01.configure

2015-03-11 17:31:56 +1100

./configure
--prefix=/home/linuxbrew/Cellar/infernal/1.1.1

configure: Configuring Infernal for your system.
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: Full Infernal source distribution - using full configuration
checking for gcc... /usr/bin/gcc
checking for C compiler default output file name... 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 /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... /usr/bin/gcc
checking for gcc... (cached) /usr/bin/gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether /usr/bin/gcc accepts -g... (cached) yes
checking for /usr/bin/gcc option to accept ISO C89... (cached) none needed
checking for a BSD-compatible install... /bin/install -c
checking how to run the C preprocessor... /usr/bin/gcc -E
checking for C compiler vendor... (cached) gnu
checking for /usr/bin/gcc option to accept ISO C99... -std=gnu99
checking for /usr/bin/gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
checking for ranlib... ranlib
checking for ar... /bin/ar
checking whether ln -s works... yes
checking whether you have a GNU make... yes, you do; and we assume you will use it!
checking for /usr/bin/gcc -std=gnu99 option to produce PIC... -fPIC
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse2 -msse3... yes
checking compiler support for sse2 cast functions... yes
checking whether SSE2 is supported... yes
checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes
configure: Activating Intel/AMD SSE optimized DP implementation
checking compiler support --start-group... yes
checking for gzip... /bin/gzip
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... yes
checking emmintrin.h usability... yes
checking emmintrin.h presence... yes
checking for emmintrin.h... yes
checking pmmintrin.h usability... yes
checking pmmintrin.h presence... no
configure: WARNING: pmmintrin.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: pmmintrin.h: proceeding with the compiler's result
checking for pmmintrin.h... yes
checking xmmintrin.h usability... yes
checking xmmintrin.h presence... yes
checking for xmmintrin.h... yes
checking whether byte ordering is bigendian... no
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for off_t... yes
checking for mkstemp... yes
checking for popen... yes
checking for strcasecmp... yes
checking for times... yes
checking for getpid... yes
checking for sysctl... yes
checking for sysconf... yes
checking for getcwd... yes
checking for stat... yes
checking for fstat... yes
checking for ntohs... yes
checking for ntohl... yes
checking for htons... yes
checking for htonl... yes
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating src/impl_sse/Makefile
config.status: creating testsuite/Makefile
config.status: creating rmark/Makefile
config.status: creating documentation/Makefile
config.status: creating documentation/manpages/Makefile
config.status: creating documentation/userguide/Makefile
config.status: creating hmmer/documentation/Makefile
config.status: creating hmmer/documentation/man/Makefile
config.status: creating hmmer/documentation/userguide/Makefile
config.status: creating hmmer/src/Makefile
config.status: creating hmmer/testsuite/Makefile
config.status: creating hmmer/profmark/Makefile
config.status: creating hmmer/src/impl_sse/Makefile
config.status: creating hmmer/libdivsufsort/Makefile
config.status: creating hmmer/Makefile
config.status: creating easel/miniapps/Makefile
config.status: creating easel/testsuite/Makefile
config.status: creating easel/Makefile
config.status: creating easel/documentation/Makefile
config.status: creating Makefile
config.status: creating src/config.h
config.status: creating hmmer/src/p7_config.h
config.status: creating hmmer/libdivsufsort/divsufsort.h
config.status: creating easel/esl_config.h
config.status: linking hmmer/src/impl_sse to hmmer/src/impl


INFERNAL configuration:

     compiler:             /usr/bin/gcc -std=gnu99 -Os -w -pipe -march=core2 -msse2 -msse3 -pthread -fPIC
     linker:               -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib
     libraries:              
     DP implementation:    sse

