printf '

' | fink --no-use-binary-dist --yes  --build-as-nobody rebuild hmmer 2>&1
The package 'hmmer' will be built without being installed.
Reading build dependency for hmmer-2.2g-3...
Reading dependency for hmmer-2.2g-3...
Reading build conflict for hmmer-2.2g-3...
The following package will be rebuilt:
 hmmer
curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/hmmer-2.2g.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 45  909k   45  411k    0     0   428k      0  0:00:02 --:--:--  0:00:02  427k
100  909k  100  909k    0     0   628k      0  0:00:01  0:00:01 --:--:--  628k
curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -o 7tm_1 http://distfiles.master.finkmirrors.net/distfiles/7tm_1
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 43  100k   43 44679    0     0   100k      0  0:00:01 --:--:--  0:00:01  100k
100  100k  100  100k    0     0   187k      0 --:--:-- --:--:-- --:--:--  187k
curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -o P08908.fasta http://distfiles.master.finkmirrors.net/distfiles/P08908.fasta
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   556  100   556    0     0   1034      0 --:--:-- --:--:-- --:--:--  1035
Setting runtime build-lock...
dpkg-deb -b /sw/build.build/root-fink-buildlock-hmmer-2.2g-3 /sw/build.build
dpkg-deb: building package `fink-buildlock-hmmer-2.2g-3' in `/sw/build.build/fink-buildlock-hmmer-2.2g-3_2014.08.02-12.40.28_darwin-x86_64.deb'.
Installing build-lock package...
/sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-hmmer-2.2g-3_2014.08.02-12.40.28_darwin-x86_64.deb
Selecting previously deselected package fink-buildlock-hmmer-2.2g-3.
(Reading database ... 4296 files and directories currently installed.)
Unpacking fink-buildlock-hmmer-2.2g-3 (from .../fink-buildlock-hmmer-2.2g-3_2014.08.02-12.40.28_darwin-x86_64.deb) ...
Setting up fink-buildlock-hmmer-2.2g-3 (2014.08.02-12.40.28) ...

sudo -u fink-bld [ENV] sh -c /tmp/fink.0dgDI
env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner --no-same-permissions -xvf /sw/src/hmmer-2.2g.tar.gz
hmmer-2.2g/
hmmer-2.2g/src/
hmmer-2.2g/src/hmmpfam.c
hmmer-2.2g/src/pvm.c
hmmer-2.2g/src/trace.c
hmmer-2.2g/src/plan7.c
hmmer-2.2g/src/plan9.c
hmmer-2.2g/src/hmmindex.c
hmmer-2.2g/src/hmmfetch.c
hmmer-2.2g/src/camJul97.c
hmmer-2.2g/src/Makefile.in
hmmer-2.2g/src/weetest.c
hmmer-2.2g/src/debug.c
hmmer-2.2g/src/masks.c
hmmer-2.2g/src/postprob.h
hmmer-2.2g/src/postprob.c
hmmer-2.2g/src/states.c
hmmer-2.2g/src/structs.h
hmmer-2.2g/src/core_algorithms.c
hmmer-2.2g/src/hmmcalibrate-pvm.c
hmmer-2.2g/src/emulation.c
hmmer-2.2g/src/threads.c
hmmer-2.2g/src/config.h
hmmer-2.2g/src/hmmpfam-pvm.c
