Bug#1048321: netcdf-fortran: Fails to build source after successful build

To: submit@bugs.debian.org
Subject: Bug#1048321: netcdf-fortran: Fails to build source after successful build
From: Lucas Nussbaum <lucas@debian.org>
Date: Sun, 13 Aug 2023 21:21:01 +0200
Message-id: <[🔎] 1691954461.065243.1279476.nullmailer@grub.nussbaum.fr>
Reply-to: Lucas Nussbaum <lucas@debian.org>, 1048321@bugs.debian.org
Source: netcdf-fortran
Version: 4.6.0+really4.5.4+ds-3
Severity: minor
Tags: trixie sid ftbfs
User: lucas@debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa@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 netcdf-fortran
> dpkg-buildpackage: info: source version 4.6.0+really4.5.4+ds-3
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Jelmer VernooÄ³ <jelmer@debian.org>
>  dpkg-source --before-build .
>  fakeroot debian/rules clean
> dh clean
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in libsrc
> make[2]: Entering directory '/<<PKGBUILDDIR>>/libsrc'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/libsrc'
> Making distclean in fortran
> make[2]: Entering directory '/<<PKGBUILDDIR>>/fortran'
> test -z "libnetcdff.la" || rm -f libnetcdff.la
> rm -rf .libs _libs
> test -z "libtypeSizes.la libnetcdf_nc_data.la libnetcdf_nf_data.la libnetcdf_nc_interfaces.la libnetcdf_nf_interfaces.la libnetcdfm.la libnetcdf_f03.la libnetcdf_fortv2_c_interfaces.la libnetcdf4_nc_interfaces.la libnetcdf4_nf_interfaces.la libnetcdf4_f03.la" || rm -f libtypeSizes.la libnetcdf_nc_data.la libnetcdf_nf_data.la libnetcdf_nc_interfaces.la libnetcdf_nf_interfaces.la libnetcdfm.la libnetcdf_f03.la libnetcdf_fortv2_c_interfaces.la libnetcdf4_nc_interfaces.la libnetcdf4_nf_interfaces.la libnetcdf4_f03.la
> rm -f *.o
> test -z "*.mod netcdf.inc" || rm -f *.mod netcdf.inc
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./so_locations
> rm -f ./so_locations
> rm -f ./.deps/nf_lib.Plo
> rm -f ./.deps/nf_v2compat.Plo
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/fortran'
> Making distclean in nf_test
> make[2]: Entering directory '/<<PKGBUILDDIR>>/nf_test'
> test -z "scratch*.nc test*.nc copy*.nc tst_*.nc ftst_*.nc f90tst_*.nc f03test*.nc *.tmp *.tmp2 fort.* tst03*.nc f03tst*.nc ftest.nc fcopy.nc nf03_error.F test03_read.F test03_write.F nf03_test.F test03_get.F f03test.F tst03_f77_v2.F" || rm -f scratch*.nc test*.nc copy*.nc tst_*.nc ftst_*.nc f90tst_*.nc f03test*.nc *.tmp *.tmp2 fort.* tst03*.nc f03tst*.nc ftest.nc fcopy.nc nf03_error.F test03_read.F test03_write.F nf03_test.F test03_get.F f03test.F tst03_f77_v2.F
> rm -rf .libs _libs
> test -z "libtests.la" || rm -f libtests.la
> rm -f *.o
> test -z "*.mod   test-suite-memcheck.log test-suite-helgrind.log test-suite-drd.log test-suite-sgcheck.log" || rm -f *.mod   test-suite-memcheck.log test-suite-helgrind.log test-suite-drd.log test-suite-sgcheck.log
>  rm -f nf_test tst_int64 tst_f77_v2 ftest nf03_test f03test tst03_f77_v2
> rm -f *.lo
> rm -f *.tab.c
> test -z "fills.nc" || rm -f fills.nc
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test -z "nf_test.log tst_int64.log tst_f77_v2.log ftest.log nf03_test.log f03test.log tst03_f77_v2.log" || rm -f nf_test.log tst_int64.log tst_f77_v2.log ftest.log nf03_test.log f03test.log tst03_f77_v2.log
> test . = "." || test -z "" || rm -f 
> rm -f ./so_locations
> test -z "fills.nc" || rm -f fills.nc
