Bug#1046864: hypre: Fails to build source after successful build

[Lucas Nussbaum]

Source: hypre
Version: 2.28.0-6
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> ------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package hypre
> dpkg-buildpackage: info: source version 2.28.0-6
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Drew Parsons <dparsons at debian.org>
>  dpkg-source --before-build .
>  fakeroot debian/rules clean
> dh clean --sourcedirectory=src
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> echo "Running clean"
> Running clean
> rm -rf /<<PKGBUILDDIR>>/debian/tmp
> rm -f src/configure.in
> rm -f src/config.log
> rm -f src/config/config.guess
> rm -f src/config/config.sub
> cd src/test; \
> for TEST in TEST_*; do \
>   rm -f ${TEST}.stdout ${TEST}.stderr; \
> done
> dh_auto_clean
> 	cd src && make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> Dist-Cleaning blas ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/blas'
> rm -rf *.o
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/blas'
> Dist-Cleaning lapack ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/lapack'
> rm -rf *.o
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/lapack'
> Dist-Cleaning utilities ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/utilities'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/utilities'
> Dist-Cleaning multivector ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/multivector'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/multivector'
> Dist-Cleaning krylov ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/krylov'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/krylov'
> Dist-Cleaning seq_mv ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/seq_mv'
> rm -f csr_spgemm_device_numer[1-9].c
> rm -f csr_spgemm_device_numer10.c
> rm -f csr_spgemm_device_symbl[1-9].c
> rm -f csr_spgemm_device_symbl10.c
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/seq_mv'
> Dist-Cleaning parcsr_mv ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/parcsr_mv'
> rm -f *.o *.obj libHYPRE*
> rm -f driver driver_matvec driver_matmul
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/parcsr_mv'
> Dist-Cleaning parcsr_block_mv ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/parcsr_block_mv'
> rm -rf *.o libHYPRE_*
> rm -f driver driver_matvec driver_matmul
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/parcsr_block_mv'
> Dist-Cleaning distributed_matrix ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/distributed_matrix'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/distributed_matrix'
> Dist-Cleaning IJ_mv ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/IJ_mv'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/IJ_mv'
> Dist-Cleaning matrix_matrix ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/matrix_matrix'
> rm -f *.o lib*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/matrix_matrix'
> Dist-Cleaning parcsr_ls ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/parcsr_ls'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/parcsr_ls'
> Dist-Cleaning struct_mv ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/struct_mv'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/struct_mv'
> Dist-Cleaning struct_ls ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/struct_ls'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/struct_ls'
> Dist-Cleaning sstruct_mv ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/sstruct_mv'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/sstruct_mv'
> Dist-Cleaning sstruct_ls ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/sstruct_ls'
> rm -f *.o *.obj libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/sstruct_ls'
> Dist-Cleaning /<<PKGBUILDDIR>>/src/distributed_ls ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/distributed_ls'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/distributed_ls/pilut'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/distributed_ls/pilut'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/distributed_ls/ParaSails'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/distributed_ls/ParaSails'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/distributed_ls/Euclid'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/distributed_ls/Euclid'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/distributed_ls'
> Dist-Cleaning lib ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/lib'
> rm -f *.o libHYPRE*
> rm -rf pchdir tca.map *inslog*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/lib'
> Dist-Cleaning docs ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/docs'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/docs/usr-manual'
> make[4]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> rm -rf _build/*
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/docs/usr-manual'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/docs/ref-manual'
> make[4]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/docs/ref-manual'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/docs'
> Dist-Cleaning test ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/test'
> rm -f *.o *.obj *.csv
> rm -rf pchdir tca.map *inslog*
> rm -f ij ij_assembly sstruct struct ams_driver maxwell_unscaled struct_migrate sstruct_fac ij_mv ij_mm zboxloop
> rm -f ex1_for ex3_for ex5_for ex6_for ex7_for
> rm -f f77_ij f77_ij_mv f77_struct
> rm -f cxx_ij cxx_sstruct cxx_struct cxx_*
> rm -f TEST_examples/*.out*
> rm -f TEST_examples/*.err*
> rm -f TEST_fac/*.out*
> rm -f TEST_fac/*.err*