hmmer-2.2g/src/globals.h
hmmer-2.2g/src/mathsupport.c
hmmer-2.2g/src/hmmsearch-pvm.c
hmmer-2.2g/src/prior.c
hmmer-2.2g/src/misc.c
hmmer-2.2g/src/hmmpostal.c
hmmer-2.2g/src/display.c
hmmer-2.2g/src/modelmakers.c
hmmer-2.2g/src/hmmcalibrate.c
hmmer-2.2g/src/hmmemit.c
hmmer-2.2g/src/hmmconvert.c
hmmer-2.2g/src/alphabet.c
hmmer-2.2g/src/hmmsearch.c
hmmer-2.2g/src/hmmio.c
hmmer-2.2g/src/emit.c
hmmer-2.2g/src/histogram.c
hmmer-2.2g/src/tophits.c
hmmer-2.2g/src/version.h
hmmer-2.2g/src/funcs.h
hmmer-2.2g/src/hmmbuild.c
hmmer-2.2g/src/hmmalign.c
hmmer-2.2g/config.guess
hmmer-2.2g/install-sh
hmmer-2.2g/Makefile.in
hmmer-2.2g/Userguide.pdf
hmmer-2.2g/LICENSE
hmmer-2.2g/INSTALL
hmmer-2.2g/squid/
hmmer-2.2g/squid/Man/
hmmer-2.2g/squid/Man/shuffle.man
hmmer-2.2g/squid/Man/alistat.man
hmmer-2.2g/squid/Man/sreformat.man
hmmer-2.2g/squid/Man/afetch.man
hmmer-2.2g/squid/Man/sfetch.man
hmmer-2.2g/squid/Man/seqstat.man
hmmer-2.2g/squid/aligneval.c
hmmer-2.2g/squid/Docs/
hmmer-2.2g/squid/Docs/gsi-format.tex
hmmer-2.2g/squid/Docs/squid-format.tex
hmmer-2.2g/squid/Docs/intro.tex
hmmer-2.2g/squid/Docs/abstract.tex
hmmer-2.2g/squid/Docs/ssi-format.tex
hmmer-2.2g/squid/Docs/formats.tex
hmmer-2.2g/squid/Docs/main.tex
hmmer-2.2g/squid/Docs/selex.tex
hmmer-2.2g/squid/squidcore.c
hmmer-2.2g/squid/iupac.c
hmmer-2.2g/squid/types.c
hmmer-2.2g/squid/seqencode.c
hmmer-2.2g/squid/rk.c
hmmer-2.2g/squid/rk.h
hmmer-2.2g/squid/squidconf.h.in
hmmer-2.2g/squid/hsregex.c
hmmer-2.2g/squid/a2m.c
hmmer-2.2g/squid/stack.c
hmmer-2.2g/squid/squid.h.in
hmmer-2.2g/squid/sqio.c
hmmer-2.2g/squid/shuffle.c
hmmer-2.2g/squid/install-sh
hmmer-2.2g/squid/stopwatch.c
hmmer-2.2g/squid/stopwatch.h
hmmer-2.2g/squid/Makefile.in
hmmer-2.2g/squid/Formats/
hmmer-2.2g/squid/Formats/a2m
hmmer-2.2g/squid/Formats/gcg
hmmer-2.2g/squid/Formats/msf
hmmer-2.2g/squid/Formats/pir
hmmer-2.2g/squid/Formats/embl
hmmer-2.2g/squid/Formats/swissprot
hmmer-2.2g/squid/Formats/clustal
hmmer-2.2g/squid/Formats/fasta
hmmer-2.2g/squid/Formats/gcgdata.2
hmmer-2.2g/squid/Formats/gcgdata.1
hmmer-2.2g/squid/Formats/regression.dat
hmmer-2.2g/squid/Formats/phylip
hmmer-2.2g/squid/Formats/stockholm.1
hmmer-2.2g/squid/Formats/stockholm.2
hmmer-2.2g/squid/Formats/selex.2
hmmer-2.2g/squid/Formats/selex.1
hmmer-2.2g/squid/Formats/formattest.pl
hmmer-2.2g/squid/Formats/genbank
hmmer-2.2g/squid/cluster.c
hmmer-2.2g/squid/clustal.c
hmmer-2.2g/squid/INSTALL
hmmer-2.2g/squid/ssi.c
hmmer-2.2g/squid/ssi.h
hmmer-2.2g/squid/sre_string.c
hmmer-2.2g/squid/00README
hmmer-2.2g/squid/seqsplit_main.c
hmmer-2.2g/squid/eps.c
hmmer-2.2g/squid/sqerror.c
hmmer-2.2g/squid/revcomp_main.c
hmmer-2.2g/squid/alistat_main.c