02.make

2015-03-11 17:31:59 +1100

make

     SUBDIR easel
make[1]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/easel'
     CC easel.o
     CC esl_alphabet.o
     CC esl_buffer.o
     CC esl_cluster.o
     CC esl_dirichlet.o
     CC esl_distance.o
     CC esl_dmatrix.o
     CC esl_exponential.o
     CC esl_fileparser.o
     CC esl_gamma.o
     CC esl_getopts.o
     CC esl_gumbel.o
     CC esl_gev.o
     CC esl_histogram.o
     CC esl_hmm.o
     CC esl_hyperexp.o
     CC esl_keyhash.o
     CC esl_mem.o
     CC esl_minimizer.o
     CC esl_mixgev.o
     CC esl_mpi.o
     CC esl_msa.o
     CC esl_msafile.o
     CC esl_msacluster.o
     CC esl_msafile2.o
     CC esl_msafile_a2m.o
     CC esl_msafile_afa.o
     CC esl_msafile_clustal.o
     CC esl_msafile_phylip.o
     CC esl_msafile_psiblast.o
     CC esl_msafile_selex.o
     CC esl_msafile_stockholm.o
     CC esl_msashuffle.o
     CC esl_msaweight.o
     CC esl_normal.o
     CC esl_paml.o
     CC esl_randomseq.o
     CC esl_random.o
     CC esl_recorder.o
     CC esl_ratematrix.o
     CC esl_sqio.o
     CC esl_sse.o
     CC esl_rootfinder.o
     CC esl_ssi.o
     CC esl_scorematrix.o
     CC esl_sq.o
     CC esl_sqio_ascii.o
     CC esl_sqio_ncbi.o
     CC esl_stack.o
     CC esl_stats.o
     CC esl_stopwatch.o
     CC esl_stretchexp.o
     CC esl_threads.o
     CC esl_tree.o
     CC esl_vectorops.o
     CC esl_vmx.o
     CC esl_workqueue.o
     CC esl_weibull.o
     CC esl_wuss.o
     AR libeasel.a
     SUBDIR miniapps
make[2]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/easel/miniapps'
     CC esl-afetch.o
     CC esl-alimanip.o
     CC esl-alimap.o
     CC esl-alimask.o
     CC esl-alimerge.o
     CC esl-alipid.o
     CC esl-alistat.o
     CC esl-cluster.o
     CC esl-compalign.o
     CC esl-compstruct.o
     CC esl-construct.o
     CC esl-histplot.o
     CC esl-mask.o
     CC esl-reformat.o
     CC esl-selectn.o
     CC esl-seqstat.o
     CC esl-seqrange.o
     CC esl-sfetch.o
     CC esl-shuffle.o
     CC esl-ssdraw.o
     CC esl-weight.o
     GEN esl-alipid
     GEN esl-selectn
     GEN esl-weight
     GEN esl-seqrange
     GEN esl-histplot
     GEN esl-cluster
     GEN esl-seqstat
     GEN esl-compstruct
     GEN esl-mask
     GEN esl-afetch
     GEN esl-shuffle
     GEN esl-sfetch
     GEN esl-alimap
     GEN esl-construct
     GEN esl-compalign
     GEN esl-reformat
     GEN esl-alimask
     GEN esl-alistat
     GEN esl-alimerge
     GEN esl-alimanip
     GEN esl-ssdraw
make[2]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/easel/miniapps'
make[1]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/easel'
     SUBDIR hmmer/libdivsufsort
make[1]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/libdivsufsort'
     CC divsufsort.o
     AR libdivsufsort.a
make[1]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/libdivsufsort'
     SUBDIR hmmer
make[1]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer'
     SUBDIR ../easel
make[2]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/easel'
     SUBDIR miniapps
make[3]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/easel/miniapps'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/easel/miniapps'
make[2]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/easel'
     SUBDIR libdivsufsort
make[2]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/libdivsufsort'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/libdivsufsort'
     SUBDIR src
make[2]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/src'
     CC alimask.o
     CC build.o
     CC cachedb.o
     CC emit.o
     CC evalues.o
     CC errors.o
     CC eweight.o
     CC generic_decoding.o
     CC generic_fwdback.o
     CC generic_fwdback_chk.o
     CC generic_fwdback_banded.o
     CC generic_null2.o
     CC generic_msv.o
     CC generic_optacc.o
     CC generic_stotrace.o
     CC generic_viterbi.o
     CC generic_vtrace.o
     CC h2_io.o
     CC hmmlogo.o
     CC heatmap.o
     CC hmmdmstr.o
     CC hmmdwrkr.o
     CC hmmdutils.o
     CC hmmer.o
     CC logsum.o
     CC modelconfig.o
     CC modelstats.o
     CC mpisupport.o
     CC seqmodel.o
     CC tracealign.o
     CC p7_alidisplay.o
     CC p7_bg.o
     CC p7_builder.o
     CC p7_gbands.o
     CC p7_domaindef.o
     CC p7_gmx.o
     CC p7_gmxb.o
     CC p7_gmxchk.o
     CC p7_hmm.o
     CC p7_hmmfile.o
     CC p7_hmmcache.o
     CC p7_hmmwindow.o
     CC p7_null3.o
     CC p7_pipeline.o
     CC p7_prior.o
     CC p7_profile.o
     CC p7_spensemble.o
     CC p7_tophits.o
     CC p7_trace.o
     CC p7_msvdata.o
     CC fm_alphabet.o
     CC fm_general.o
     CC fm_msv.o
     CC hmmpgmd2msa.o
     CC exactmatch.o
     CC hmmalign.o
     CC hmmbuild.o
     CC hmmconvert.o
     CC hmmemit.o
     CC hmmfetch.o
     CC hmmpress.o
     CC hmmscan.o
     CC hmmsearch.o
     CC hmmsim.o