> rm -f TEST_ij/*.out*
> rm -f TEST_ij/*.err*
> rm -f TEST_ij/*.txt*
> rm -f TEST_ij/vectors.*
> rm -f TEST_sstruct/*.out*
> rm -f TEST_sstruct/*.err*
> rm -f TEST_struct/*.out*
> rm -f TEST_struct/*.err*
> rm -f ex1 ex2 ex3 ex4 ex5 ex5big ex5b ex5b77 ex6 ex7 ex8 ex9 ex15big ex18comp
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/test'
> Dist-Cleaning examples ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/examples'
> rm -f ex1.o ex2.o ex3.o ex4.o ex5.o ex5f.o ex6.o ex7.o ex8.o ex9.o ex11.o ex12.o ex12f.o ex13.o ex14.o ex15.o ex16.o
> rm -f ex5big.o ex15big.o
> rm -f ex5f.o ex12f.o
> rm -f ex17.o ex18.o
> rm -f ex18comp.o
> rm -f cudaf.o cudaf.mod ex*.o
> cd vis; make clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/examples/vis'
> make[4]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> rm -f *mesh* *sol* *data*
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/examples/vis'
> rm -f ex1 ex2 ex3 ex4 ex5 ex5f ex6 ex7 ex8 ex9 ex11 ex12 ex12f ex13 ex14 ex15 ex16 ex1*~ ex2*~ ex3*~ ex4*~ ex5*~ ex5f*~ ex6*~ ex7*~ ex8*~ ex9*~ ex11*~ ex12*~ ex12f*~ ex13*~ ex14*~ ex15*~ ex16*~
> rm -f ex5big ex15big ex5big*~ ex15big*~
> rm -f  ex5f*~ ex12f*~
> rm -f ex17 ex18 ex17*~ ex18*~
> rm -f ex18comp ex18comp*~
> rm -fr README*
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/examples'
> Dist-Cleaning examples/docs ...
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/examples/docs'
> rm -f *.html
> rm -f *~
> rm -rf ../*.html ../README_files
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/examples/docs'
> rm -rf tca.map pchdir *inslog*
> rm -rf ./config/Makefile.config
> rm -rf ./TAGS
> rm -rf ./autom4te.cache
> rm -rf ./config.log
> rm -rf ./config.status
> rm -rf ./HYPRE_config.h
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--sourcedirectory=src
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> rm -rf src64 src64m
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building hypre using existing ./hypre_2.28.0.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file src/config/config.sub, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file src/config/config.guess, use --include-removal to override
> dpkg-source: error: cannot represent change to src-static/IJ_mv/F90_HYPRE_IJMatrix.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/F90_HYPRE_IJMatrix.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/F90_HYPRE_IJVector.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/F90_HYPRE_IJVector.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/F90_IJMatrix.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/F90_IJMatrix.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/HYPRE_IJMatrix.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/HYPRE_IJMatrix.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/HYPRE_IJVector.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/HYPRE_IJVector.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJMatrix.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJMatrix.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJMatrix_parcsr.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJMatrix_parcsr.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJMatrix_parcsr_device.obj: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJMatrix_parcsr_device.obj in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJVector.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJVector.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJVector_parcsr.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJVector_parcsr.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJVector_parcsr_device.obj: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJVector_parcsr_device.obj in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/IJ_assumed_part.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/IJ_assumed_part.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/aux_par_vector.o: binary file contents changed
> dpkg-source: error: add src-static/IJ_mv/aux_par_vector.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src-static/IJ_mv/aux_parcsr_matrix.o: binary file contents changed
[...]
> dpkg-source: error: add src64m-static/utilities/qsort.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src64m-static/utilities/qsplit.o: binary file contents changed
> dpkg-source: error: add src64m-static/utilities/qsplit.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src64m-static/utilities/random.o: binary file contents changed
> dpkg-source: error: add src64m-static/utilities/random.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src64m-static/utilities/threading.o: binary file contents changed
> dpkg-source: error: add src64m-static/utilities/threading.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src64m-static/utilities/timer.o: binary file contents changed
> dpkg-source: error: add src64m-static/utilities/timer.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src64m-static/utilities/timing.o: binary file contents changed
> dpkg-source: error: add src64m-static/utilities/timing.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src64m-static/utilities/utilities.o: binary file contents changed
> dpkg-source: error: add src64m-static/utilities/utilities.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'src64m-static/utilities/version.sh' will not be represented in diff
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.


The full build log is available from:
http://qa-logs.debian.net/2023/08/13/hypre_2.28.0-6_unstable.log

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.