hmmer-2.2g/squid/afetch_main.c
hmmer-2.2g/squid/compstruct_main.c
hmmer-2.2g/squid/sfetch_main.c
hmmer-2.2g/squid/gki.c
hmmer-2.2g/squid/gki.h
hmmer-2.2g/squid/weight.c
hmmer-2.2g/squid/gsi.c
hmmer-2.2g/squid/gsi.h
hmmer-2.2g/squid/translate.c
hmmer-2.2g/squid/sindex_main.c
hmmer-2.2g/squid/alignio.c
hmmer-2.2g/squid/revcomp.c
hmmer-2.2g/squid/stockholm.h
hmmer-2.2g/squid/stockholm.c
hmmer-2.2g/squid/compalign_main.c
hmmer-2.2g/squid/gsi64.h
hmmer-2.2g/squid/gsi64.c
hmmer-2.2g/squid/dayhoff.c
hmmer-2.2g/squid/file.c
hmmer-2.2g/squid/sqfuncs.h
hmmer-2.2g/squid/selex.c
hmmer-2.2g/squid/phylip.c
hmmer-2.2g/squid/sreformat_main.c
hmmer-2.2g/squid/msa.c
hmmer-2.2g/squid/msa.h
hmmer-2.2g/squid/msf.c
hmmer-2.2g/squid/seqstat_main.c
hmmer-2.2g/squid/translate_main.c
hmmer-2.2g/squid/sre_math.c
hmmer-2.2g/squid/test_main.c
hmmer-2.2g/squid/shuffle_main.c
hmmer-2.2g/squid/weight_main.c
hmmer-2.2g/squid/sre_ctype.c
hmmer-2.2g/squid/getopt.c
hmmer-2.2g/squid/configure
hmmer-2.2g/testsuite/
hmmer-2.2g/testsuite/tophits_test.c
hmmer-2.2g/testsuite/Makefile.in
hmmer-2.2g/testsuite/Optiontests.nslx
hmmer-2.2g/testsuite/parsingviterbi_test.c
hmmer-2.2g/testsuite/fn3-bin
hmmer-2.2g/testsuite/fn3.hmm
hmmer-2.2g/testsuite/trace_test.slx
hmmer-2.2g/testsuite/trace_test.seq
hmmer-2.2g/testsuite/trace_test.hmm
hmmer-2.2g/testsuite/README
hmmer-2.2g/testsuite/fn3-bin-swap
hmmer-2.2g/testsuite/fitting_test.c
hmmer-2.2g/testsuite/alignalign_test.c
hmmer-2.2g/testsuite/weeviterbi_test.c
hmmer-2.2g/testsuite/titin.fa
hmmer-2.2g/testsuite/evd_test.c
hmmer-2.2g/testsuite/Exercises.sh
hmmer-2.2g/testsuite/masks_test.c
hmmer-2.2g/testsuite/trace_test.c
hmmer-2.2g/testsuite/Optiontests.slx
hmmer-2.2g/testsuite/Optiontests.pam
hmmer-2.2g/testsuite/Optiontests.pri
hmmer-2.2g/testsuite/Optiontests.nfa
hmmer-2.2g/testsuite/viterbi_exercise.c
hmmer-2.2g/testsuite/weeviterbi_test.hmm
hmmer-2.2g/testsuite/weeviterbi_test.seq
hmmer-2.2g/testsuite/Optiontests.pl
hmmer-2.2g/testsuite/Optiontests.fa
hmmer-2.2g/testsuite/fn3.seed
hmmer-2.2g/00README
hmmer-2.2g/COPYRIGHT
hmmer-2.2g/config.sub
hmmer-2.2g/NOTES
hmmer-2.2g/documentation/
hmmer-2.2g/documentation/man/
hmmer-2.2g/documentation/man/hmmalign.man
hmmer-2.2g/documentation/man/hmmpfam.man
hmmer-2.2g/documentation/man/hmmer.man
hmmer-2.2g/documentation/man/hmmfetch.man
hmmer-2.2g/documentation/man/hmmsearch.man
hmmer-2.2g/documentation/man/hmmindex.man
hmmer-2.2g/documentation/man/hmmbuild.man
hmmer-2.2g/documentation/man/hmmemit.man
hmmer-2.2g/documentation/man/hmmcalibrate.man
hmmer-2.2g/documentation/man/hmmconvert.man
hmmer-2.2g/tutorial/
hmmer-2.2g/tutorial/amino.null
hmmer-2.2g/tutorial/nucleic.null
