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Bug 1841811 - sagemath fails to build and install: fatal error: gap/system.h: No such file or directory
Summary: sagemath fails to build and install: fatal error: gap/system.h: No such file ...
Keywords:
Status: CLOSED RAWHIDE
Alias: None
Product: Fedora
Classification: Fedora
Component: sagemath
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Paulo Andrade
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: F33FTBFS PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-05-29 14:38 UTC by Igor Raits
Modified: 2020-07-11 23:42 UTC (History)
2 users (show)

Fixed In Version: sagemath-9.1-1.fc33
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2020-07-11 23:42:34 UTC
Type: ---
Embargoed:

Attachments (Terms of Use)

Description Igor Raits 2020-05-29 14:38:59 UTC 
Hello,

Please note that this comment was generated automatically. If you feel that this output has mistakes, please contact me via email (ignatenkobrain).

Your package (sagemath) Fails To Install in Fedora 33:

can't install sagemath-jupyter:
  - nothing provides python3.8dist(notebook) >= 4.4.1 needed by sagemath-jupyter-9.0-7.fc33.x86_64
  
If you don't react accordingly to the policy for FTBFS/FTI bugs (https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/), your package may be orphaned in 8+ weeks.

P.S. The data was generated solely from koji buildroot, so it might be newer than the latest compose or the content on mirrors.

P.P.S. If this bug has been reported in the middle of upgrading multiple dependent packages, please consider using side tags: https://docs.fedoraproject.org/en-US/rawhide-gating/multi-builds/

Thanks!
Comment 1 Igor Raits 2020-06-08 07:00:04 UTC 
Hello,

This is the first reminder (step 3 from https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs).

If you know about this problem and are planning on fixing it, please acknowledge so by setting the bug status to ASSIGNED. If you don't have time to maintain this package, consider orphaning it, so maintainers of dependent packages realize the problem.
Comment 2 Miro Hrončok 2020-06-11 15:24:42 UTC 
This was blocked by some dependencies but no longer is so. Attempting a rebuild.
Comment 3 Miro Hrončok 2020-06-11 16:24:21 UTC 
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.9/build/cythonized/sage/schemes/toric/divisor_class.o -L/builddir/build/BUILDROOT/sagemath-9.0-8.fc33.i386/usr/lib/sagemath/local/lib -L/usr/lib -lgmp -o build/lib.linux-i686-3.9/sage/schemes/toric/divisor_class.cpython-39-i386-linux-gnu.so
[471/510] creating build/temp.linux-i686-3.9/build/cythonized/sage/sets
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I./sage/groups/perm_gps/partn_ref2 -I./sage/cpython -I/usr/include -I/builddir/build/BUILD/sage-9.0/src -I/builddir/build/BUILD/sage-9.0/src/sage/ext -I/usr/include/python3.9 -I/usr/lib/python3.9/site-packages/numpy/core/include -I/usr/lib/python3.9/site-packages/cysignals -Ibuild/cythonized -I/usr/include/python3.9 -c build/cythonized/sage/sets/disjoint_set.c -o build/temp.linux-i686-3.9/build/cythonized/sage/sets/disjoint_set.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1 -std=c99
build/cythonized/sage/sets/disjoint_set.c:646:10: fatal error: gap/system.h: No such file or directory
  646 | #include "gap/system.h"
      |          ^~~~~~~~~~~~~~
compilation terminated.
Comment 4 Igor Raits 2020-06-29 20:21:47 UTC 
Hello,

This is the second reminder (step 4 from https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs).

If you know about this problem and are planning on fixing it, please acknowledge so by setting the bug status to ASSIGNED. If you don't have time to maintain this package, consider orphaning it, so maintainers of dependent packages realize the problem.
Comment 5 Igor Raits 2020-07-11 15:56:46 UTC 
Hello,

Please note that this comment was generated automatically. If you feel that this output has mistakes, please contact me via email (ignatenkobrain).

All subpackages of a package against which this bug was filled are now installable or removed from Fedora 33.

Thanks for taking care of it!
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