     CC hmmstat.o
     CC jackhmmer.o
     CC phmmer.o
     CC nhmmer.o
     CC hmmpgmd.o
     CC hmmc2.o
     CC makenhmmerdb.o
     AR libhmmer-src.stamp
     SUBDIR impl_sse
make[3]: Entering directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/src/impl_sse'
     CC decoding.o
     CC fwdback.o
     CC io.o
     CC ssvfilter.o
     CC msvfilter.o
     CC null2.o
     CC optacc.o
     CC stotrace.o
     CC vitfilter.o
     CC p7_omx.o
     CC p7_oprofile.o
     CC mpi.o
     CC fm.o
     AR libhmmer-impl.stamp
make[3]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/src/impl_sse'
     GEN alimask
     GEN exactmatch
     GEN hmmalign
     GEN hmmbuild
     GEN hmmconvert
     GEN hmmemit
     GEN hmmfetch
     GEN hmmlogo
     GEN hmmpress
     GEN hmmscan
     GEN hmmsearch
     GEN hmmsim
     GEN jackhmmer
     GEN phmmer
     GEN nhmmer
     GEN hmmc2
     GEN hmmpgmd
     GEN makenhmmerdb
exactmatch.o: In function `getFMHits':
exactmatch.c:(.text+0x12b): undefined reference to `fm_getChar'
exactmatch.c:(.text+0x144): undefined reference to `fm_getOccCount'
exactmatch.o: In function `main':
exactmatch.c:(.text.startup+0x3e2): undefined reference to `fm_configAlloc'
exactmatch.c:(.text.startup+0x40c): undefined reference to `fm_readFMmeta'
exactmatch.c:(.text.startup+0x4c4): undefined reference to `fm_readFM'
exactmatch.c:(.text.startup+0x4d7): undefined reference to `fm_readFM'
exactmatch.c:(.text.startup+0x726): undefined reference to `fm_initConfig'
exactmatch.c:(.text.startup+0x730): undefined reference to `fm_createAlphabet'
exactmatch.c:(.text.startup+0x850): undefined reference to `fm_getSARangeForward'
exactmatch.c:(.text.startup+0x99a): undefined reference to `fm_getSARangeReverse'
exactmatch.c:(.text.startup+0xa8e): undefined reference to `fm_getOriginalPosition'
exactmatch.c:(.text.startup+0xc2a): undefined reference to `fm_freeFM'
exactmatch.c:(.text.startup+0xc3a): undefined reference to `fm_freeFM'
exactmatch.c:(.text.startup+0xc9a): undefined reference to `fm_destroyConfig'
collect2: error: ld returned 1 exit status
make[2]: *** [exactmatch] Error 1
make[2]: *** Waiting for unfinished jobs....
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
make[2]: *** [hmmsearch] Error 1
/home/linuxbrew/lib/libhmmer.a(hmmdutils.o): In function `hmmpgmd_GetRanges':
hmmdutils.c:(.text+0x369): undefined reference to `esl_regexp_ParseCoordString'
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
make[2]: *** [hmmpgmd] Error 1
hmmemit.o: In function `main':
hmmemit.c:(.text.startup+0x72a): undefined reference to `p7_hmm_GetSimpleRepeats'
collect2: error: ld returned 1 exit status
make[2]: *** [hmmemit] Error 1
nhmmer.o: In function `main':
nhmmer.c:(.text.startup+0x6cd): undefined reference to `fm_configAlloc'
nhmmer.c:(.text.startup+0x71c): undefined reference to `fm_readFMmeta'
nhmmer.c:(.text.startup+0x72c): undefined reference to `fm_initConfig'
nhmmer.c:(.text.startup+0x736): undefined reference to `fm_createAlphabet'
nhmmer.c:(.text.startup+0xf0b): undefined reference to `p7_hmm_MSVDataCreate'
nhmmer.c:(.text.startup+0x10d8): undefined reference to `p7_hmm_MSVDataClone'
nhmmer.c:(.text.startup+0x11e7): undefined reference to `fm_readFM'
nhmmer.c:(.text.startup+0x11fc): undefined reference to `fm_readFM'
nhmmer.c:(.text.startup+0x125e): undefined reference to `p7_Pipeline_FM'
nhmmer.c:(.text.startup+0x174b): undefined reference to `p7_tophits_SortBySeqidx'
nhmmer.c:(.text.startup+0x1932): undefined reference to `p7_tophits_LongInserts'
nhmmer.c:(.text.startup+0x1a7b): undefined reference to `p7_hmm_MSVDataDestroy'
nhmmer.c:(.text.startup+0x1a8a): undefined reference to `p7_hmm_MSVDataDestroy'
nhmmer.c:(.text.startup+0x1c9c): undefined reference to `fm_destroyConfig'
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
make[2]: *** [nhmmer] Error 1
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
make[2]: *** [jackhmmer] Error 1
make[2]: *** [phmmer] Error 1
/home/linuxbrew/lib/libhmmer.a(hmmdutils.o): In function `hmmpgmd_GetRanges':
hmmdutils.c:(.text+0x369): undefined reference to `esl_regexp_ParseCoordString'
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
make[2]: *** [hmmc2] Error 1
makenhmmerdb.o: In function `main':
makenhmmerdb.c:(.text.startup+0x729): undefined reference to `fm_createAlphabet'
makenhmmerdb.c:(.text.startup+0x127e): undefined reference to `fm_reverseString'
collect2: error: ld returned 1 exit status
make[2]: *** [makenhmmerdb] Error 1
/home/linuxbrew/lib/libhmmer.a(p7_domaindef.o): In function `reparameterize_model':
p7_domaindef.c:(.text+0xa7): undefined reference to `esl_sq_CountResidues'
collect2: error: ld returned 1 exit status
make[2]: *** [hmmscan] Error 1
make[2]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/tmp/infernal-accMcR/infernal-1.1.1/hmmer'
make: *** [all] Error 2