hmmer-2.2g/tutorial/fn3.slx
hmmer-2.2g/tutorial/globins630.fa
hmmer-2.2g/tutorial/globins50.msf
hmmer-2.2g/tutorial/Artemia.fa
hmmer-2.2g/tutorial/7LES_DROME
hmmer-2.2g/tutorial/amino.pri
hmmer-2.2g/tutorial/pkinase.slx
hmmer-2.2g/tutorial/rrm.hmm
hmmer-2.2g/tutorial/rrm.slx
hmmer-2.2g/tutorial/nucleic.pri
hmmer-2.2g/tutorial/RU1A_HUMAN
hmmer-2.2g/configure
sudo -u fink-bld [ENV] sh -c /tmp/fink.dZm6Z
cp /sw/src/7tm_1 .
sudo -u fink-bld [ENV] sh -c /tmp/fink.s_GDF
cp /sw/src/P08908.fasta .
sudo -u fink-bld [ENV] sh -c /tmp/fink.Fwt_D
[ -r /sw/fink/dists/stable/main/finkinfo/sci/hmmer.patch ]
sudo -u fink-bld [ENV] sh -c /tmp/fink.5ign4
patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/hmmer.patch
patching file config.guess
patching file config.sub
patching file Makefile.in
sudo -u fink-bld [ENV] sh -c /tmp/fink.jIykG
./configure --prefix=/sw --bindir=/sw/build.build/root-hmmer-2.2g-3/sw/bin --mandir=/sw/build.build/root-hmmer-2.2g-3/sw/share/man
creating cache ./config.cache
   Welcome to HMMER... configuring for your system.
checking for gcc... gcc
checking whether the C compiler (gcc  -L/sw/lib) works... yes
checking whether the C compiler (gcc  -L/sw/lib) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking whether ln -s works... yes
checking for ranlib... ranlib
checking whether your make is GNU make... yes, it is.
checking host system type... i386-apple-darwin13.3.0
checking how to run the C preprocessor... gcc -E
   Trying to enable default POSIX threads support
checking for pthread.h... 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... gcc
checking for pthread_setconcurrency... yes
checking for pthread_attr_setscope... yes
checking for ntohs... yes
checking for ntohl... yes
checking for htons... yes
checking for htonl... yes
   Configuration complete. Writing Makefiles and such...
updating cache ./config.cache
creating ./config.status
creating Makefile
creating src/Makefile
creating testsuite/Makefile
configuring in squid
running /bin/sh ./configure  --prefix=/sw --bindir=/sw/build.build/root-hmmer-2.2g-3/sw/bin --mandir=/sw/build.build/root-hmmer-2.2g-3/sw/share/man --cache-file=.././config.cache --srcdir=.
loading cache .././config.cache
   Welcome to SQUID... configuring for your system.
checking for gcc... (cached) gcc
checking whether the C compiler (gcc  -L/sw/lib) works... yes
checking whether the C compiler (gcc  -L/sw/lib) is a cross-compiler... no
checking whether we are using GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking whether ln -s works... (cached) yes
checking for ranlib... (cached) ranlib
checking whether your make is GNU make... yes, it is.
