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Gentoo's Bugzilla – Attachment 641712 Details for
Bug 725306
sci-biology/hmmer-2.3.2-r4 fails to compile: ld: cannot find -lsquid
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build.log
build.log (text/plain), 24.23 KB, created by
Agostino Sarubbo
on 2020-05-25 13:10:21 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-05-25 13:10:21 UTC
Size:
24.23 KB
patch
obsolete
> * Package: sci-biology/hmmer-2.3.2-r4 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking hmmer-2.3.2.tar.gz to /var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work >>>> Source unpacked in /var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work >>>> Preparing source in /var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2 ... > * Applying hmmer-2.3.2-fix-perl-shebangs.patch ... > [ ok ] > * Applying hmmer-2.3.2-fix-build-system-destdir.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2 ... > * econf: updating hmmer-2.3.2/squid/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating hmmer-2.3.2/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating hmmer-2.3.2/config.guess with /usr/share/gnuconfig/config.guess >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --enable-lfs --disable-altivec --disable-threads >configure: configuring HMMER for your system. >configure: This is a full source distribution - using full config >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking for C compiler default output... a.out >checking whether the C compiler works... yes >checking whether we are cross compiling... no >checking for suffix of executables... >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ANSI C... none needed >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking for ar... : >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking whether your make is GNU make... yes, it is. >configure: Altivec/PowerPC optimization disabled >configure: configured for optional LFS, large file support >configure: POSIX multithreading support disabled >checking for ntohs... yes >checking for ntohl... yes >checking for htons... yes >checking for htonl... yes >configure: creating ./config.status >config.status: creating src/Makefile >config.status: creating testsuite/Makefile >config.status: creating Makefile >config.status: creating src/config.h >configure: configuring in squid >configure: running /bin/sh './configure' --prefix=/usr '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--enable-lfs' '--disable-altivec' '--disable-threads' 'CC=x86_64-pc-linux-gnu-gcc' 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' --cache-file=/dev/null --srcdir=. >configure: configuring the SQUID library for your system. >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking for C compiler default output... a.out >checking whether the C compiler works... yes >checking whether we are cross compiling... no >checking for suffix of executables... >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ANSI C... none needed >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking for ar... : >checking whether your make is GNU make... yes, it is. >checking whether byte ordering is bigendian... no >checking for ntohs... yes >checking for ntohl... yes >checking for htons... yes >checking for htonl... yes >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for egrep... grep -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for unsigned short... yes >checking size of unsigned short... 2 >checking for unsigned int... yes >checking size of unsigned int... 4 >checking for unsigned long... yes >checking size of unsigned long... 8 >checking for unsigned long long... yes >checking size of unsigned long long... 8 >checking for strtoul... yes >checking for strtoull... yes >checking whether fpos_t is an arithmetic datatype... no. >checking for strtoull... (cached) yes >checking for ftello... yes >checking for fseeko... yes >checking for ftello64... yes >checking for fseeko64... yes >checking for ftell64... no >checking for fseek64... no >checking for stat64... yes >checking for struct stat64... no! >checking for off_t... yes >checking size of off_t... 8 >checking for off64_t... no >checking size of off64_t... 0 >checking for fpos_t... yes >checking size of fpos_t... 16 >configure: configured for optional LFS, large file support >configure: creating ./config.status >config.status: creating Makefile >config.status: creating Testsuite/Makefile >config.status: creating squid.h >config.status: creating squidconf.h >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2 ... >make -j4 >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/squid' >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c afetch_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c a2m.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c aligneval.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c alignio.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c clustal.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c cluster.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c dayhoff.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c eps.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c file.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c getopt.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c gki.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c gsi.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c hsregex.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c iupac.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c msa.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c msf.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c phylip.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c revcomp.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c rk.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c selex.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c seqencode.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c shuffle.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sqerror.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sqio.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c squidcore.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sre_ctype.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sre_math.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sre_random.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sre_string.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c ssi.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c stack.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c stockholm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c stopwatch.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c translate.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c types.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c vectorops.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c weight.