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew.git
HEAD: 325f1adf2ad6c24b624c36b50455fbe152e6a46e
Last commit: 32 hours ago
HOMEBREW_PREFIX: /home/linuxbrew
HOMEBREW_CELLAR: /home/linuxbrew/Cellar
CPU: 72-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 2.0.0-p598 => /usr/bin/ruby
Perl: /bin/perl => /usr/bin/perl
Python: /bin/python => /usr/bin/python2.7
Ruby: /bin/ruby => /usr/bin/ruby
Java: 1.7.0_75

CC: /usr/bin/gcc
CXX: /usr/bin/g++
OBJC: /usr/bin/gcc
OBJCXX: /usr/bin/g++
CFLAGS: -Os -w -pipe -march=core2
CXXFLAGS: -Os -w -pipe -march=core2
CPPFLAGS: -isystem/home/linuxbrew/include
LDFLAGS: -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /home/linuxbrew
PKG_CONFIG_LIBDIR: /home/linuxbrew/lib/pkgconfig
PATH: /home/linuxbrew/bin:/home/perl5/bin:/usr/local/sbin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/home/linuxbrew/Library/ENV/scm

config.log

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by Infernal configure 1.1.1, which was
generated by GNU Autoconf 2.63.  Invocation command line was

  $ ./configure --prefix=/home/linuxbrew/Cellar/infernal/1.1.1

## --------- ##
## Platform. ##
## --------- ##

hostname = 526080-s598782
uname -m = x86_64
uname -r = 3.10.0-123.20.1.el7.x86_64
uname -s = Linux
uname -v = #1 SMP Wed Jan 21 09:45:55 EST 2015

/usr/bin/uname -p = x86_64
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /home/linuxbrew/bin
PATH: /home/perl5/bin
PATH: /usr/local/sbin
PATH: /sbin
PATH: /bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /root/bin
PATH: /home/linuxbrew/Library/ENV/scm