checking whether byte ordering is bigendian... no
checking for ntohs... (cached) yes
checking for ntohl... (cached) yes
checking for htons... (cached) yes
checking for htonl... (cached) yes
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking whether fpos_t is an arithmetic datatype... no.
checking for ftello... yes
checking for fseeko... yes
checking for ftello64... no
checking for fseeko64... no
checking for ftell64... no
checking for fseek64... no
checking for stat64... yes
checking size of off_t... 8
checking size of off64_t... 0
checking size of fpos_t... 8
   Configuration complete. Writing Makefiles and such...
updating cache .././config.cache
creating ./config.status
creating Makefile
creating squid.h
creating squidconf.h
make
echo "/* version.h -- automatically generated by a Makefile. DO NOT EDIT. */" > version.h
echo "#define PACKAGE     \""HMMER"\""     >> version.h
echo "#define RELEASE     \""2.2g"\""     >> version.h
echo "#define RELEASEDATE \""August 2001"\"" >> version.h
echo "#define COPYRIGHT   \""Copyright \(C\) 1992-2001 HHMI/Washington University School of Medicine"\""   >> version.h
echo "#define LICENSE     \""Freely distributed under the GNU General Public License \(GPL\)"\""     >> version.h
cp version.h squid/
cp version.h src/
gcc -g -O2   -DHAVE_CONFIG_H -c afetch_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c a2m.c		
gcc -g -O2   -DHAVE_CONFIG_H -c aligneval.c		
gcc -g -O2   -DHAVE_CONFIG_H -c alignio.c		
gcc -g -O2   -DHAVE_CONFIG_H -c clustal.c		
gcc -g -O2   -DHAVE_CONFIG_H -c cluster.c		
gcc -g -O2   -DHAVE_CONFIG_H -c dayhoff.c		
gcc -g -O2   -DHAVE_CONFIG_H -c eps.c		
eps.c:67:22: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)'
    if ((len = (int) strlen(msa->sqname[i])) > namewidth)
                     ^
eps.c:67:22: note: please include the header <string.h> or explicitly provide a declaration for 'strlen'
1 warning generated.
gcc -g -O2   -DHAVE_CONFIG_H -c file.c		
gcc -g -O2   -DHAVE_CONFIG_H -c getopt.c		
gcc -g -O2   -DHAVE_CONFIG_H -c gki.c		
gcc -g -O2   -DHAVE_CONFIG_H -c gsi.c		
gcc -g -O2   -DHAVE_CONFIG_H -c hsregex.c		
gcc -g -O2   -DHAVE_CONFIG_H -c iupac.c		
gcc -g -O2   -DHAVE_CONFIG_H -c msa.c		
gcc -g -O2   -DHAVE_CONFIG_H -c msf.c		
gcc -g -O2   -DHAVE_CONFIG_H -c phylip.c		
gcc -g -O2   -DHAVE_CONFIG_H -c revcomp.c		
gcc -g -O2   -DHAVE_CONFIG_H -c rk.c		
gcc -g -O2   -DHAVE_CONFIG_H -c selex.c		
gcc -g -O2   -DHAVE_CONFIG_H -c seqencode.c		
gcc -g -O2   -DHAVE_CONFIG_H -c shuffle.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sqerror.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sqio.c		
gcc -g -O2   -DHAVE_CONFIG_H -c squidcore.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sre_ctype.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sre_math.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sre_string.c		
gcc -g -O2   -DHAVE_CONFIG_H -c ssi.c		
gcc -g -O2   -DHAVE_CONFIG_H -c stack.c		
gcc -g -O2   -DHAVE_CONFIG_H -c stockholm.c		
gcc -g -O2   -DHAVE_CONFIG_H -c stopwatch.c		
gcc -g -O2   -DHAVE_CONFIG_H -c translate.c		
gcc -g -O2   -DHAVE_CONFIG_H -c types.c		
gcc -g -O2   -DHAVE_CONFIG_H -c weight.c		
gcc -g -O2   -DHAVE_CONFIG_H -c alistat_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c compalign_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c compstruct_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sfetch_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sreformat_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c revcomp_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c seqsplit_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c seqstat_main.c		
sreformat_main.c:214:19: warning: implicit declaration of function 'WriteSELEXOneBlock' is invalid in C99 [-Wimplicit-function-declaration]
            if (do_pfam) WriteSELEXOneBlock(stdout, msa);
                         ^
gcc -g -O2   -DHAVE_CONFIG_H -c shuffle_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c sindex_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c translate_main.c		
gcc -g -O2   -DHAVE_CONFIG_H -c weight_main.c		
1 warning generated.
