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Gentoo's Bugzilla – Attachment 835117 Details for
Bug 882279
sci-biology/hmmer-2.3.2-r5: hmmcalibrate.c:646:3: warning: implicit declaration of function ‘pthread_setconcurrency’ [-Wimplicit-function-declaration]
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sci-biology:hmmer-2.3.2-r5:20221120-173030.log
sci-biology:hmmer-2.3.2-r5:20221120-173030.log (text/plain), 32.52 KB, created by
Toralf Förster
on 2022-11-20 17:38:24 UTC
(
hide
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Description:
sci-biology:hmmer-2.3.2-r5:20221120-173030.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2022-11-20 17:38:24 UTC
Size:
32.52 KB
patch
obsolete
> * Package: sci-biology/hmmer-2.3.2-r5:2 > * 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-r5/work >>>> Source unpacked in /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work >>>> Preparing source in /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/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-r5/work/hmmer-2.3.2 ... > * 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 > * econf: updating hmmer-2.3.2/squid/config.sub with /usr/share/gnuconfig/config.sub >./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 --enable-threads --disable-altivec >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... /usr/bin/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: enabled POSIX multithreading support >checking for pthread_setconcurrency... yes >checking for pthread_attr_setscope... yes >checking for the pthreads library -lpthreads... no >checking whether pthreads work without any flags... yes >checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE >checking if more special flags are required for pthreads... no >checking for cc_r... x86_64-pc-linux-gnu-gcc >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' '--enable-threads' '--disable-altivec' 'CFLAGS=-pipe -march=native -fno-diagnostics-color -O2' '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... /usr/bin/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-r5/work/hmmer-2.3.2 ... >make -j4 'AR=x86_64-pc-linux-gnu-ar rcs' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/squid' >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c afetch_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c a2m.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c aligneval.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c alignio.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c clustal.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c cluster.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c dayhoff.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c eps.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c file.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c getopt.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c gki.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c gsi.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c hsregex.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c iupac.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c msa.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c msf.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c phylip.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c revcomp.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c rk.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c selex.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c seqencode.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c shuffle.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sqerror.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sqio.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c squidcore.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sre_ctype.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sre_math.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sre_random.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sre_string.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c ssi.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c stack.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c stockholm.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c stopwatch.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c translate.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c types.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c vectorops.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c weight.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c alistat_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c compalign_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c compstruct_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c revcomp_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c seqsplit_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c seqstat_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sfetch_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c shuffle_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sindex_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c sreformat_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c translate_main.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -c weight_main.c >x86_64-pc-linux-gnu-ar rcs 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-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o afetch afetch_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o alistat alistat_main.o 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 -lm >x86_64-pc-linux-gnu-ranlib libsquid.a >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o compalign compalign_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o compstruct compstruct_main.o 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 -lm >chmod 644 libsquid.a >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o revcomp revcomp_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o seqsplit seqsplit_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o seqstat seqstat_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o sfetch sfetch_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o shuffle shuffle_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o sindex sindex_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o sreformat sreformat_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o translate translate_main.o 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 -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o weight weight_main.o 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 -lm >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/squid' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/squid' >make[1]: Nothing to be done for 'module'. >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/squid' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/src' >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmalign.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c alphabet.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c core_algorithms.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c debug.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c display.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c emit.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c emulation.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c fast_algorithms.