeyer @videlec @kcrisman @dimpase @fchapoton @stumpc5 @mo271 @vbraun

Component: packages: optional

Author: Matthias Koeppe

Branch: c0c0427

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/20901

The text was updated successfully, but these errors were encountered:

mkoeppe · 2016-07-07T05:11:11Z

Dependencies: #20692

mkoeppe · 2016-07-15T19:46:48Z

Branch: u/mkoeppe/upgrade_bliss_package_to_0_73_with_debian_patches__install_header_files_in_location_expected_by_polymake

mkoeppe · 2016-07-15T19:50:08Z

Commit: 3837a48

mkoeppe · 2016-07-15T19:50:08Z

New commits:

`3837a48`	`bliss: Use autotoolized package from Debian`

mkoeppe · 2016-07-15T19:50:08Z

Author: Matthias Koeppe

mkoeppe · 2016-07-15T19:50:08Z

Changed dependencies from #20692 to none

mkoeppe · 2016-07-16T12:20:10Z

comment:5

Needs review. Prerequisite for polymake (#20892).

dimpase · 2016-07-16T14:58:44Z

comment:6

what are the new goodies? a shared library?

mkoeppe · 2016-07-16T16:18:15Z

comment:7

Replying to @dimpase:

what are the new goodies? a shared library?

A shared library, proper include files location, and as a result works as a prerequisite for polymake.
New upstream version -- but upstream is silent about what has changed compared to 0.72.

sagetrac-git · 2016-07-16T18:57:43Z

Branch pushed to git repo; I updated commit sha1. New commits:

`225755e`	`bliss: Add more info in SPKG.txt`

sagetrac-git · 2016-07-16T18:57:43Z

Changed commit from 3837a48 to 225755e

jdemeyer · 2016-07-17T07:33:56Z

comment:9

The usual way to ship packages in Sage is to start from the original unmodified sources and then apply patches (either at packaging time or at build time). Here, you are instead forking upstream for no clear reason.

sagetrac-git · 2016-07-17T09:34:19Z

Changed commit from 225755e to 4b22211

sagetrac-git · 2016-07-17T09:34:19Z

Branch pushed to git repo; I updated commit sha1. New commits:

`4b22211`	`bliss: Use upstream tarball and patches`

mkoeppe · 2016-07-17T09:37:40Z

comment:11

Replying to @jdemeyer:

The usual way to ship packages in Sage is to start from the original unmodified sources and then apply patches (either at packaging time or at build time). Here, you are instead forking upstream for no clear reason.

OK, I've changed it to using upstream + a patch.
Unfortunately our patches cannot be as elegant as Debian's because we cannot rely on the availability of autotools. So my patch has to ship the whole autogenerated build system.

kiwifb · 2016-07-18T11:19:03Z

comment:12

Learn to write a spkg-src file like for ecl
https://github.com/sagemath/sage-prod/blob/master/build/pkgs/ecl/spkg-src
or glpk at #20710. It will require you to produce a new tarball and host it somewhere until the ticket is merged.

dimpase · 2016-07-20T08:47:54Z

comment:13

yeah, spkg-src is important, as you don't want to become the only one in state to perform an update...

mkoeppe · 2016-07-26T07:11:55Z

comment:14

Unfortunately this update causes some tests to fail with segfault.

age:             sage: g3 = polytopes.hypercube(3).vertex_graph(); g3
Graph on 8 vertices
sage:             sage: g3.automorphism_group().cardinality()
python(2197,0x7fff7b8f9000) malloc: *** error for object 0x1001d3fff: pointer being realloc'd was not allocated
*** set a breakpoint in malloc_error_break to debug