> test -z "nf_test.trs tst_int64.trs tst_f77_v2.trs ftest.trs nf03_test.trs f03test.trs tst03_f77_v2.trs" || rm -f nf_test.trs tst_int64.trs tst_f77_v2.trs ftest.trs nf03_test.trs f03test.trs tst03_f77_v2.trs
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f ./.deps/f03lib.Po
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/nf_test'
> Making distclean in nf03_test
> make[2]: Entering directory '/<<PKGBUILDDIR>>/nf03_test'
> test -z "tst*.nc" || rm -f tst*.nc
> rm -rf .libs _libs
> rm -f *.o
>  rm -f tst_f90 tst_fill_int64
> test -z "tst_f90.log tst_fill_int64.log" || rm -f tst_f90.log tst_fill_int64.log
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test -z "tst_f90.trs tst_fill_int64.trs" || rm -f tst_f90.trs tst_fill_int64.trs
> test . = "." || test -z "" || rm -f 
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/nf03_test'
> Making distclean in nf_test4
> make[2]: Entering directory '/<<PKGBUILDDIR>>/nf_test4'
> test -z "ftst_*.nc f03tst_*.nc *.tmp *.tmp2 f03tst_groups.F f03tst_vars.F f03tst_vars2.F f03tst_vars3.F f03tst_vars4.F f03tst_vars5.F f03tst_vars6.F f03tst_types.F f03tst_types2.F f03tst_types3.F f03tst_v2.F  f03tst_var_szip.F" || rm -f ftst_*.nc f03tst_*.nc *.tmp *.tmp2 f03tst_groups.F f03tst_vars.F f03tst_vars2.F f03tst_vars3.F f03tst_vars4.F f03tst_vars5.F f03tst_vars6.F f03tst_types.F f03tst_types2.F f03tst_types3.F f03tst_v2.F  f03tst_var_szip.F
> rm -rf .libs _libs
> rm -f *.o
> test -z "ftst_groups.log ftst_vars.log ftst_vars2.log ftst_vars3.log ftst_vars4.log ftst_vars5.log ftst_vars6.log ftst_types.log ftst_types2.log ftst_types3.log ftst_path.log ftst_rengrps.log f03tst_open_mem.log ftst_var_compact.log ftst_v2.log ftst_var_szip.log f03tst_groups.log f03tst_vars.log f03tst_vars2.log f03tst_vars3.log f03tst_vars4.log f03tst_vars5.log f03tst_vars6.log f03tst_types.log f03tst_types2.log f03tst_types3.log f03tst_v2.log f03tst_var_szip.log" || rm -f ftst_groups.log ftst_vars.log ftst_vars2.log ftst_vars3.log ftst_vars4.log ftst_vars5.log ftst_vars6.log ftst_types.log ftst_types2.log ftst_types3.log ftst_path.log ftst_rengrps.log f03tst_open_mem.log ftst_var_compact.log ftst_v2.log ftst_var_szip.log f03tst_groups.log f03tst_vars.log f03tst_vars2.log f03tst_vars3.log 
> f03tst_vars4.log f03tst_vars5.log f03tst_vars6.log f03tst_types.log f03tst_types2.log f03tst_types3.log f03tst_v2.log f03tst_var_szip.log
> rm -f *.lo
>  rm -f ftst_groups ftst_vars ftst_vars2 ftst_vars3 ftst_vars4 ftst_vars5 ftst_vars6 ftst_types ftst_types2 ftst_types3 ftst_path ftst_rengrps f03tst_open_mem ftst_var_compact ftst_v2 ftst_var_szip f03tst_groups f03tst_vars f03tst_vars2 f03tst_vars3 f03tst_vars4 f03tst_vars5 f03tst_vars6 f03tst_types f03tst_types2 f03tst_types3 f03tst_v2 f03tst_var_szip
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> test -z "ftst_groups.trs ftst_vars.trs ftst_vars2.trs ftst_vars3.trs ftst_vars4.trs ftst_vars5.trs ftst_vars6.trs ftst_types.trs ftst_types2.trs ftst_types3.trs ftst_path.trs ftst_rengrps.trs f03tst_open_mem.trs ftst_var_compact.trs ftst_v2.trs ftst_var_szip.trs f03tst_groups.trs f03tst_vars.trs f03tst_vars2.trs f03tst_vars3.trs f03tst_vars4.trs f03tst_vars5.trs f03tst_vars6.trs f03tst_types.trs f03tst_types2.trs f03tst_types3.trs f03tst_v2.trs f03tst_var_szip.trs" || rm -f ftst_groups.trs ftst_vars.trs ftst_vars2.trs ftst_vars3.trs ftst_vars4.trs ftst_vars5.trs ftst_vars6.trs ftst_types.trs ftst_types2.trs ftst_types3.trs ftst_path.trs ftst_rengrps.trs f03tst_open_mem.trs ftst_var_compact.trs ftst_v2.trs ftst_var_szip.trs f03tst_groups.trs f03tst_vars.trs f03tst_vars2.trs f03tst_vars3.trs 