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c histogram.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmio.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c mathsupport.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c masks.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c misc.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c modelmakers.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c plan7.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c plan9.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c postprob.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c prior.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c pvm.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c threads.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c tophits.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c trace.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmbuild.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmcalibrate.c >hmmcalibrate.c: In function âworkpool_startâ: >hmmcalibrate.c:646:3: warning: implicit declaration of function âpthread_setconcurrencyâ [-Wimplicit-function-declaration] > 646 | pthread_setconcurrency(num_threads+1); > | ^~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmconvert.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmemit.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmfetch.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmindex.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmpfam.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -c hmmsearch.c >hmmpfam.c: In function âworkpool_startâ: >hmmpfam.c:1032:3: warning: implicit declaration of function âpthread_setconcurrencyâ [-Wimplicit-function-declaration] > 1032 | pthread_setconcurrency(num_threads+1); > | ^~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -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 >hmmsearch.c: In function âworkpool_startâ: >hmmsearch.c:1021:3: warning: implicit declaration of function âpthread_setconcurrencyâ [-Wimplicit-function-declaration] > 1021 | pthread_setconcurrency(num_threads+1); > | ^~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmcalibrate hmmcalibrate.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmconvert hmmconvert.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmemit hmmemit.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmfetch hmmfetch.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmindex hmmindex.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmpfam hmmpfam.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmbuild hmmbuild.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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -L../squid -o hmmsearch hmmsearch.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 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/src' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/src' >x86_64-pc-linux-gnu-ar rcs 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 >chmod 644 libhmmer.a >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/src' >make[1]: Entering directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/testsuite' >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c alignalign_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c evd_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c masks_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c parsingviterbi_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c tophits_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c trace_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c viterbi_exercise.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -DHAVE_CONFIG_H -I../squid -I../src -c weeviterbi_test.c >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -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 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o evd_test -L../squid -L../src evd_test.o -lhmmer -lsquid -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o masks_test -L../squid -L../src masks_test.o -lhmmer -lsquid -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o parsingviterbi_test -L../squid -L../src parsingviterbi_test.o -lhmmer -lsquid -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o tophits_test -L../squid -L../src tophits_test.o -lhmmer -lsquid -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o trace_test -L../squid -L../src trace_test.o -lhmmer -lsquid -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o viterbi_exercise -L../squid -L../src viterbi_exercise.o -lhmmer -lsquid -lm >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DHAVE_CONFIG_H -o weeviterbi_test -L../squid -L../src weeviterbi_test.o -lhmmer -lsquid -lm >make[1]: Leaving directory '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2/testsuite' >>>> Source compiled. > * Skipping make test/check due to ebuild restriction. >>>> Test phase [disabled because of RESTRICT=test]: sci-biology/hmmer-2.3.2-r5 > >>>> Install sci-biology/hmmer-2.3.2-r5 into /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image >make -j4 DESTDIR=/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image install >mkdir -p /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/bin >mkdir -p /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/share/man/man1 >for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ > cp src/$file /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/bin/;\ >done >for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ > cp documentation/man/$file.man /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/share/man/man1/$file.1;\ >done >>>> Completed installing sci-biology/hmmer-2.3.2-r5 into /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image > > * Final size of build directory: 12124 KiB (11.8 MiB) > * Final size of installed tree: 6300 KiB ( 6.1 MiB) > > * > * QA Notice: Package triggers severe warnings which indicate that it > * may exhibit random runtime failures. > * > * hmmcalibrate.c:646:3: warning: implicit declaration of function âpthread_setconcurrencyâ [-Wimplicit-function-declaration] > * hmmpfam.c:1032:3: warning: implicit declaration of function âpthread_setconcurrencyâ [-Wimplicit-function-declaration] > * hmmsearch.c:1021:3: warning: implicit declaration of function âpthread_setconcurrencyâ [-Wimplicit-function-declaration] > * > * Please file a bug about this at https://bugs.gentoo.org/ > * with the maintainer of the package. > * > * ERROR: sci-biology/hmmer-2.3.2-r5::gentoo failed: > * install aborted due to severe warnings shown above > * > * Call stack: > * misc-functions.sh, line 670: Called install_qa_check > * misc-functions.sh, line 134: Called source 'install_symlink_html_docs' > * 90gcc-warnings, line 197: Called gcc_warn_check > * 90gcc-warnings, line 183: Called die > * The specific snippet of code: > * die "install aborted due to severe warnings shown above" > * > * If you need support, post the output of `emerge --info '=sci-biology/hmmer-2.3.2-r5::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/hmmer-2.3.2-r5::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:hmmer-2.3.2-r5:20221120-173030.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image' > * S: '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2' >
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