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1875: Configuring Infernal for your system.
configure:2062: checking build system type
configure:2080: result: x86_64-unknown-linux-gnu
configure:2102: checking host system type
configure:2117: result: x86_64-unknown-linux-gnu
configure:2150: Full Infernal source distribution - using full configuration
configure:2351: checking for gcc
configure:2378: result: /usr/bin/gcc
configure:2610: checking for C compiler version
configure:2618: /usr/bin/gcc --version >&5
gcc (GCC) 4.8.3 20140911 (Red Hat 4.8.3-9)
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2622: $? = 0
configure:2629: /usr/bin/gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.3/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.3 20140911 (Red Hat 4.8.3-9) (GCC) 
configure:2633: $? = 0
configure:2640: /usr/bin/gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2644: $? = 4
configure:2667: checking for C compiler default output file name
configure:2689: /usr/bin/gcc -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:2693: $? = 0
configure:2731: result: a.out
configure:2750: checking whether the C compiler works
configure:2760: ./a.out
configure:2764: $? = 0
configure:2783: result: yes
configure:2790: checking whether we are cross compiling
configure:2792: result: no
configure:2795: checking for suffix of executables
configure:2802: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:2806: $? = 0
configure:2832: result: 
configure:2838: checking for suffix of object files
configure:2864: /usr/bin/gcc -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:2868: $? = 0
configure:2893: result: o
configure:2897: checking whether we are using the GNU C compiler
configure:2926: /usr/bin/gcc -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:2933: $? = 0
configure:2950: result: yes
configure:2959: checking whether /usr/bin/gcc accepts -g
configure:2989: /usr/bin/gcc -c -g -isystem/home/linuxbrew/include conftest.c >&5
configure:2996: $? = 0
configure:3097: result: yes
configure:3114: checking for /usr/bin/gcc option to accept ISO C89
configure:3188: /usr/bin/gcc  -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:3195: $? = 0
configure:3218: result: none needed
configure:3238: checking for C compiler vendor
configure:3272: /usr/bin/gcc -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:30:7: error: 'thisisanerror' undeclared (first use in this function)
       thisisanerror;
       ^
conftest.c:30:7: note: each undeclared identifier is reported only once for each function it appears in
configure:3279: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| 
| #if !(defined(__ICC) || defined(__ECC) || defined(__INTEL_COMPILER))
|       thisisanerror;
| #endif
| 
|   ;
|   return 0;
| }
configure:3272: /usr/bin/gcc -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:30:7: error: 'thisisanerror' undeclared (first use in this function)
       thisisanerror;
       ^
conftest.c:30:7: note: each undeclared identifier is reported only once for each function it appears in
configure:3279: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| 
| #if !(defined(__xlc__) || defined(__xlC__) || defined(__IBMC__) || defined(__IBMCPP__))
|       thisisanerror;
| #endif
| 
|   ;
|   return 0;
| }
configure:3272: /usr/bin/gcc -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:30:7: error: 'thisisanerror' undeclared (first use in this function)
       thisisanerror;
       ^
conftest.c:30:7: note: each undeclared identifier is reported only once for each function it appears in
configure:3279: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| 
| #if !(defined(__PATHCC__) || defined(__PATHSCALE__))
|       thisisanerror;
| #endif
| 
|   ;
|   return 0;
| }
configure:3272: /usr/bin/gcc -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:3279: $? = 0
configure:3296: result: gnu
configure:3536: checking for the pthreads library -lpthreads
configure:3579: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2  -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c -lpthreads  >&5
/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
configure:3586: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| #include <pthread.h>
| int
| main ()
| {
| pthread_t th; pthread_join(th, 0);
|                      pthread_attr_init(0); pthread_cleanup_push(0, 0);
|                      pthread_create(0,0,0,0); pthread_cleanup_pop(0);
|   ;
|   return 0;
| }
configure:3609: result: no
configure:3481: checking whether pthreads work without any flags
configure:3579: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2  -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c   >&5
/tmp/cc1yvz2c.o: In function `main':
conftest.c:(.text.startup+0x9): undefined reference to `pthread_join'
conftest.c:(.text.startup+0x34): undefined reference to `__pthread_register_cancel'
conftest.c:(.text.startup+0x41): undefined reference to `pthread_create'
conftest.c:(.text.startup+0x49): undefined reference to `__pthread_unregister_cancel'
collect2: error: ld returned 1 exit status
configure:3586: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| #include <pthread.h>
| int
| main ()
| {
| pthread_t th; pthread_join(th, 0);
|                      pthread_attr_init(0); pthread_cleanup_push(0, 0);
|                      pthread_create(0,0,0,0); pthread_cleanup_pop(0);
|   ;
|   return 0;
| }
configure:3609: result: no
configure:3486: checking whether pthreads work with -Kthread
configure:3579: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2 -Kthread -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c   >&5
