[Debian-med-packaging] Bug#1043622: art-nextgen-simulation-tools: Fails to build source after successful build
Lucas Nussbaum
lucas at debian.org
Sun Aug 13 14:17:54 BST 2023
Source: art-nextgen-simulation-tools
Version: 20160605+dfsg-4
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 art-nextgen-simulation-tools
> dpkg-buildpackage: info: source version 20160605+dfsg-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <npatra974 at gmail.com>
> dpkg-source --before-build .
> debian/rules clean
> dh clean
> dh_auto_clean
> make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "art_illumina art_454 art_SOLiD" || rm -f art_illumina art_454 art_SOLiD
> rm -f *.o
> rm -f *.tab.c
> rm -f art_454_src/*.o
> test -z "" || rm -f
> rm -f art_SOLiD_src/*.o
> test . = "." || test -z "" || rm -f
> rm -f art_illumina_src/*.o
> rm -f art_454_src/.deps/.dirstamp
> rm -f config.h stamp-h1
> rm -f art_454_src/.dirstamp
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f art_SOLiD_src/.deps/.dirstamp
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> rm -f art_SOLiD_src/.dirstamp
> rm -f art_illumina_src/.deps/.dirstamp
> rm -f art_illumina_src/.dirstamp
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f art_454_src/.deps/art.Po
> rm -f art_454_src/.deps/art_454.Po
> rm -f art_454_src/.deps/readSeqFile.Po
> rm -f art_454_src/.deps/read_profile.Po
> rm -f art_454_src/.deps/samRead.Po
> rm -f art_454_src/.deps/seqRead.Po
> rm -f art_SOLiD_src/.deps/art.Po
> rm -f art_SOLiD_src/.deps/art_SOLiD.Po
> rm -f art_SOLiD_src/.deps/readSeqFile.Po
> rm -f art_SOLiD_src/.deps/read_SOLiD.Po
> rm -f art_SOLiD_src/.deps/samRead.Po
> rm -f art_illumina_src/.deps/art_illumina.Po
> rm -f art_illumina_src/.deps/art_qual_scale.Po
> rm -f art_illumina_src/.deps/empdist.Po
> rm -f art_illumina_src/.deps/readSeqFile.Po
> rm -f art_illumina_src/.deps/samRead.Po
> rm -f art_illumina_src/.deps/seqRead.Po
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean
> dh_clean
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building art-nextgen-simulation-tools using existing ./art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file config.h.in, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_5_end_com.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_5_end_com.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_5_end_com.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_5_end_com.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair_F3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair_F3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair_R3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_matepair_R3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_pair.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_pair.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_pair1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_pair1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_pair2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_pair2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_454.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_454.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_454.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_454.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_4542.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_4542.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_F3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_F3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_F5.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_paired_F5.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single_454.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single_454.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single_454.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/amp_single_454.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/dat_userProfile.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/dat_userProfile.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/dat_userProfile.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_com.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_com.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_com1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_com1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_com2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_com2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_dat.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_dat_F3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_dat_F3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_dat_R3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_dat_R3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs1.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs1_F3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs1_F3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs1_R3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs1_R3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs2.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs2_F3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs2_F3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs2_R3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/matepair_fs2_R3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flx2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_454_flxTitan2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_dat.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_dat_F3.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_dat_F3.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_dat_F5.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_dat_F5.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f1.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f11.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f11.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f12.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f12.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f2.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f21.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f21.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f22.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_com_f22.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_sep.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_sep.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_sep1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_sep1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_sep2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_end_sep2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_nomask.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_nomask1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_nomask1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_nomask2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/paired_nomask2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_flx.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_flx.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_flx.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_flx.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_flx.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t1.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t1.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t1.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t1.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t2.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t2.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t2.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t2.stat
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_454_t2_normalised.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_dat.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_dat.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_dat.map
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_dat.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_com.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_com.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_com.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_com.sam
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_sep.aln
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_sep.bed
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_sep.fq
> art-nextgen-simulation-tools-20160605+dfsg/examples/single_end_sep.sam
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/art-nextgen-simulation-tools_20160605+dfsg-4.diff.ZwTS1y
> 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/art-nextgen-simulation-tools_20160605+dfsg-4_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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