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c alistat_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c compalign_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c compstruct_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c revcomp_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c seqsplit_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c seqstat_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sfetch_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c shuffle_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sindex_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c sreformat_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c translate_main.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -c weight_main.c >: rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o >x86_64-pc-linux-gnu-ranlib libsquid.a >x86_64-pc-linux-gnu-ranlib: 'libsquid.a': No such file >make[1]: *** [Makefile:169: libsquid.a] Error 1 >make[1]: *** Waiting for unfinished jobs.... >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/squid' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/squid' >: rcv libsquid.a a2m.o aligneval.o alignio.o clustal.o cluster.o dayhoff.o eps.o file.o getopt.o gki.o gsi.o hsregex.o iupac.o msa.o msf.o phylip.o revcomp.o rk.o selex.o seqencode.o shuffle.o sqerror.o sqio.o squidcore.o sre_ctype.o sre_math.o sre_random.o sre_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o vectorops.o weight.o >x86_64-pc-linux-gnu-ranlib libsquid.a >x86_64-pc-linux-gnu-ranlib: 'libsquid.a': No such file >make[1]: *** [Makefile:169: libsquid.a] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/squid' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/src' >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmalign.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c alphabet.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c core_algorithms.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c debug.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c display.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c emit.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c emulation.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c fast_algorithms.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c histogram.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmio.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c mathsupport.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c masks.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c misc.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c modelmakers.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c plan7.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c plan9.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c postprob.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c prior.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c pvm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c threads.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c tophits.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c trace.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmbuild.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmcalibrate.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmconvert.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmemit.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmfetch.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmindex.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmpfam.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -c hmmsearch.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lsquid -lm >/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lsquid >collect2: error: ld returned 1 exit status >make[1]: *** [Makefile:97: hmmalign] Error 1 >make[1]: *** Waiting for unfinished jobs.... >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/src' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/src' >: rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o >x86_64-pc-linux-gnu-ranlib libhmmer.a >x86_64-pc-linux-gnu-ranlib: 'libhmmer.a': No such file >make[1]: *** [Makefile:107: libhmmer.a] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/src' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/testsuite' >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c alignalign_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c evd_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c masks_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c parsingviterbi_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c tophits_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c trace_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c viterbi_exercise.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -DHAVE_CONFIG_H -I../squid -I../src -c weeviterbi_test.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o alignalign_test -L../squid -L../src alignalign_test.o -lhmmer -lsquid -lm >/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lhmmer >/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lsquid >collect2: error: ld returned 1 exit status >make[1]: *** [Makefile:48: alignalign_test] Error 1 >make[1]: *** Waiting for unfinished jobs.... >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2/testsuite' >make: *** [Makefile:84: all] Error 2 > * ERROR: sci-biology/hmmer-2.3.2-r4::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/hmmer-2.3.2-r4::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/hmmer-2.3.2-r4::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-biology/hmmer-2.3.2-r4:20200525-121430.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2' > * S: '/var/tmp/portage/sci-biology/hmmer-2.3.2-r4/work/hmmer-2.3.2' > > > >emerge --info: >Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 >KiB Mem: 16011344 total, 1832892 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Mon, 25 May 2020 12:35:49 +0000 >sh bash 5.0_p17 >ld GNU ld (Gentoo 2.34 p4) 2.34.0 >app-shells/bash: 5.0_p17::gentoo >dev-lang/perl: 5.30.2-r2::gentoo >dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.18::gentoo >sys-devel/autoconf: 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r1::gentoo >sys-devel/gcc: 10.1.0::gentoo >sys-devel/gcc-config: 2.3::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) >sys-libs/glibc: 2.31-r3::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-jobs: 1 > sync-rsync-verify-max-age: 24 > sync-rsync-extra-opts: > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="*" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-gcc" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-g++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >DISTDIR="/usr/portage/distfiles" >EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" >ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" >MAKEOPTS="-j4" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS >
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bug 725306
: 641712