gcc: error: unrecognized command line option '-Kthread'
configure:3586: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| #include <pthread.h>
| int
| main ()
| {
| pthread_t th; pthread_join(th, 0);
|                      pthread_attr_init(0); pthread_cleanup_push(0, 0);
|                      pthread_create(0,0,0,0); pthread_cleanup_pop(0);
|   ;
|   return 0;
| }
configure:3609: result: no
configure:3486: checking whether pthreads work with -kthread
configure:3579: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2 -kthread -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c   >&5
gcc: error: unrecognized command line option '-kthread'
configure:3586: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| #include <pthread.h>
| int
| main ()
| {
| pthread_t th; pthread_join(th, 0);
|                      pthread_attr_init(0); pthread_cleanup_push(0, 0);
|                      pthread_create(0,0,0,0); pthread_cleanup_pop(0);
|   ;
|   return 0;
| }
configure:3609: result: no
configure:3536: checking for the pthreads library -llthread
configure:3579: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2  -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c -llthread  >&5
/bin/ld: cannot find -llthread
collect2: error: ld returned 1 exit status
configure:3586: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| /* end confdefs.h.  */
| #include <pthread.h>
| int
| main ()
| {
| pthread_t th; pthread_join(th, 0);
|                      pthread_attr_init(0); pthread_cleanup_push(0, 0);
|                      pthread_create(0,0,0,0); pthread_cleanup_pop(0);
|   ;
|   return 0;
| }
configure:3609: result: no
configure:3486: checking whether pthreads work with -pthread
configure:3579: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2 -pthread -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c   >&5
configure:3586: $? = 0
configure:3609: result: yes
configure:3629: checking for joinable pthread attribute
configure:3652: /usr/bin/gcc -o conftest -Os -w -pipe -march=core2 -pthread -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c   >&5
configure:3659: $? = 0
configure:3734: result: PTHREAD_CREATE_JOINABLE
configure:3741: checking if more special flags are required for pthreads
configure:3751: result: no
configure:3763: checking for cc_r
configure:3791: result: /usr/bin/gcc
configure:3952: checking for gcc
configure:3979: result: /usr/bin/gcc
configure:4211: checking for C compiler version
configure:4219: /usr/bin/gcc --version >&5
gcc (GCC) 4.8.3 20140911 (Red Hat 4.8.3-9)
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:4223: $? = 0
configure:4230: /usr/bin/gcc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.3/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.3-20140911/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.3 20140911 (Red Hat 4.8.3-9) (GCC) 
configure:4234: $? = 0
configure:4241: /usr/bin/gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:4245: $? = 4
configure:4248: checking whether we are using the GNU C compiler
configure:4301: result: yes
configure:4310: checking whether /usr/bin/gcc accepts -g
configure:4448: result: yes
configure:4465: checking for /usr/bin/gcc option to accept ISO C89
configure:4569: result: none needed
configure:4601: checking for a BSD-compatible install
configure:4669: result: /bin/install -c
configure:5049: checking how to run the C preprocessor
configure:5089: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:5096: $? = 0
configure:5127: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
conftest.c:26:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:5134: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5167: result: /usr/bin/gcc -E
configure:5196: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:5203: $? = 0
configure:5234: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
conftest.c:26:28: fatal error: ac_nonexistent.h: No such file or directory
 #include <ac_nonexistent.h>
                            ^
compilation terminated.
configure:5241: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:5281: checking for C compiler vendor
configure:5339: result: gnu
configure:5346: checking for /usr/bin/gcc option to accept ISO C99
configure:5505: /usr/bin/gcc  -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c:76:29: error: expected ';', ',' or ')' before 'text'
 test_restrict (ccp restrict text)
                             ^
conftest.c: In function 'main':
conftest.c:130:18: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'newvar'
   char *restrict newvar = "Another string";
                  ^
conftest.c:130:18: error: 'newvar' undeclared (first use in this function)
conftest.c:130:18: note: each undeclared identifier is reported only once for each function it appears in
conftest.c:140:3: error: 'for' loop initial declarations are only allowed in C99 mode
   for (int i = 0; i < ia->datasize; ++i)
   ^
conftest.c:140:3: note: use option -std=c99 or -std=gnu99 to compile your code
configure:5512: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| /* end confdefs.h.  */
| #include <stdarg.h>
| #include <stdbool.h>
| #include <stdlib.h>
| #include <wchar.h>
| #include <stdio.h>
| 
| // Check varargs macros.  These examples are taken from C99 6.10.3.5.
| #define debug(...) fprintf (stderr, __VA_ARGS__)
| #define showlist(...) puts (#__VA_ARGS__)
| #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__))
| static void
| test_varargs_macros (void)
| {
|   int x = 1234;
|   int y = 5678;
|   debug ("Flag");
|   debug ("X = %d\n", x);
|   showlist (The first, second, and third items.);
|   report (x>y, "x is %d but y is %d", x, y);
| }