Program received signal SIGABRT, Aborted.
0x00007fff8b2cff06 in __pthread_kill () from /usr/lib/system/libsystem_kernel.dylib
(gdb) where
#0  0x00007fff8b2cff06 in __pthread_kill () from /usr/lib/system/libsystem_kernel.dylib
#1  0x00007fff92ea14ec in pthread_kill () from /usr/lib/system/libsystem_pthread.dylib
#2  0x00007fff8ec5c6e7 in abort () from /usr/lib/system/libsystem_c.dylib
#3  0x00007fff933d879d in realloc () from /usr/lib/system/libsystem_malloc.dylib
#4  0x0000000107284ddd in __pyx_f_4sage_3ext_6memory_sage_sig_realloc () from /Users/mkoeppe/cvs/sage/local/lib/python2.7/site-packages/sage/ext/memory.so
#5  0x0000000106afca01 in __gmpz_realloc () from /Users/mkoeppe/cvs/sage/local/lib/libgmp.16.dylib
#6  0x0000000106af8c0e in __gmpz_mul_si () from /Users/mkoeppe/cvs/sage/local/lib/libgmp.16.dylib
#7  0x00000001aefad6f0 in ?? () from /Users/mkoeppe/cvs/sage/local/lib/libbliss.2.dylib
#8  0x00000001aefaf43c in ?? () from /Users/mkoeppe/cvs/sage/local/lib/libbliss.2.dylib
#9  0x00000001aef96e13 in __pyx_pw_4sage_6graphs_5bliss_1automorphism_group(_object*, _object*, _object*) ()
   from /Users/mkoeppe/cvs/sage/local/lib/python2.7/site-packages/sage/graphs/bliss.so
#10 0x00000001000e92a4 in PyEval_EvalFrameEx () from /Users/mkoeppe/cvs/sage/local/lib/libpython2.7.dylib
#

I could use some help here.

kiwifb · 2016-07-26T07:16:15Z

comment:15

Well known problem. Disable gmp in bliss that's the culprit.

mkoeppe · 2016-07-26T08:05:48Z

comment:16

Replying to @kiwifb:

Well known problem. Disable gmp in bliss that's the culprit.

Thanks!

dimpase · 2016-07-26T09:40:43Z

comment:17

Why would bliss need gmp? Looks strange to me.

kiwifb · 2016-07-26T09:44:45Z

comment:18

It's a build option, ask the author.

sagetrac-git · 2016-08-03T07:53:11Z

Changed commit from 4b22211 to 1d2707c

sagetrac-git · 2016-08-03T07:53:11Z

Branch pushed to git repo; I updated commit sha1. New commits:

`3111091`	`Merge tag '7.3.beta9' into t/20901/upgrade_bliss_package_to_0_73_with_debian_patches__install_header_files_in_location_expected_by_polymake`
`1c398a3`	`Merge tag '7.3.rc0' into t/20901/upgrade_bliss_package_to_0_73_with_debian_patches__install_header_files_in_location_expected_by_polymake`
`1d2707c`	`Use repackaged archive instead of huge patch`

mkoeppe · 2016-08-03T07:54:37Z

comment:21

Replying to @kiwifb:

Learn to write a spkg-src file

Thanks, done.

Ready for review.

dimpase · 2016-08-03T08:43:36Z

comment:22

there is something funny with tarball name: if I do sage -i bliss it looks for bliss-0.73+debian-1+sage-2016-08-02.tar.gz, while wget with your URL gives bliss-0.73.debian-1.sage-2016-08-02.tar.gz.

OK, I renamed the tarball, and was able to run sage -i bliss, but the following make fails:

[sagelib-7.3.rc0] building 'sage.graphs.bliss' extension
[sagelib-7.3.rc0] Executing 1 command (using 1 thread)
[sagelib-7.3.rc0] [1/1] gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I/home/scratch/dimpase/sage/sage/local/include -I/home/scratch/dimpase/sage/sage/local/include/python2.7 -I/home/scratch/dimpase/sage/sage/local/lib/python2.7/site-packages/numpy/core/include -I/home/scratch/dimpase/sage/sage/src -I/home/scratch/dimpase/sage/sage/src/sage/ext -I/home/scratch/dimpase/sage/sage/src/build/cythonized -I/home/scratch/dimpase/sage/sage/src/build/cythonized/sage/ext -I/home/scratch/dimpase/sage/sage/local/include/python2.7 -c /home/scratch/dimpase/sage/sage/src/build/cythonized/sage/graphs/bliss.cpp -o build/temp.linux-x86_64-2.7/home/scratch/dimpase/sage/sage/src/build/cythonized/sage/graphs/bliss.o -fno-strict-aliasing
[sagelib-7.3.rc0] /home/scratch/dimpase/sage/sage/src/build/cythonized/sage/graphs/bliss.cpp:317:20: fatal error: graph.hh: No such file or directory
[sagelib-7.3.rc0] compilation terminated.
[sagelib-7.3.rc0] error: command 'gcc' failed with exit status 1

This is on Fedora23, Sage 7.3.rc0, with gcc version 5.3.1 20160406 (Red Hat 5.3.1-6) (GCC).

mkoeppe · 2016-08-03T08:49:22Z

comment:23

Replying to @dimpase:

there is something funny with tarball name: if I do sage -i bliss it looks for bliss-0.73+debian-1+sage-2016-08-02.tar.gz, while wget with your URL gives bliss-0.73.debian-1.sage-2016-08-02.tar.gz.

