Source: freebayes Version: 1.3.6-2 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230216 ftbfs-bookworm
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ > libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF > libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o > libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp > In file included from ../src/AlleleParser.h:32, > from ../src/DataLikelihood.h:20, > from ../src/DataLikelihood.cpp:1: > /usr/include/vcflib/Variant.h:36:10: fatal error: wavefront/wfa.hpp: No such > file or directory > 36 | #include "wavefront/wfa.hpp" > | ^~~~~~~~~~~~~~~~~~~ > compilation terminated. > [2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ > libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF > libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o > libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp > FAILED: libfreebayes_common.a.p/src_AlleleParser.cpp.o > c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ > libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF > libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o > libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp > In file included from ../src/AlleleParser.h:32, > from ../src/AlleleParser.cpp:1: > /usr/include/vcflib/Variant.h:36:10: fatal error: wavefront/wfa.hpp: No such > file or directory > 36 | #include "wavefront/wfa.hpp" > | ^~~~~~~~~~~~~~~~~~~ > compilation terminated. > [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ > libfreebayes_common.a.p/src_Contamination.cpp.o -MF > libfreebayes_common.a.p/src_Contamination.cpp.o.d -o > libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp > [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o > -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o > libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp > [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ > libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF > libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o > libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp > [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o > -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o > libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp > [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ > libfreebayes_common.a.p/src_BedReader.cpp.o -MF > libfreebayes_common.a.p/src_BedReader.cpp.o.d -o > libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp > [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath > -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack > -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always > -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 > -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread > -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable > -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o > -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o > libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp > ../src/Allele.cpp: In member function ‘const short int > Allele::currentQuality() const’: > ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not > handled in switch [-Wswitch] > 160 | switch (this->type) { > | ^ > ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not > handled in switch [-Wswitch] > ninja: build stopped: subcommand failed. > dh_auto_build: error: cd build && LC_ALL=C.UTF-8 ninja -j8 -v returned exit > code 1 > make: *** [debian/rules:6: binary] Error 25 The full build log is available from: http://qa-logs.debian.net/2023/02/16/freebayes_1.3.6-2_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230216;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230216&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! 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.