| 
| // Check long long types.
| #define BIG64 18446744073709551615ull
| #define BIG32 4294967295ul
| #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0)
| #if !BIG_OK
|   your preprocessor is broken;
| #endif
| #if BIG_OK
| #else
|   your preprocessor is broken;
| #endif
| static long long int bignum = -9223372036854775807LL;
| static unsigned long long int ubignum = BIG64;
| 
| struct incomplete_array
| {
|   int datasize;
|   double data[];
| };
| 
| struct named_init {
|   int number;
|   const wchar_t *name;
|   double average;
| };
| 
| typedef const char *ccp;
| 
| static inline int
| test_restrict (ccp restrict text)
| {
|   // See if C++-style comments work.
|   // Iterate through items via the restricted pointer.
|   // Also check for declarations in for loops.
|   for (unsigned int i = 0; *(text+i) != '\0'; ++i)
|     continue;
|   return 0;
| }
| 
| // Check varargs and va_copy.
| static void
| test_varargs (const char *format, ...)
| {
|   va_list args;
|   va_start (args, format);
|   va_list args_copy;
|   va_copy (args_copy, args);
| 
|   const char *str;
|   int number;
|   float fnumber;
| 
|   while (*format)
|     {
|       switch (*format++)
| 	{
| 	case 's': // string
| 	  str = va_arg (args_copy, const char *);
| 	  break;
| 	case 'd': // int
| 	  number = va_arg (args_copy, int);
| 	  break;
| 	case 'f': // float
| 	  fnumber = va_arg (args_copy, double);
| 	  break;
| 	default:
| 	  break;
| 	}
|     }
|   va_end (args_copy);
|   va_end (args);
| }
| 
| int
| main ()
| {
| 
|   // Check bool.
|   _Bool success = false;
| 
|   // Check restrict.
|   if (test_restrict ("String literal") == 0)
|     success = true;
|   char *restrict newvar = "Another string";
| 
|   // Check varargs.
|   test_varargs ("s, d' f .", "string", 65, 34.234);
|   test_varargs_macros ();
| 
|   // Check flexible array members.
|   struct incomplete_array *ia =
|     malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10));
|   ia->datasize = 10;
|   for (int i = 0; i < ia->datasize; ++i)
|     ia->data[i] = i * 1.234;
| 
|   // Check named initializers.
|   struct named_init ni = {
|     .number = 34,
|     .name = L"Test wide string",
|     .average = 543.34343,
|   };
| 
|   ni.number = 58;
| 
|   int dynamic_array[ni.number];
|   dynamic_array[ni.number - 1] = 543;
| 
|   // work around unused variable warnings
|   return (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == 'x'
| 	  || dynamic_array[ni.number - 1] != 543);
| 
|   ;
|   return 0;
| }
configure:5505: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:5512: $? = 0
configure:5542: result: -std=gnu99
configure:5673: checking for /usr/bin/gcc -std=gnu99 option to accept ISO Standard C
configure:5684: result: -std=gnu99
configure:5733: checking for ranlib
configure:5749: found /bin/ranlib
configure:5760: result: ranlib
configure:5784: checking for ar
configure:5803: found /bin/ar
configure:5816: result: /bin/ar
configure:5825: checking whether ln -s works
configure:5829: result: yes
configure:5837: checking whether you have a GNU make
configure:5848: result: yes, you do; and we assume you will use it!
configure:6933: checking for /usr/bin/gcc -std=gnu99 option to produce PIC
configure:7019: result: -fPIC
configure:7028: checking whether C compiler accepts -msse2
configure:7057: /usr/bin/gcc -std=gnu99 -c -msse2 -isystem/home/linuxbrew/include conftest.c >&5
configure:7064: $? = 0
configure:7082: result: yes
configure:7090: checking whether C compiler accepts -msse2 -msse3
configure:7119: /usr/bin/gcc -std=gnu99 -c -msse2 -msse3 -isystem/home/linuxbrew/include conftest.c >&5
configure:7126: $? = 0
configure:7144: result: yes
configure:7614: checking compiler support for sse2 cast functions
configure:7649: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -msse2 -msse3 -isystem/home/linuxbrew/include conftest.c >&5
configure:7656: $? = 0
configure:7674: result: yes
configure:7686: checking whether SSE2 is supported
configure:7719: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -msse2 -msse3 -isystem/home/linuxbrew/include conftest.c >&5
configure:7726: $? = 0
configure:7731: result: yes
configure:7829: checking whether _MM_SET_FLUSH_ZERO_MODE is supported
configure:7855: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -msse2 -msse3 -isystem/home/linuxbrew/include conftest.c >&5
configure:7862: $? = 0
configure:7867: result: yes
configure:7888: Activating Intel/AMD SSE optimized DP implementation
configure:7934: checking compiler support --start-group
configure:7959: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -Wl,--start-group -Wl,--end-group -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:7966: $? = 0
configure:7974: result: yes
configure:8001: checking for gzip
configure:8019: found /bin/gzip
configure:8032: result: /bin/gzip
configure:8062: checking for grep that handles long lines and -e
configure:8122: result: /bin/grep
configure:8127: checking for egrep
configure:8191: result: /bin/grep -E
configure:8196: checking for ANSI C header files
configure:8226: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8233: $? = 0
configure:8332: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:8336: $? = 0
configure:8342: ./conftest
configure:8346: $? = 0
configure:8364: result: yes
configure:8388: checking for sys/types.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for sys/stat.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for stdlib.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for string.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for memory.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for strings.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for inttypes.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for stdint.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8388: checking for unistd.h