It's a limitation of github, it renames + to .

OK, I renamed the tarball, and was able to run sage -i bliss, but the following make fails:

[sagelib-7.3.rc0] building 'sage.graphs.bliss' extension
[sagelib-7.3.rc0] Executing 1 command (using 1 thread)
[sagelib-7.3.rc0] [1/1] gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -fPIC -I/home/scratch/dimpase/sage/sage/local/include -I/home/scratch/dimpase/sage/sage/local/include/python2.7 -I/home/scratch/dimpase/sage/sage/local/lib/python2.7/site-packages/numpy/core/include -I/home/scratch/dimpase/sage/sage/src -I/home/scratch/dimpase/sage/sage/src/sage/ext -I/home/scratch/dimpase/sage/sage/src/build/cythonized -I/home/scratch/dimpase/sage/sage/src/build/cythonized/sage/ext -I/home/scratch/dimpase/sage/sage/local/include/python2.7 -c /home/scratch/dimpase/sage/sage/src/build/cythonized/sage/graphs/bliss.cpp -o build/temp.linux-x86_64-2.7/home/scratch/dimpase/sage/sage/src/build/cythonized/sage/graphs/bliss.o -fno-strict-aliasing
[sagelib-7.3.rc0] /home/scratch/dimpase/sage/sage/src/build/cythonized/sage/graphs/bliss.cpp:317:20: fatal error: graph.hh: No such file or directory
[sagelib-7.3.rc0] compilation terminated.
[sagelib-7.3.rc0] error: command 'gcc' failed with exit status 1

This is on Fedora23, Sage 7.3.rc0, with gcc version 5.3.1 20160406 (Red Hat 5.3.1-6) (GCC).

Thanks for catching this. Fix coming shortly.

sagetrac-git · 2016-08-03T10:00:33Z

Changed commit from 1d2707c to c0c0427

sagetrac-git · 2016-08-03T10:00:33Z

Branch pushed to git repo; I updated commit sha1. New commits:

`c0c0427`	`Adjust to changed bliss header file locations`

mkoeppe · 2016-08-03T10:01:04Z

comment:25

Fixed.

dimpase · 2016-08-03T10:55:01Z

comment:27

OK, this works. In order to keep the release manager happy, I suggest that you put the tarball somewhere where it can be wget'ed without renaming hassle...

mkoeppe · 2016-08-04T19:02:33Z

comment:28

Is this a "positive_review"?

dimpase · 2016-08-04T19:09:20Z

comment:29

I trust you are able to put the tarball somewhere where the name mangling does not happen. :-)

dimpase · 2016-08-04T19:09:20Z

Reviewer: Dima Pasechnik

mkoeppe · 2016-08-04T19:29:25Z

comment:30

Thanks, Dima.

Volker - does the upload location of the tarball work for you?

vbraun · 2016-08-07T20:01:33Z

Changed branch from u/mkoeppe/upgrade_bliss_package_to_0_73_with_debian_patches__install_header_files_in_location_expected_by_polymake to c0c0427

mkoeppe · 2016-08-10T17:49:13Z

Changed commit from c0c0427 to none

mkoeppe · 2016-08-10T17:49:13Z

Upstream: Reported upstream. No feedback yet.

fchapoton · 2016-08-18T10:26:32Z

comment:33

some patchbots meet compilation problems:

[sagelib-7.4.beta1] /home/worker/sage-patchbot/src/build/cythonized/sage/graphs/bliss.cpp:317:26: fatal error: bliss/graph.hh: No such file or directory
[sagelib-7.4.beta1]  #include "bliss/graph.hh"
[sagelib-7.4.beta1]                           ^
[sagelib-7.4.beta1] compilation terminated.

mkoeppe · 2016-08-18T16:12:52Z

comment:34

Well, the install location of this header file changed with this upgrade, so the patchbots will have to reinstall the package.

jdemeyer · 2016-08-19T09:26:31Z

comment:35

I hope that #21288 will fix this.

mkoeppe added this to the sage-7.3 milestone Jun 28, 2016

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vbraun closed this as completed in e68bc34 Aug 7, 2016

videlec mentioned this issue Jan 12, 2017

package polymake 3.0 #20892

Closed

Upgrade bliss package to 0.73 with Debian patches; install header files in location expected by polymake #20901

Upgrade bliss package to 0.73 with Debian patches; install header files in location expected by polymake #20901

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