Source: bowtie Version: 1.2.0+dfsg-1 Severity: serious Hi,
bowtie FTBFS on mips64el with this error: > g++ -w -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DWITH_TBB > -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 > -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat > -Werror=format-security -g -O2 -fdebug-prefix-map=.=. > -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro > -Wl,-z,now\"" -Wl,--hash-style=both -DWITH_TBB -DNO_SPINLOCK > -DWITH_QUEUELOCK=1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 > -fdebug-prefix-map=/«BUILDDIR»/bowtie-1.2.0+dfsg=. -fstack-protector-strong > -Wformat -Werror=format-security -g -O2 > -fdebug-prefix-map=/«BUILDDIR»/bowtie-1.2.0+dfsg=. -fstack-protector-strong > -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" > -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog > --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1 | sed > 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE > -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ > -I /usr/include/seqan \ > -o bowtie-build-s ebwt_build.cpp \ > ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp > bowtie_build_main.cpp \ > -lpthread -ltbb -ltbbmalloc_proxy > /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI > collect2: error: ld returned 1 exit status > Makefile:258: recipe for target 'bowtie-build-s' failed > make[2]: *** [bowtie-build-s] Error 1 > make[2]: Leaving directory '/«BUILDDIR»/bowtie-1.2.0+dfsg' > debian/rules:17: recipe for target 'override_dh_auto_build' failed > make[1]: *** [override_dh_auto_build] Error 2 > make[1]: Leaving directory '/«BUILDDIR»/bowtie-1.2.0+dfsg' > debian/rules:14: recipe for target 'build-arch' failed > make: *** [build-arch] Error 2 > dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 This is because mips* does not currently support -Wl,--hash-style=both. Unfortunately the MIPS linker (ab)uses the dynamic symbol table making it much harded to add support for this to BFD so it has not been done yet. I think the gnu hash style is just an optimization, so it should be OK to remove this option completely. --hash-style=gnu is already the default on all all other architectures and has been for a few years now so removing it on Debian should not affect other architectures. Thanks, James
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