Bug 2259556

Summary: F40FailsToInstall: Macaulay2
Product: [Fedora] Fedora Reporter: Fedora Fails To Install <fti-bugs>
Component: Macaulay2Assignee: Rex Dieter <rdieter>
Status: CLOSED NEXTRELEASE QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: 40CC: code, jwakely, loganjerry, rdieter
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: Macaulay2-1.22-6.fc40 Doc Type: If docs needed, set a value
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2024-02-27 15:42:11 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:
Bug Depends On:    
Bug Blocks: 2260877, 2231790, 2258089    

Description Fedora Fails To Install 2024-01-22 10:49:41 UTC
Hello,

Please note that this comment was generated automatically by https://pagure.io/releng/blob/main/f/scripts/ftbfs-fti/follow-policy.py
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Your package (Macaulay2) Fails To Install in Fedora 40:

can't install Macaulay2:
  - nothing provides libboost_stacktrace_addr2line.so.1.81.0()(64bit) needed by Macaulay2-1.22-1.fc40.x86_64
  
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.


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. To reproduce, use the koji/local repo only, e.g. in mock:

    $ mock -r fedora-40-x86_64 --config-opts mirrored=False install Macaulay2


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/fesco/Updates_Policy/#updating-inter-dependent-packages

Thanks!

Comment 1 Jonathan Wakely 2024-01-22 11:19:03 UTC
Dunno what happened here, the build just seemed to stop halfway through:
https://koji.fedoraproject.org/koji/taskinfo?taskID=111963353

Comment 2 Ben Beasley 2024-01-27 15:08:05 UTC
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/builddir/build/BUILD/M2-release-1.22/M2/BUILD/x86_64-redhat-linux-gnu/../../include -I/builddir/build/BUILD/M2-release-1.22/M2/BUILD/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/M2-release-1.22/M2/BUILD/x86_64-redhat-linux-gnu/usr-host/include -isystem /usr/include/libxml2 -I/usr/include/cddlib -I/usr/include/frobby -DNDEBUG -I/usr/include/cddlib -I/usr/include/eigen3 -I/usr/include -DBOOST_STACKTRACE_LINK -O2 -Wall -DNDEBUG -UDEBUG -I/usr/include/flexiblas/ -D__FFLASFFPACK_HAVE_CBLAS=1 -fopenmp -pthread -O2 -std=gnu++14 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fsigned-char -g -Wno-mismatched-tags -w -MT diophantine-solver.lo -MD -MP -MF .deps/diophantine-solver.Tpo -c diophantine-solver.C -o diophantine-solver.o
In file included from ../../linbox/matrix/sparse-matrix.h:76,
                 from ../../linbox/blackbox/lambda-sparse.h:29,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:26:
../../linbox/matrix/sparsematrix/sparse-ell-matrix.h: In member function 'LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>& LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>::operator=(const LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>&)':
../../linbox/matrix/sparsematrix/sparse-ell-matrix.h:1216:44: error: assignment of read-only location '((LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>*)this)->LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>::_ld'
 1216 |                                 _ld        = iter._ld ;
      |                                 ~~~~~~~~~~~^~~~~~~~~~ 

I fixed a problem like this in linbox by adding a patch 0001-const_cast-missing.patch in https://src.fedoraproject.org/rpms/linbox/c/7389d46e81dc00dcb952b2ccbbbec3fb4fcc6c8b?branch=rawhide. I tried to fix the above problem in the bundled linbox here by concatenating that patch to the existing linbox-1.7.0.patch, and that applied without complaint, but the build still failed in the same way:

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -I/builddir/build/BUILD
/M2-release-1.22/M2/BUILD/x86_64-redhat-linux-gnu/../../include -I/builddir/build/
BUILD/M2-release-1.22/M2/BUILD/x86_64-redhat-linux-gnu/include -I/builddir/build/B
UILD/M2-release-1.22/M2/BUILD/x86_64-redhat-linux-gnu/usr-host/include -isystem /u
sr/include/libxml2 -I/usr/include/cddlib -I/usr/include/frobby -DNDEBUG -I/usr/inc
lude/cddlib -I/usr/include/eigen3 -I/usr/include -DBOOST_STACKTRACE_LINK -O2 -Wall
 -DNDEBUG -UDEBUG -I/usr/include/flexiblas/ -D__FFLASFFPACK_HAVE_CBLAS=1 -fopenmp 
-pthread -O2 -std=gnu++14 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werro
r=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTI
ONS -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchrono
us-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer 
-mno-omit-leaf-frame-pointer -fsigned-char -g -Wno-mismatched-tags -w -MT diophant
ine-solver.lo -MD -MP -MF .deps/diophantine-solver.Tpo -c diophantine-solver.C -o 
diophantine-solver.o
In file included from ../../linbox/matrix/sparse-matrix.h:76,
                 from ../../linbox/blackbox/lambda-sparse.h:29,
                 from ../../linbox/algorithms/rational-solver.h:44,
                 from ../../linbox/algorithms/diophantine-solver.h:29,
                 from diophantine-solver.C:26:
../../linbox/matrix/sparsematrix/sparse-ell-matrix.h: In member function 'LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>& LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>::operator=(const LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>&)':
../../linbox/matrix/sparsematrix/sparse-ell-matrix.h:1216:44: error: assignment of read-only location '((LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>*)this)->LinBox::SparseMatrix<_Field, LinBox::SparseMatrixFormat::ELL>::_IndexedIterator<index_iterator, element_iterator, Field>::_ld'
 1216 |                                 _ld        = iter._ld ;
      |                                 ~~~~~~~~~~~^~~~~~~~~~

I’m sure there is something I’ve simply overlooked here, but I haven’t found it yet. I’m not planning to keep working on this at the moment.

Comment 3 Jonathan Wakely 2024-01-27 21:23:15 UTC
Those const_casts seem like quite the code smell ... is there some underlying const-correctness bug that they're papering over?

Comment 4 Ben Beasley 2024-01-28 14:08:40 UTC
(In reply to Jonathan Wakely from comment #3)
> Those const_casts seem like quite the code smell ... is there some
> underlying const-correctness bug that they're papering over?

The patch does look a little suspicious that way, and you may be right. I’m pretty sure I won’t have a chance to dig into their design, though.

Comment 5 Fedora Fails To Install 2024-01-29 16:07:18 UTC
Hello,

Please note that this comment was generated automatically by https://pagure.io/releng/blob/main/f/scripts/ftbfs-fti/follow-policy.py
If you feel that this output has mistakes, please open an issue at https://pagure.io/releng/

This package fails to install and maintainers are advised to take one of the following actions:

 - Fix this bug and close this bugzilla once the update makes it to the repository.
   (The same script that posted this comment will eventually close this bugzilla
   when the fixed package reaches the repository, so you don't have to worry about it.)

or

 - Move this bug to ASSIGNED if you plan on fixing this, but simply haven't done so yet.

or

 - Orphan the package if you no longer plan to maintain it.


If you do not take one of these actions, the process at https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs will continue.
This package may be orphaned in 7+ weeks.
This is the first reminder (step 3) from the policy.

Don't hesitate to ask for help on https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/ if you are unsure how to fix this bug.

Comment 6 Aoife Moloney 2024-02-15 23:11:25 UTC
This bug appears to have been reported against 'rawhide' during the Fedora Linux 40 development cycle.
Changing version to 40.

Comment 7 Fedora Fails To Install 2024-02-19 19:05:52 UTC
Hello,

Please note that this comment was generated automatically by https://pagure.io/releng/blob/main/f/scripts/ftbfs-fti/follow-policy.py
If you feel that this output has mistakes, please open an issue at https://pagure.io/releng/

This package fails to install and maintainers are advised to take one of the following actions:

 - Fix this bug and close this bugzilla once the update makes it to the repository.
   (The same script that posted this comment will eventually close this bugzilla
   when the fixed package reaches the repository, so you don't have to worry about it.)

or

 - Move this bug to ASSIGNED if you plan on fixing this, but simply haven't done so yet.

or

 - Orphan the package if you no longer plan to maintain it.


If you do not take one of these actions, the process at https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs will continue.
This package may be orphaned in 4+ weeks.
This is the second reminder (step 4) from the policy.

Don't hesitate to ask for help on https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/ if you are unsure how to fix this bug.

Comment 8 Jerry James 2024-02-27 15:42:11 UTC
I updated linbox-1.7.0.patch to match the current linbox package and built this package as part of the SCIP/SoPlex effort.  The build succeeded.  The const issues referred to above are part of the linbox codebase, rather than Macaulay2.  I don't know what they are trying to do there.