> f03tst_vars4.trs f03tst_vars5.trs f03tst_vars6.trs f03tst_types.trs f03tst_types2.trs f03tst_types3.trs f03tst_v2.trs f03tst_var_szip.trs
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/nf_test4'
> Making distclean in nf03_test4
> make[2]: Entering directory '/<<PKGBUILDDIR>>/nf03_test4'
> test -z "f90tst_*.nc fort.*" || rm -f f90tst_*.nc fort.*
> rm -rf .libs _libs
> rm -f *.o
> test -z "f90tst_vars.log f90tst_vars_vlen.log f90tst_grps.log f90tst_fill.log f90tst_fill2.log f90tst_vars2.log f90tst_vars3.log f90tst_vars4.log f90tst_path.log f90tst_rengrps.log f90tst_nc4.log f90tst_types.log f90tst_types2.log f90tst_io.log f90tst_var_szip.log" || rm -f f90tst_vars.log f90tst_vars_vlen.log f90tst_grps.log f90tst_fill.log f90tst_fill2.log f90tst_vars2.log f90tst_vars3.log f90tst_vars4.log f90tst_path.log f90tst_rengrps.log f90tst_nc4.log f90tst_types.log f90tst_types2.log f90tst_io.log f90tst_var_szip.log
> rm -f *.lo
> rm -f *.tab.c
>  rm -f f90tst_vars f90tst_vars_vlen f90tst_grps f90tst_fill f90tst_fill2 f90tst_vars2 f90tst_vars3 f90tst_vars4 f90tst_path f90tst_rengrps f90tst_nc4 f90tst_types f90tst_types2 f90tst_io f90tst_var_szip
> test -z "run_f90_par_test.sh" || rm -f run_f90_par_test.sh
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> test -z "f90tst_vars.trs f90tst_vars_vlen.trs f90tst_grps.trs f90tst_fill.trs f90tst_fill2.trs f90tst_vars2.trs f90tst_vars3.trs f90tst_vars4.trs f90tst_path.trs f90tst_rengrps.trs f90tst_nc4.trs f90tst_types.trs f90tst_types2.trs f90tst_io.trs f90tst_var_szip.trs" || rm -f f90tst_vars.trs f90tst_vars_vlen.trs f90tst_grps.trs f90tst_fill.trs f90tst_fill2.trs f90tst_vars2.trs f90tst_vars3.trs f90tst_vars4.trs f90tst_path.trs f90tst_rengrps.trs f90tst_nc4.trs f90tst_types.trs f90tst_types2.trs f90tst_io.trs f90tst_var_szip.trs
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/nf03_test4'
> Making distclean in docs
> make[2]: Entering directory '/<<PKGBUILDDIR>>/docs'
> test -z "doxyfile.stamp" || rm -f doxyfile.stamp
> rm -rf .libs _libs
> rm -rf ../docs/man
> rm -f *.lo
> test -z "Doxyfile" || rm -f Doxyfile
> rm -rf ../docs/html
> test . = "." || test -z "" || rm -f 
> rm -rf ../docs/latex
> rm -rf ../docs/latex_main
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/docs'
> Making distclean in examples
> make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
> Making distclean in F77
> make[3]: Entering directory '/<<PKGBUILDDIR>>/examples/F77'
> test -z "simple_xy.nc sfc_pres_temp.nc pres_temp_4D.nc simple_xy_nc4.nc" || rm -f simple_xy.nc sfc_pres_temp.nc pres_temp_4D.nc simple_xy_nc4.nc
> rm -rf .libs _libs
> rm -f *.o
> test -z "run_examples.sh.log run_examples_4.sh.log" || rm -f run_examples.sh.log run_examples_4.sh.log
> rm -f *.lo
> rm -f *.tab.c
>  rm -f simple_xy_wr simple_xy_rd sfc_pres_temp_wr sfc_pres_temp_rd pres_temp_4D_wr pres_temp_4D_rd simple_xy_nc4_wr simple_xy_nc4_rd
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> test -z "run_examples.sh.trs run_examples_4.sh.trs" || rm -f run_examples.sh.trs run_examples_4.sh.trs
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples/F77'
> Making distclean in F90
> make[3]: Entering directory '/<<PKGBUILDDIR>>/examples/F90'
>  rm -f simple_xy_wr simple_xy_rd sfc_pres_temp_wr sfc_pres_temp_rd pres_temp_4D_wr pres_temp_4D_rd nc4_simple_xy_wr nc4_sfc_pres_temp_wr nc4_pres_temp_4D_wr simple_xy_nc4_wr simple_xy_nc4_rd