sindex_main.c:75:16: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
      if      (strcmp(optname, "--64") == 0) mode    = SSI_OFFSET_I64;
               ^
sindex_main.c:75:16: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
1 warning generated.
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
gcc -g -O2 -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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o  -lm
ar 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_string.o ssi.o stack.o stockholm.o stopwatch.o translate.o types.o weight.o
a - a2m.o
a - aligneval.o
a - alignio.o
a - clustal.o
a - cluster.o
a - dayhoff.o
a - eps.o
a - file.o
a - getopt.o
a - gki.o
a - gsi.o
a - hsregex.o
a - iupac.o
a - msa.o
a - msf.o
a - phylip.o
a - revcomp.o
a - rk.o
a - selex.o
a - seqencode.o
a - shuffle.o
a - sqerror.o
a - sqio.o
a - squidcore.o
a - sre_ctype.o
a - sre_math.o
a - sre_string.o
a - ssi.o
a - stack.o
a - stockholm.o
a - stopwatch.o
a - translate.o
a - types.o
a - weight.o
ranlib libsquid.a
chmod 644 libsquid.a
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmalign.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c alphabet.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c core_algorithms.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c debug.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c display.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c emit.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c emulation.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c histogram.c
hmmalign.c:100:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-m")        == 0) matchonly= TRUE;
             ^
hmmalign.c:100:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmio.c
1 warning generated.
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c mathsupport.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c masks.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c misc.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c modelmakers.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c plan7.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c plan9.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c postprob.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c prior.c
prior.c:112:12: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
  if      (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET;
           ^
prior.c:112:12: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c pvm.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c threads.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c tophits.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c trace.c
1 warning generated.
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmbuild.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmcalibrate.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmconvert.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmemit.c
hmmconvert.c:90:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-a") == 0) { outfmt    = P7ASCII;    }
             ^
hmmconvert.c:90:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmfetch.c
hmmemit.c:92:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-a")     == 0) do_alignment = TRUE;
             ^
hmmemit.c:92:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
hmmemit.c:177:2: warning: implicitly declaring library function 'strcpy' with type 'char *(char *, const char *)'
        strcpy(sqinfo.name, hmm->name);
        ^
hmmemit.c:177:2: note: please include the header <string.h> or explicitly provide a declaration for 'strcpy'
1 warning generated.
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmindex.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmpfam.c
gcc -g -O2 -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1    -I../squid  -c hmmsearch.c
2 warnings generated.
