Your message dated Mon, 3 Sep 2018 16:07:59 +0200 with message-id <[email protected]> and subject line gmap: FTBFS on stretch/amd64 if CPU has SSE2 and nothing more has caused the Debian Bug report #902820, regarding gmap: FTBFS on stretch/amd64 if CPU has SSE2 and nothing more 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 [email protected] immediately.) -- 902820: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=902820 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: src:gmap Version: 2017-01-14-1 Severity: serious Tags: ftbfs Dear maintainer: I tried to build this package in stretch but it failed: -------------------------------------------------------------------------------- [...] debian/rules build-arch dh build-arch --parallel --with autotools_dev dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel dh_autotools-dev_updateconfig -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --enable-shared --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap checking package version... 2017-01-14 loading default site script ./config.site checking CFLAGS... -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security checking MPI_CFLAGS... [... snipped ...] gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function 'SAM_header_change_HD_tosorted': samheader.c:201:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),CHUNK,input); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:206:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof(char),headerlen,input); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-uintlist.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-genome128_hr.o gmap_sse2-genome_sites.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-merge.o gmap_sse2-in dexdb.o gmap_sse2-indexdb_hr.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_s se2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getopt.o gmap_sse2-getopt1.o gmap_sse2-gmap.o -lz -lbz2 -lm libtool: link: gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-uintlist.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-genome128_hr.o gmap_sse2-genome_sites.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-merge.o gmap_sse2-indexdb.o gmap_sse2-indexdb _hr.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-outbuffer.o gmap_sse2 -chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getopt.o gmap_sse2-getopt1.o gmap_sse2-gmap.o -lz -lbz2 -lm -pthread gmap_sse2-oligoindex_hr.o: In function `store_positions_fwd_simd': ./src/oligoindex_hr.c:21180: undefined reference to `Atoi_reduce_ct' ./src/oligoindex_hr.c:21180: undefined reference to `Atoi_reduce_ct' ./src/oligoindex_hr.c:21181: undefined reference to `Atoi_reduce_ct' ./src/oligoindex_hr.c:21181: undefined reference to `Atoi_reduce_ct' ./src/oligoindex_hr.c:21182: undefined reference to `Atoi_reduce_ct' ./src/oligoindex_hr.c:21184: undefined reference to `Atoi_reduce_ga' ./src/oligoindex_hr.c:21184: undefined reference to `Atoi_reduce_ga' ./src/oligoindex_hr.c:21185: undefined reference to `Atoi_reduce_ga' ./src/oligoindex_hr.c:21185: undefined reference to `Atoi_reduce_ga' ./src/oligoindex_hr.c:21186: undefined reference to `Atoi_reduce_ga' collect2: error: ld returned 1 exit status Makefile:3423: recipe for target 'gmap.sse2' failed make[3]: *** [gmap.sse2] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/src' Makefile:3292: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' Makefile:432: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: make -j1 returned exit code 2 debian/rules:19: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- A diff between a failed build and a successful build (in a machine having the extra features) yields this result: @@ -448,16 +448,25 @@ checking compiler is defective and requires an immediate in sse2 shift commands... no checking for whether simd is enabled... not specified so enabled by default checking for sse2 support... yes -checking for ssse3 support... no -checking for sse4.1 support... no -checking for sse4.2 support... no -checking for popcnt support... no +checking for ssse3 support... yes +checking for sse4.1 support... yes +checking for sse4.2 support... yes +checking for popcnt support... yes checking for bmi1 support... no -checking for avx2 support... no +checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes +checking whether C compiler accepts -msse2 -mssse3... yes +checking for tmmintrin.h header file... yes +checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes +checking for smmintrin.h header file... yes +checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes +checking for nmmintrin.h header file... yes +checking for mm_popcnt support... yes +checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2... yes +checking for immintrin.h header file... yes checking gmapdb... /var/cache/gmap checking MAX_STACK_READLENGTH... 300 checking for zlib support... enabled @@ -516,8 +525,8 @@ checking standard linker flags to be used... checking pthread compiler flags to be used... -pthread checking popcnt flags to be used... -mpopcnt -checking compile level... sse2 -checking SSE2 compiler flags to be used... -msse2 +checking compile level... avx2 +checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 AFAIK on Debian/amd64 only SSE2 is allowed to be assumed by default. I tried to compare my build logs with official ones, but there is none: https://buildd.debian.org/status/package.php?p=gmap (( Could you please consider source-only uploads? i.e. "dpkg-buildpackage -S" )). In either case, I'm putting my failed build logs here in case you need them, they were made with sbuild on different virtual machines running Debian stretch: https://people.debian.org/~sanvila/build-logs/gmap/ (Note: All the failures seem to be related to detection of CPU features, but since the machines are diverse, the failures are not always the same). Thanks.
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--- Begin Message ---Package: gmap Version: 2018-07-04-3 Upstream provided patch fixing the issue.
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