* 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... clang 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 clang accepts -g... yes checking for clang 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... clang 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' 'CC=clang' 'CFLAGS=-pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int' '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... clang 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 clang accepts -g... yes checking for clang 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... clang -E checking for egrep... grep -E checking for ANSI C header files... no 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. '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/temp/clang14.log' -> '/var/tmp/clang/sci-biology/hmmer-2.3.2-r5/clang14.log' '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/temp/clang15.log' -> '/var/tmp/clang/sci-biology/hmmer-2.3.2-r5/clang15.log' >>> 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' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c afetch_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c a2m.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c aligneval.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c alignio.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c clustal.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c cluster.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c dayhoff.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c eps.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c file.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c getopt.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c gki.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c gsi.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c hsregex.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c iupac.c hsregex.c:334:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regcomp(exp) ^ hsregex.c:423:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] reg(cp, paren, flagp) ^ hsregex.c:423:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:493:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regbranch(cp, flagp) ^ hsregex.c:493:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:534:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regpiece(cp, flagp) ^ hsregex.c:534:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:603:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regatom(cp, flagp) ^ hsregex.c:603:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:714:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regnode(cp, op) ^ hsregex.c:714:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:739:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regc(cp, b) ^ hsregex.c:739:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:755:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] reginsert(cp, op, opnd) ^ hsregex.c:755:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:780:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regtail(cp, p, val) ^ hsregex.c:780:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:805:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regoptail(cp, p, val) ^ hsregex.c:805:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:847:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regexec(prog, str) ^ hsregex.c:901:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regtry(ep, prog, string) ^ hsregex.c:901:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:937:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regmatch(ep, prog) ^ hsregex.c:937:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:1096:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regrepeat(ep, node) ^ hsregex.c:1096:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:1135:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regnext(p) ^ hsregex.c:1135:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] hsregex.c:1281:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regsub(rp, source, dest) ^ hsregex.c:1330:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regerror(s) ^ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c msa.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c msf.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c phylip.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c revcomp.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c rk.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c selex.c 30 warnings generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c seqencode.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c shuffle.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sqerror.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sqio.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c squidcore.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_ctype.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_math.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_random.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sre_string.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c ssi.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c stack.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c stockholm.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c stopwatch.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c translate.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c types.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c vectorops.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c weight.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c alistat_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c compalign_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c compstruct_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c revcomp_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c seqsplit_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c seqstat_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sfetch_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c shuffle_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sindex_main.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c sreformat_main.c sindex_main.c:178:58: warning: comparison of array 'sqinfo.desc' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (do_pfamseq && sfp->format == SQFILE_FASTA && sqinfo.desc != NULL) { ~~~~~~~^~~~ ~~~~ clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -c translate_main.c 1 warning generated. clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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-ranlib libsquid.a chmod 644 libsquid.a clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c hmmalign.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c alphabet.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c core_algorithms.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c debug.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c display.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c emit.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c emulation.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c fast_algorithms.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c histogram.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c hmmio.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c mathsupport.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c masks.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c misc.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c modelmakers.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c plan7.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c plan9.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c postprob.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c prior.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c pvm.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c threads.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c tophits.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c trace.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c hmmbuild.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c hmmcalibrate.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -c hmmconvert.c hmmcalibrate.c:646:3: error: call to undeclared function 'pthread_setconcurrency'; ISO C99 and later do not support implicit function declarations [-Werror,-Wimplicit-function-declaration] pthread_setconcurrency(num_threads+1); ^ 1 error generated. make[1]: *** [Makefile:89: hmmcalibrate.o] Error 1 make[1]: *** Waiting for unfinished jobs.... 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' clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c alignalign_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c evd_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c masks_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c parsingviterbi_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c tophits_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c trace_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c viterbi_exercise.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -DHAVE_CONFIG_H -I../squid -I../src -c weeviterbi_test.c clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 clang -pipe -march=native -fno-diagnostics-color -O2 -Werror=implicit-function-declaration -Werror=implicit-int -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 cp: cannot stat 'src/hmmalign': No such file or directory cp: cannot stat 'src/hmmbuild': No such file or directory cp: cannot stat 'src/hmmcalibrate': No such file or directory cp: cannot stat 'src/hmmconvert': No such file or directory cp: cannot stat 'src/hmmemit': No such file or directory cp: cannot stat 'src/hmmfetch': No such file or directory cp: cannot stat 'src/hmmindex': No such file or directory cp: cannot stat 'src/hmmpfam': No such file or directory cp: cannot stat 'src/hmmsearch': No such file or directory make: *** [Makefile:114: install] Error 1 * ERROR: sci-biology/hmmer-2.3.2-r5::gentoo failed (install phase): * emake failed * * 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-r5:20221028-235120.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/work/hmmer-2.3.2' * S: '/var/tmp/portage/sci-biology/hmmer-2.3.2-r5/work/hmmer-2.3.2'