* 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