[Debian-med-packaging] Bug#864439: bowtie: FTBFS on mips64el - /usr/bin/ld: .gnu.hash is incompatible with the MIPS ABI

James Cowgill jcowgill at debian.org
Thu Jun 8 16:37:00 UTC 2017


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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