> test -z "simple_xy.nc sfc_pres_temp.nc pres_temp_4D.nc simple_xy_nc4.nc simple_xy_par.nc nc4_simple_xy_wr.f90 simple_xy.cdl nc4_sfc_pres_temp_wr.f90 sfc_pres_temp.cdl nc4_pres_temp_4d_wr.f90 pres_temp_4d.cdl nc4_simple_xy.nc nc4_pres_temp_4D.nc nc4_sfc_pres_temp.nc " || rm -f simple_xy.nc sfc_pres_temp.nc pres_temp_4D.nc simple_xy_nc4.nc simple_xy_par.nc nc4_simple_xy_wr.f90 simple_xy.cdl nc4_sfc_pres_temp_wr.f90 sfc_pres_temp.cdl nc4_pres_temp_4d_wr.f90 pres_temp_4d.cdl nc4_simple_xy.nc nc4_pres_temp_4D.nc nc4_sfc_pres_temp.nc 
> rm -rf .libs _libs
> rm -f *.o
> test -z "run_examples.sh.log run_examples_4.sh.log" || rm -f run_examples.sh.log run_examples_4.sh.log
> test -z "run_examples.sh.trs run_examples_4.sh.trs" || rm -f run_examples.sh.trs run_examples_4.sh.trs
> test -z "test-suite.log" || rm -f test-suite.log
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples/F90'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> Making distclean in CMakeExtras
> make[2]: Entering directory '/<<PKGBUILDDIR>>/CMakeExtras'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/CMakeExtras'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "nf-config netcdf-fortran.pc libnetcdff.settings" || rm -f nf-config netcdf-fortran.pc libnetcdff.settings
> rm -f libtool config.lt
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> test -z "VERSION libnetcdf.settings" || rm -f VERSION libnetcdf.settings
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> rm -f -r docs/doxygen_sqlite3.db docs/html/ docs/man/ docs/latex/
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building netcdf-fortran using existing ./netcdf-fortran_4.6.0+really4.5.4+ds.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file ltmain.sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file configure, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file fortran/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file nf03_test4/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file nf_test4/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltsugar.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/lt~obsolete.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltversion.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/libtool.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file m4/ltoptions.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file nf_test/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file examples/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file examples/F90/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file examples/F77/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file nf03_test/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file docs/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file CMakeExtras/Makefile.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file libsrc/Makefile.in, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  netcdf-fortran-4.6.0+really4.5.4+ds/docs/netcdf_f77.3
>  netcdf-fortran-4.6.0+really4.5.4+ds/examples/F90/nc4_pres_temp_4D_wr.f90
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/netcdf-fortran_4.6.0+really4.5.4+ds-3.diff.y7XdSS
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> 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/netcdf-fortran_4.6.0+really4.5.4+ds-3_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.
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