Source: fastqtl Version: 2.184+v7+dfsg-3 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build User: [email protected] Usertags: qa-doublebuild
Hi, This package fails to do build a binary-only build (not source) after a successful build (dpkg-buildpackage ; dpkg-buildpackage -b). 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/DoubleBuild Relevant part of the build log: > cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env > -us -uc -rfakeroot -b > ----------------------------------------------------------------------------------------------------------------------------- > > dpkg-buildpackage: info: source package fastqtl > dpkg-buildpackage: info: source version 2.184+v7+dfsg-3 > dpkg-buildpackage: info: source distribution unstable > dpkg-buildpackage: info: source changed by Ãtienne Mollier > <[email protected]> > dpkg-source --before-build . > dpkg-buildpackage: info: host architecture amd64 > debian/rules clean > dh clean --with python3 > dh_auto_clean > make -j8 clean > make[1]: Entering directory '/<<PKGBUILDDIR>>' > rm -f obj/*.o bin/fastQTL > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > dh_clean > debian/rules binary > dh binary --with python3 > dh_update_autotools_config > dh_autoreconf > dh_auto_configure > debian/rules override_dh_auto_build > make[1]: Entering directory '/<<PKGBUILDDIR>>' > mkdir -p /<<PKGBUILDDIR>>/obj/ > mkdir -p /<<PKGBUILDDIR>>/bin/ > dh_auto_build -- CXXFLAGS='-g -ffile-prefix-map=/<<PKGBUILDDIR>>=. > -fstack-protector-strong -Wformat -Werror=format-security -std=c++14' > make -j8 "INSTALL=install --strip-program=true" "CXXFLAGS=-g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14" > make[2]: Entering directory '/<<PKGBUILDDIR>>' > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisMapping.o -c src/analysisMapping.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisNominal.o -c src/analysisNominal.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisNominalBest.o -c src/analysisNominalBest.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisPermutation.o -c src/analysisPermutation.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisPermutationInteraction.o -c > src/analysisPermutationInteraction.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisPermutationPerGroup.o -c src/analysisPermutationPerGroup.cpp > -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/analysisPermutationSequence.o -c src/analysisPermutationSequence.cpp > -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/commands.o -c src/commands.cpp -Isrc > In file included from src/analysisPermutationPerGroup.cpp:17: > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > In file included from src/analysisPermutationSequence.cpp:17: > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > In file included from src/analysisNominal.cpp:17: > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > src/analysisPermutation.cpp: In member function âvoid > data::runPermutation(std::string, std::vector<int>)â: > src/analysisPermutation.cpp:75:27: warning: âvoid > std::random_shuffle(_RAIter, _RAIter) [with _RAIter = > __gnu_cxx::__normal_iterator<float*, vector<float> >]â is deprecated: use > 'std::shuffle' instead [-Wdeprecated-declarations] > 75 | random_shuffle(phenotype_curr.begin(), > phenotype_curr.end()); > | > ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > In file included from /usr/include/c++/13/algorithm:61, > from src/utils/utils.h:54, > from src/data.h:25, > from src/analysisPermutation.cpp:17: > /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here > 4581 | random_shuffle(_RandomAccessIterator __first, > _RandomAccessIterator __last) > | ^~~~~~~~~~~~~~ > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > src/analysisPermutationInteraction.cpp: In member function âvoid > data::runPermutationInteraction(std::string, int)â: > src/analysisPermutationInteraction.cpp:48:39: warning: âvoid > std::random_shuffle(_RAIter, _RAIter) [with _RAIter = > __gnu_cxx::__normal_iterator<float*, vector<float> >]â is deprecated: use > 'std::shuffle' instead [-Wdeprecated-declarations] > 48 | > random_shuffle(permuted_phenotypes[perm].begin(), > permuted_phenotypes[perm].end()); > | > ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > In file included from /usr/include/c++/13/algorithm:61, > from src/utils/utils.h:54, > from src/data.h:25, > from src/analysisPermutationInteraction.cpp:17: > /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here > 4581 | random_shuffle(_RandomAccessIterator __first, > _RandomAccessIterator __last) > | ^~~~~~~~~~~~~~ > src/analysisPermutationInteraction.cpp:76:47: warning: âvoid > std::random_shuffle(_RAIter, _RAIter) [with _RAIter = > __gnu_cxx::__normal_iterator<float*, vector<float> >]â is deprecated: use > 'std::shuffle' instead [-Wdeprecated-declarations] > 76 | > random_shuffle(phenotype_curr.begin(), phenotype_curr.end()); > | > ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here > 4581 | random_shuffle(_RandomAccessIterator __first, > _RandomAccessIterator __last) > | ^~~~~~~~~~~~~~ > In file included from src/analysisMapping.cpp:17: > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/df.o -c src/df.cpp -Isrc > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/fastQTL.o -c src/fastQTL.cpp -Isrc > In file included from src/analysisNominalBest.cpp:17: > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/management.o -c src/management.