Your message dated Tue, 09 Oct 2018 06:42:05 +0000 with message-id <e1g9lix-000iqt...@fasolo.debian.org> and subject line Bug#910324: fixed in freebayes 1.2.0-2 has caused the Debian Bug report #910324, regarding freebayes parallel FTBFS to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 910324: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=910324 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: freebayes Version: 1.2.0-1 Severity: serious Tags: ftbfs freebayes fails to build from source in sbuild on unstable/amd64 when performing a parallel build. The linker invocation is run before all relevant objects are compiled. A build log ends with: | g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` bamleftalign.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/bamleftalign -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp` | g++: error: AlleleParser.o: No such file or directory | g++: error: Genotype.o: No such file or directory | g++: error: ResultData.o: No such file or directory | make[2]: *** [Makefile:81: ../bin/bamleftalign] Error 1 | make[2]: *** Waiting for unfinished jobs.... | make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' | make[1]: *** [Makefile:2: all] Error 2 | make[1]: Leaving directory '/<<PKGBUILDDIR>>' | dh_auto_build: make -j12 "INSTALL=install --strip-program=true" returned exit code 2 | make: *** [debian/rules:6: build] Error 2 | dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 The issue is also seen during reproducible builds: https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/freebayes_1.2.0-1.rbuild.log.gz Helmut
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--- Begin Message ---Source: freebayes Source-Version: 1.2.0-2 We believe that the bug you reported is fixed in the latest version of freebayes, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 910...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated freebayes package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 09 Oct 2018 07:56:21 +0200 Source: freebayes Binary: freebayes Architecture: source Version: 1.2.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Closes: 910324 Changes: freebayes (1.2.0-2) unstable; urgency=medium . * Standards-Version: 4.2.1 * Versioned Build-Depends: libvcflib-dev (>= 1.0.0~rc2+dfsg-2~) * debian/rules: + --no-parallel Closes: #910324 + Respect DEB_BUILD_OPTIONS in override_dh_auto_test Checksums-Sha1: 264b0b942abc6274a1cf0d0f6b3945c8fb660aa9 2171 freebayes_1.2.0-2.dsc 7ff12ab788e7865b025859c9eda94213a9b39915 10780 freebayes_1.2.0-2.debian.tar.xz Checksums-Sha256: 3f75bdb409afe1ef2004e460a7478e537a8f742bb01c1be197d10154e54cca8f 2171 freebayes_1.2.0-2.dsc a8b8e2c729adffb8d7d347f06edce1cb3d866da99fc59feec7ff3531db09e4fe 10780 freebayes_1.2.0-2.debian.tar.xz Files: 0523d4aa8d667e75a545f7deb7e692af 2171 science optional freebayes_1.2.0-2.dsc e0972cf8355275e1e775ed92235b7f34 10780 science optional freebayes_1.2.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlu8RVQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE1kg/+Kq+BfJ99buzqucq/kAGE4J/C8uxo7DXv /bhPsnhZPJKzyTGg99ovT+enH8fZJfk0z3EiNvWNXN2FLQh9vjHyBzi21VBt7IIV eybXG0+S7ryQP+kjPXM3cWvQHppOmelCU+WfCp0TAON9eyR1+XqZ4NDZcYd2Zh1s H4B7NAVz5R0ZrxmWqDmI1sG1GanCC4i+xQfLCtsvrXUiY3ih9g9Y/Fj3NfrZ/Gga r3HRHx31+RnZn6jqW4O942z/dzaMa/H+VsPRp1iZFnQtkdPKGYQj/LdV7tQMa7Ly YkLyfTnkYYugzfrvRkvbzTwI7GXejT7Gly+w5cSNo86urN9ZYw5Jp9L7gKAh4lBV AarvH0+v14ERKnKHTtdlCXMM2avnYoUvT0QUJ6XMBtmJ9msvRp9lZzt7t6E+Qmxo /N+YCX6WKt/ChgbYOIK6NNFQ7D0bS0TCLB5hNO+oe2+ldWtn72cAZtVN7SdmCOQy yZpXxju2Ay844h1offN74eGh6wujN0NtZ7FRsXpXdn0+WuYR92WxFpeXr/ddkGAm I3y5/eKI2GSPom7QrzKFo7W755Mk8ytnucZJvdyYyFC471nL5Uko5dVkTlvFPE8A 65/bFiDRddcMqr9wcchUnW6xovFbhRHWUnKQAYEUODZpmYktBQ2Ecq5U+6QlPd9f 9KNRC83bg30= =sqfP -----END PGP SIGNATURE-----
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