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -L../squid  -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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
ar rcv  libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.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  
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libhmmer.a(pvm.o) has no symbols
a - alphabet.o
a - core_algorithms.o
a - debug.o
a - display.o
a - emit.o
a - emulation.o
a - histogram.o
a - hmmio.o
a - mathsupport.o
a - masks.o
a - misc.o
a - modelmakers.o
a - plan7.o
a - plan9.o
a - postprob.o
a - prior.o
a - pvm.o
a - threads.o
a - tophits.o
a - trace.o
ranlib libhmmer.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libhmmer.a(pvm.o) has no symbols
chmod 644 libhmmer.a
make check
(cd testsuite; make CC="gcc" CFLAGS="-g -O2")
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c alignalign_test.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c evd_test.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c masks_test.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c parsingviterbi_test.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c tophits_test.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c trace_test.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c viterbi_exercise.c		
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -I../squid -I../src -c weeviterbi_test.c		
alignalign_test.c:91:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-v")       == 0) be_verbose = TRUE;
             ^
alignalign_test.c:91:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
alignalign_test.c:165:14: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)'
      rlen = strlen(rseq[idx]);
             ^
alignalign_test.c:165:14: note: please include the header <string.h> or explicitly provide a declaration for 'strlen'
masks_test.c:76:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-v")       == 0) { be_verbose = TRUE;   }
             ^
masks_test.c:76:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
evd_test.c:132:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-e")       == 0) { nevd       = atoi(optarg); } 
             ^
evd_test.c:132:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
masks_test.c:93:15: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)'
  len = (int) strlen(seq);
              ^
masks_test.c:93:15: note: please include the header <string.h> or explicitly provide a declaration for 'strlen'
tophits_test.c:68:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-s") == 0) { seed       = atoi(optarg); }
             ^
tophits_test.c:68:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
parsingviterbi_test.c:73:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-v")       == 0) be_verbose = TRUE;
             ^
parsingviterbi_test.c:73:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
trace_test.c:78:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-v")       == 0) be_verbose = TRUE;
             ^
trace_test.c:78:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
weeviterbi_test.c:73:14: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)'
    if      (strcmp(optname, "-v")       == 0) be_verbose = TRUE;
             ^
weeviterbi_test.c:73:14: note: please include the header <string.h> or explicitly provide a declaration for 'strcmp'
1 warning generated.
1 warning generated.
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o trace_test -L../squid -L../src trace_test.o -lhmmer -lsquid  -lm
2 warnings generated.
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o weeviterbi_test -L../squid -L../src weeviterbi_test.o -lhmmer -lsquid  -lm
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o masks_test -L../squid -L../src masks_test.o -lhmmer -lsquid  -lm
1 warning generated.
2 warnings generated.
1 warning generated.
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o tophits_test -L../squid -L../src tophits_test.o -lhmmer -lsquid  -lm
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o alignalign_test -L../squid -L../src alignalign_test.o -lhmmer -lsquid  -lm
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o parsingviterbi_test -L../squid -L../src parsingviterbi_test.o -lhmmer -lsquid  -lm
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o viterbi_exercise -L../squid -L../src viterbi_exercise.o -lhmmer -lsquid  -lm
1 warning generated.
gcc -g -O2  -DHMMER_THREADS  -DHAVE_PTHREAD_SETCONCURRENCY=1 -DHAVE_PTHREAD_ATTR_SETSCOPE=1 -DHAVE_NTOHS=1 -DHAVE_NTOHL=1 -DHAVE_HTONS=1 -DHAVE_HTONL=1  -o evd_test -L../squid -L../src evd_test.o -lhmmer -lsquid  -lm
(cd testsuite; make check)

Running compiled Shiva exercises:
Warning: some tests may take several minutes to complete.
alignalign_test: ok
evd_test: ok
masks_test: ok
parsingviterbi_test: ok
tophits_test: ok
trace_test: ok
viterbi_exercise: ok
weeviterbi_test: ok

Running scripted Shiva exercises:
Warning: This also may take several minutes.