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/mle.o -c src/mle.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readCovariates.o -c src/readCovariates.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readGroups.o -c src/readGroups.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc > In file included from src/management.cpp:20: > src/data.h: In member function âdouble > data::getCorrelation(std::vector<float>&, std::vector<float>&)â: > src/data.h:180:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; > src/data.h:181:9: note: here > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > | ^~~~ > src/data.h:181:22: warning: this statement may fall through > [-Wimplicit-fallthrough=] > 181 | case 2: sum0 += vec1[i+1] * vec2[i+1]; > src/data.h:182:9: note: here > 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; > | ^~~~ > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readInteractions.o -c src/readInteractions.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/readThresholds.o -c src/readThresholds.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/residualizer.o -c src/residualizer.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/tabix.o -c src/utils/tabix.cpp -Isrc > g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o > obj/utils.o -c src/utils/utils.cpp -Isrc > src/utils/tabix.cpp: In constructor âTabix::Tabix(std::string&)â: > src/utils/tabix.cpp:17:22: warning: âint bgzf_is_bgzf(const char*)â is > deprecated: Use bgzf_compression() or hts_detect_format() instead > [-Wdeprecated-declarations] > 17 | if ( bgzf_is_bgzf(cfilename)!=1 ) > | ~~~~~~~~~~~~^~~~~~~~~~~ > In file included from src/utils/tabix.hpp:12, > from src/utils/tabix.cpp:6: > /usr/include/htslib/bgzf.h:270:9: note: declared here > 270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use > bgzf_compression() or hts_detect_format() instead"); > | ^~~~~~~~~~~~ > src/utils/utils.cpp: In function âvoid > putils::random_shuffle(std::vector<std::vector<float> >&)â: > src/utils/utils.cpp:133:31: warning: âvoid std::random_shuffle(_RAIter, > _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<int*, vector<int> >]â > is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] > 133 | random_shuffle(O.begin(), O.end()); > | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ > In file included from /usr/include/c++/13/algorithm:61, > from src/utils/utils.h:54, > from src/utils/utils.cpp:17: > /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here > 4581 | random_shuffle(_RandomAccessIterator __first, > _RandomAccessIterator __last) > | ^~~~~~~~~~~~~~ > g++ -std=c++11 -O3 -Wl,-z,relro -Wl,-z,now obj/analysisMapping.o > obj/analysisNominal.o obj/analysisNominalBest.o obj/analysisPermutation.o > obj/analysisPermutationInteraction.o obj/analysisPermutationPerGroup.o > obj/analysisPermutationSequence.o obj/commands.o obj/df.o obj/fastQTL.o > obj/management.o obj/mle.o obj/readCovariates.o obj/readGenotypes.o > obj/readGroups.o obj/readInclusionsExclusions.o obj/readInteractions.o > obj/readPhenotypes.o obj/readThresholds.o obj/residualizer.o obj/tabix.o > obj/utils.o -lRmath -lhts -lm -lz -lbz2 -lboost_iostreams > -lboost_program_options -lgslcblas -lgsl -lblas -o bin/fastQTL > make[2]: Leaving directory '/<<PKGBUILDDIR>>' > cd /<<PKGBUILDDIR>>/example/ && \ > tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s > --owner=root --group=root --numeric-owner > covariates.txt.gz > examples.tar.xz > tar: examples.tar.xz: File shrank by 16262880 bytes; padding with zeros > genotypes.vcf.gz > genotypes.vcf.gz.tbi > interaction.txt > phenotypes.bed.gz > phenotypes.bed.gz.tbi > make[1]: *** [debian/rules:16: override_dh_auto_build] Error 1 > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > make: *** [debian/rules:10: binary] Error 2 > dpkg-buildpackage: error: debian/rules binary subprocess returned exit status > 2 > > E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage > --sanitize-env -us -uc -rfakeroot -b' failed to run. The full build log is available from: http://qa-logs.debian.net/2023/08/16/fastqtl_2.184+v7+dfsg-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.
