sci-biology:hmmer-2.3.2-r5:20221028-235120.log

sci-biology:hmmer-2.3.2-r5:20221028-235120.log (text/plain), 37.08 KB, created by Toralf Förster on 2022-10-29 09:44:19 UTC

 * Package:    sci-biology/hmmer-2.3.2-r5:2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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'