perl ./Optiontests.pl
Option tests: 88. Passed: 88. Failed: 0
sh ./Exercises.sh
chmod a+r documentation/man/*
chmod a+r squid/Man/*
/bin/rm -rf /sw/build.build/root-hmmer-2.2g-3
/bin/mkdir -p /sw/build.build/root-hmmer-2.2g-3/sw
/bin/mkdir -p /sw/build.build/root-hmmer-2.2g-3/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-hmmer-2.2g-3
sudo -u fink-bld [ENV] sh -c /tmp/fink.RKBmL
install -d -m 755 /sw/build.build/root-hmmer-2.2g-3/sw/bin
install -d -m 755 /sw/build.build/root-hmmer-2.2g-3/sw/share/man/man1
mv INSTALL INSTALL.sav
make install prefix=/sw/build.build/root-hmmer-2.2g-3/sw
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch afetch alistat seqstat sfetch sindex shuffle sreformat ; do\
	   cp binaries/$file /sw/build.build/root-hmmer-2.2g-3/sw/bin/;\
	done
for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\
	   cp documentation/man/$file.man /sw/build.build/root-hmmer-2.2g-3/sw/share/man/man1/$file.1;\
	done
for file in afetch alistat seqstat sfetch sindex shuffle sreformat; do\
	   cp squid/Man/$file.man /sw/build.build/root-hmmer-2.2g-3/sw/share/man/man1/$file.1;\
	done
cp: squid/Man/sindex.man: No such file or directory
mv INSTALL.sav INSTALL
install -d -m 755 /sw/build.build/root-hmmer-2.2g-3/sw/include/hmmer-2.2g
install -c -p -m 644 version.h src/*.h /sw/build.build/root-hmmer-2.2g-3/sw/include/hmmer-2.2g
ln -s hmmer-2.2g /sw/build.build/root-hmmer-2.2g-3/sw/include/hmmer
install -d -m 755 /sw/build.build/root-hmmer-2.2g-3/sw/lib
install -c -p -m 644 src/libhmmer.a /sw/build.build/root-hmmer-2.2g-3/sw/lib/libhmmer-2.2g.a
ln -s libhmmer-2.2g.a /sw/build.build/root-hmmer-2.2g-3/sw/lib/libhmmer.a
install -d -m 755 /sw/build.build/root-hmmer-2.2g-3/sw/share/hmmer/demo
install -c -p -m 644 ../7tm_1 /sw/build.build/root-hmmer-2.2g-3/sw/share/hmmer/demo
install -c -p -m 644 ../P08908.fasta /sw/build.build/root-hmmer-2.2g-3/sw/share/hmmer/demo
echo "#!/bin/sh" > /sw/build.build/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh
echo "hmmsearch /sw/share/hmmer/demo/7tm_1 /sw/share/hmmer/demo/P08908.fasta" >> /sw/build.build/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh
chmod 755 /sw/build.build/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh
sudo -u fink-bld [ENV] sh -c /tmp/fink.MJ2Ms
/usr/bin/install -d -m 700 /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer
/bin/cp -r 00README /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer/
/bin/cp -r COPYRIGHT /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer/
/bin/cp -r INSTALL /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer/
/bin/cp -r LICENSE /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer/
/bin/cp -r NOTES /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer/
/bin/cp -r Userguide.pdf /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer/
/bin/chmod -R go=u-w /sw/build.build/root-hmmer-2.2g-3/sw/share/doc/hmmer
/usr/bin/install -d -m 755 /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d
echo "setenv HMMERDB '/data/hmmerdb'" >> /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.csh.env
echo "export HMMERDB='/data/hmmerdb'" >> /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.sh.env
/usr/bin/touch /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.csh
/usr/bin/touch /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.sh
/bin/cat /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.csh >> /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.csh.env
/bin/cat /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.sh >> /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.sh.env
/bin/mv -f /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.csh.env /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.csh
/bin/mv -f /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.sh.env /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.sh
/bin/chmod 755 /sw/build.build/root-hmmer-2.2g-3/sw/etc/profile.d/hmmer.*
/bin/rm -f /sw/build.build/root-hmmer-2.2g-3/sw/info/dir /sw/build.build/root-hmmer-2.2g-3/sw/info/dir.old /sw/build.build/root-hmmer-2.2g-3/sw/share/info/dir /sw/build.build/root-hmmer-2.2g-3/sw/share/info/dir.old
Reverting ownership of install dir to root
Writing control file...
Writing package script postinst...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-hmmer-2.2g-3 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `hmmer' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/hmmer_2.2g-3_darwin-x86_64.deb'.
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-hmmer-2.2g-3
(Reading database ... 4297 files and directories currently installed.)
Removing fink-buildlock-hmmer-2.2g-3 ...