[Debian-med-packaging] Bug#1046152: mcl: Fails to build source after successful build

Sun Aug 13 20:20:58 BST 2023

Source: mcl
Version: 1:22-282+ds-2
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 mcl
> dpkg-buildpackage: info: source version 1:22-282+ds-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean
>    dh_auto_clean
> 	make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in .
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "" || rm -f 
> rm -f config.h stamp-h1
> 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
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> Making distclean in img
> make[2]: Entering directory '/<<PKGBUILDDIR>>/img'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/img'
> Making distclean in graphs
> make[2]: Entering directory '/<<PKGBUILDDIR>>/graphs'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/graphs'
> Making distclean in doc
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> Making distclean in .
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making distclean in clew
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/clew'
> test -z "libclew.a" || rm -f libclew.a
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/cat.Po
> rm -f ./.deps/claw.Po
> rm -f ./.deps/clm.Po
> rm -f ./.deps/scan.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/clew'
> Making distclean in mcl
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/mcl'
> test -z "libmcl.a" || rm -f libmcl.a
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/alg.Po
> rm -f ./.deps/dpsd.Po
> rm -f ./.deps/expand.Po
> rm -f ./.deps/inflate.Po
> rm -f ./.deps/interpret.Po
> rm -f ./.deps/proc.Po
> rm -f ./.deps/procinit.Po
> rm -f ./.deps/transform.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/mcl'
> Making distclean in gryphon
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/gryphon'
> test -z "libgryphon.a" || rm -f libgryphon.a
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/path.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/gryphon'
> Making distclean in impala
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/impala'
> test -z "libimpala.a" || rm -f libimpala.a
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/app.Po
> rm -f ./.deps/compose.Po
> rm -f ./.deps/edge.Po
> rm -f ./.deps/iface.Po
> rm -f ./.deps/io.Po
> rm -f ./.deps/ivp.Po
> rm -f ./.deps/matrix.Po
> rm -f ./.deps/pval.Po
> rm -f ./.deps/stream.Po
> rm -f ./.deps/tab.Po
> rm -f ./.deps/vector.Po
> rm -f ./.deps/version.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/impala'
> Making distclean in shcl
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/shcl'
> test -z "clm" || rm -f clm
> test -z "clmdag clmframe" || rm -f clmdag clmframe
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/clm.Po
> rm -f ./.deps/clmadjust.Po
> rm -f ./.deps/clmclose.Po
> rm -f ./.deps/clmdag.Po
> rm -f ./.deps/clmdist.Po
> rm -f ./.deps/clmframe.Po
> rm -f ./.deps/clmimac.Po
> rm -f ./.deps/clminfo.Po
> rm -f ./.deps/clminfo2.Po
> rm -f ./.deps/clmmate.Po
> rm -f ./.deps/clmmeet.Po
> rm -f ./.deps/clmoptics.Po
> rm -f ./.deps/clmorder.Po
> rm -f ./.deps/clmps.Po
> rm -f ./.deps/clmresidue.Po
> rm -f ./.deps/report.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/shcl'
> Making distclean in shmcl
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/shmcl'
> test -z "mcl" || rm -f mcl
> test -z "mclcm" || rm -f mclcm
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/mcl.Po
> rm -f ./.deps/mclcm.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/shmcl'
> Making distclean in shmx
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/shmx'
> test -z "mcx mcxsubs mcxmap mcxarray mcxdump mcxload" || rm -f mcx mcxsubs mcxmap mcxarray mcxdump mcxload
> test -z "mcxtest2 mcxtest mcxminusmeet mcxmm mcxmetric mcxrand mcxassemble" || rm -f mcxtest2 mcxtest mcxminusmeet mcxmm mcxmetric mcxrand mcxassemble
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/mcx.Po
> rm -f ./.deps/mcxalter.Po
> rm -f ./.deps/mcxarray.Po
> rm -f ./.deps/mcxassemble.Po
> rm -f ./.deps/mcxclcf.Po
> rm -f ./.deps/mcxcollect.Po
> rm -f ./.deps/mcxconvert.Po
> rm -f ./.deps/mcxdiameter.Po
> rm -f ./.deps/mcxdump.Po
> rm -f ./.deps/mcxerdos.Po
> rm -f ./.deps/mcxfp.Po
> rm -f ./.deps/mcxload.Po
> rm -f ./.deps/mcxmap.Po
> rm -f ./.deps/mcxmetric.Po
> rm -f ./.deps/mcxminusmeet.Po
> rm -f ./.deps/mcxmm.Po
> rm -f ./.deps/mcxquery.Po
> rm -f ./.deps/mcxrand.Po
> rm -f ./.deps/mcxsubs.Po
> rm -f ./.deps/mcxtab.Po
> rm -f ./.deps/mcxtest.Po
> rm -f ./.deps/mcxtest2.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/shmx'
> Making distclean in shmcx
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/shmcx'
> test -z "mcxi" || rm -f mcxi
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/glob.Po
> rm -f ./.deps/mcxi.Po
> rm -f ./.deps/ops.Po
> rm -f ./.deps/stack.Po
> rm -f ./.deps/util.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/shmcx'
> Making distclean in shmcxquery
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src/shmcxquery'
> test -z "mcxquery" || rm -f mcxquery
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> rm -f ./.deps/mcxquery.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/shmcxquery'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making distclean in include
> make[2]: Entering directory '/<<PKGBUILDDIR>>/include'
> Making distclean in .
> make[3]: Entering directory '/<<PKGBUILDDIR>>/include'
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/include'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/include'
> Making distclean in scripts
> make[2]: Entering directory '/<<PKGBUILDDIR>>/scripts'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/scripts'
> Making distclean in rcl
> make[2]: Entering directory '/<<PKGBUILDDIR>>/rcl'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/rcl'
> Making distclean in testing
> make[2]: Entering directory '/<<PKGBUILDDIR>>/testing'
> Making distclean in .
> make[3]: Entering directory '/<<PKGBUILDDIR>>/testing'
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/testing'
> Making distclean in stream
> make[3]: Entering directory '/<<PKGBUILDDIR>>/testing/stream'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/testing/stream'
> Making distclean in blast
> make[3]: Entering directory '/<<PKGBUILDDIR>>/testing/blast'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/testing/blast'
> Making distclean in setops
> make[3]: Entering directory '/<<PKGBUILDDIR>>/testing/setops'
> test -z "" || rm -f 
> test . = "." || test -z "" || rm -f 
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/testing/setops'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/testing'
> Making distclean in shed
> make[2]: Entering directory '/<<PKGBUILDDIR>>/shed'
> Making distclean in .
> make[3]: Entering directory '/<<PKGBUILDDIR>>/shed'
> test -z "" || rm -f 
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f 
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/shed'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/shed'
> 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
> find . -name "*.zmr" -delete
> find . -name "*.zmt" -delete
> rm -rf doc/*.1 doc/*.html doc/*-html doc/*.ps
> rm -rf src/alien/oxygen/doc/*.1 src/alien/oxygen/doc/*.html src/alien/oxygen/doc/*.ps
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building mcl using existing ./mcl_22-282+ds.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file aclocal.m4, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file INSTALL, 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 config.h.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autofoo/install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autofoo/compile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autofoo/mkinstalldirs, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autofoo/depcomp, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autofoo/missing, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  mcl-22-282+ds/doc/mcl.txt
>  mcl-22-282+ds/doc/mclcm.txt
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/mcl_22-282+ds-2.diff.QjB7ae
> 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/mcl_22-282+ds-2_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.