[Debian-med-packaging] Bug#1046372: librcsb-core-wrapper: Fails to build source after successful build

Sun Aug 13 20:20:54 BST 2023

Source: librcsb-core-wrapper
Version: 1.005-11
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 librcsb-core-wrapper
> dpkg-buildpackage: info: source version 1.005-11
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --with python3
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	make -j8 clean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf docs
> 
> ------------------------------------------------------------
> **** Cleaning etc ****
> ------------------------------------------------------------
> 
> ------------------------------------------------------------
> **** Cleaning common ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/common'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> 
> ------------------------------------------------------------
> **** Cleaning test results in dict-obj-file ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/dict-obj-file'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/dict-obj-file'
> 
> ------------------------------------------------------------
> **** Cleaning test results in pdbml-parser ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/pdbml-parser'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/common'
> 
> ------------------------------------------------------------
> **** Cleaning tables ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/tables'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/pdbml-parser'
> rm -rf rcsb
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/tables'
> 
> ------------------------------------------------------------
> **** Cleaning regex ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/regex'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/regex'
> 
> ------------------------------------------------------------
> **** Cleaning cif-file ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/cif-file'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/cif-file'
> 
> ------------------------------------------------------------
> **** Cleaning cif-parser ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/cif-parser'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/cif-parser'
> 
> ------------------------------------------------------------
> **** Cleaning cif-file-util ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/cif-file-util'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/cif-file-util'
> 
> ------------------------------------------------------------
> **** Cleaning dict-obj-file ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/dict-obj-file'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/dict-obj-file'
> 
> ------------------------------------------------------------
> **** Cleaning pdbml-parser ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/pdbml-parser'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/pdbml-parser'
> 
> ------------------------------------------------------------
> **** Cleaning cctbx ****
> ------------------------------------------------------------
> make[3]: Entering directory '/<<PKGBUILDDIR>>/cctbx'
> make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/cctbx'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -rf wrapper/python/build
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building librcsb-core-wrapper using existing ./librcsb-core-wrapper_1.005.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to wrapper/python/src:
> dpkg-source: error:   new version is symlink to ../src
> dpkg-source: error:   old version is nonexistent
> dpkg-source: warning: ignoring deletion of file dict-obj-file/test/mmcif_std.odb, use --include-removal to override
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11/build/CorePyWrap.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11/build/CorePyWrap.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11/build/CorePyWrap.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to cif-file-util/obj/.libs/CifCorrector.o: binary file contents changed
> dpkg-source: error: add cif-file-util/obj/.libs/CifCorrector.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 cif-file-util/obj/.libs/CifFileUtil.o: binary file contents changed
> dpkg-source: error: add cif-file-util/obj/.libs/CifFileUtil.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 cif-file/obj/.libs/CifDataInfo.o: binary file contents changed
> dpkg-source: error: add cif-file/obj/.libs/CifDataInfo.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 cif-file/obj/.libs/CifExcept.o: binary file contents changed
> dpkg-source: error: add cif-file/obj/.libs/CifExcept.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 cif-file/obj/.libs/CifFile.o: binary file contents changed
> dpkg-source: error: add cif-file/obj/.libs/CifFile.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 cif-file/obj/.libs/CifParentChild.o: binary file contents changed
> dpkg-source: error: add cif-file/obj/.libs/CifParentChild.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 cif-file/obj/.libs/DicFile.o: binary file contents changed
> dpkg-source: error: add cif-file/obj/.libs/DicFile.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 cif-file/obj/.libs/ParentChild.o: binary file contents changed
> dpkg-source: error: add cif-file/obj/.libs/ParentChild.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 cif-parser/obj/.libs/CifFileReadDef.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/CifFileReadDef.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 cif-parser/obj/.libs/CifParser.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/CifParser.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 cif-parser/obj/.libs/CifParserBase.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/CifParserBase.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 cif-parser/obj/.libs/CifScanner.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/CifScanner.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 cif-parser/obj/.libs/CifScannerBase.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/CifScannerBase.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 cif-parser/obj/.libs/DICParser.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/DICParser.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 cif-parser/obj/.libs/DICParserBase.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/DICParserBase.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 cif-parser/obj/.libs/DICScanner.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/DICScanner.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 cif-parser/obj/.libs/DICScannerBase.o: binary file contents changed
> dpkg-source: error: add cif-parser/obj/.libs/DICScannerBase.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 common/obj/.libs/BlockIO.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/BlockIO.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 common/obj/.libs/CifString.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/CifString.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 common/obj/.libs/DataInfo.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/DataInfo.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 common/obj/.libs/Exceptions.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/Exceptions.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 common/obj/.libs/GenCont.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/GenCont.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 common/obj/.libs/GenString.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/GenString.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 common/obj/.libs/RcsbFile.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/RcsbFile.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 common/obj/.libs/RcsbPlatform.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/RcsbPlatform.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 common/obj/.libs/Serializer.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/Serializer.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 common/obj/.libs/mapped_ptr_vector.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/mapped_ptr_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 common/obj/.libs/mapped_vector.o: binary file contents changed
> dpkg-source: error: add common/obj/.libs/mapped_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 dict-obj-file/obj/.libs/DictDataInfo.o: binary file contents changed
> dpkg-source: error: add dict-obj-file/obj/.libs/DictDataInfo.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 dict-obj-file/obj/.libs/DictObjCont.o: binary file contents changed
> dpkg-source: error: add dict-obj-file/obj/.libs/DictObjCont.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 dict-obj-file/obj/.libs/DictObjContInfo.o: binary file contents changed
> dpkg-source: error: add dict-obj-file/obj/.libs/DictObjContInfo.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 dict-obj-file/obj/.libs/DictObjFile.o: binary file contents changed
> dpkg-source: error: add dict-obj-file/obj/.libs/DictObjFile.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 dict-obj-file/obj/.libs/DictParentChild.o: binary file contents changed
> dpkg-source: error: add dict-obj-file/obj/.libs/DictParentChild.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 pdbml-parser/obj/.libs/PdbMlFileUtil.o: binary file contents changed
> dpkg-source: error: add pdbml-parser/obj/.libs/PdbMlFileUtil.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 pdbml-parser/obj/.libs/PdbMlParserHandler.o: binary file contents changed
> dpkg-source: error: add pdbml-parser/obj/.libs/PdbMlParserHandler.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 pdbml-parser/obj/.libs/misc_util.o: binary file contents changed
> dpkg-source: error: add pdbml-parser/obj/.libs/misc_util.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 regex/obj/.libs/regcomp.o: binary file contents changed
> dpkg-source: error: add regex/obj/.libs/regcomp.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 regex/obj/.libs/regerror.o: binary file contents changed
> dpkg-source: error: add regex/obj/.libs/regerror.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 regex/obj/.libs/regexec.o: binary file contents changed
> dpkg-source: error: add regex/obj/.libs/regexec.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 regex/obj/.libs/regfree.o: binary file contents changed
> dpkg-source: error: add regex/obj/.libs/regfree.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 tables/obj/.libs/ISTable.o: binary file contents changed
> dpkg-source: error: add tables/obj/.libs/ISTable.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 tables/obj/.libs/ITTable.o: binary file contents changed
> dpkg-source: error: add tables/obj/.libs/ITTable.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 tables/obj/.libs/TTable.o: binary file contents changed
> dpkg-source: error: add tables/obj/.libs/TTable.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 tables/obj/.libs/TableFile.o: binary file contents changed
> dpkg-source: error: add tables/obj/.libs/TableFile.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> 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/librcsb-core-wrapper_1.005-11_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.