configure:8409: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8416: $? = 0
configure:8433: result: yes
configure:8475: checking endian.h usability
configure:8492: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8499: $? = 0
configure:8513: result: yes
configure:8517: checking endian.h presence
configure:8532: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:8539: $? = 0
configure:8553: result: yes
configure:8586: checking for endian.h
configure:8595: result: yes
configure:8464: checking for inttypes.h
configure:8471: result: yes
configure:8464: checking for stdint.h
configure:8471: result: yes
configure:8464: checking for unistd.h
configure:8471: result: yes
configure:8464: checking for sys/types.h
configure:8471: result: yes
configure:8475: checking netinet/in.h usability
configure:8492: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8499: $? = 0
configure:8513: result: yes
configure:8517: checking netinet/in.h presence
configure:8532: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:8539: $? = 0
configure:8553: result: yes
configure:8586: checking for netinet/in.h
configure:8595: result: yes
configure:8630: checking sys/param.h usability
configure:8647: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8654: $? = 0
configure:8668: result: yes
configure:8672: checking sys/param.h presence
configure:8687: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:8694: $? = 0
configure:8708: result: yes
configure:8741: checking for sys/param.h
configure:8750: result: yes
configure:8769: checking for sys/sysctl.h
configure:8793: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8800: $? = 0
configure:8817: result: yes
configure:8861: checking emmintrin.h usability
configure:8878: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8885: $? = 0
configure:8899: result: yes
configure:8903: checking emmintrin.h presence
configure:8918: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:8925: $? = 0
configure:8939: result: yes
configure:8972: checking for emmintrin.h
configure:8981: result: yes
configure:8861: checking pmmintrin.h usability
configure:8878: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8885: $? = 0
configure:8899: result: yes
configure:8903: checking pmmintrin.h presence
configure:8918: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
In file included from conftest.c:50:0:
/usr/lib/gcc/x86_64-redhat-linux/4.8.3/include/pmmintrin.h:31:3: error: #error "SSE3 instruction set not enabled"
 # error "SSE3 instruction set not enabled"
   ^
configure:8925: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| #define HAVE_SSE2_CAST 1
| #define HAVE_FLUSH_ZERO_MODE 1
| #define HAVE_SSE2 1
| #define p7_IMPL_SSE 1
| #define HAVE_GZIP 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ENDIAN_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_NETINET_IN_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_SYS_SYSCTL_H 1
| #define HAVE_EMMINTRIN_H 1
| /* end confdefs.h.  */
| #include <pmmintrin.h>
configure:8939: result: no
configure:8945: WARNING: pmmintrin.h: accepted by the compiler, rejected by the preprocessor!
configure:8947: WARNING: pmmintrin.h: proceeding with the compiler's result
configure:8972: checking for pmmintrin.h
configure:8981: result: yes
configure:8861: checking xmmintrin.h usability
configure:8878: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:8885: $? = 0
configure:8899: result: yes
configure:8903: checking xmmintrin.h presence
configure:8918: /usr/bin/gcc -E -isystem/home/linuxbrew/include conftest.c
configure:8925: $? = 0
configure:8939: result: yes
configure:8972: checking for xmmintrin.h
configure:8981: result: yes
configure:9162: checking whether byte ordering is bigendian
configure:9187: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c:53:9: error: unknown type name 'not'
         not a universal capable compiler
         ^
conftest.c:53:15: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'universal'
         not a universal capable compiler
               ^
conftest.c:53:15: error: unknown type name 'universal'
configure:9194: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| #define HAVE_SSE2_CAST 1
| #define HAVE_FLUSH_ZERO_MODE 1
| #define HAVE_SSE2 1
| #define p7_IMPL_SSE 1
| #define HAVE_GZIP 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ENDIAN_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_NETINET_IN_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_SYS_SYSCTL_H 1
| #define HAVE_EMMINTRIN_H 1
| #define HAVE_PMMINTRIN_H 1
| #define HAVE_XMMINTRIN_H 1
| /* end confdefs.h.  */
| #ifndef __APPLE_CC__
| 	       not a universal capable compiler
| 	     #endif
| 	     typedef int dummy;
| 
configure:9244: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:9251: $? = 0
configure:9283: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:59:4: error: unknown type name 'not'
    not big endian
    ^
conftest.c:59:12: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'endian'
    not big endian
            ^
configure:9290: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| #define HAVE_SSE2_CAST 1
| #define HAVE_FLUSH_ZERO_MODE 1
| #define HAVE_SSE2 1
| #define p7_IMPL_SSE 1
| #define HAVE_GZIP 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ENDIAN_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_NETINET_IN_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_SYS_SYSCTL_H 1
| #define HAVE_EMMINTRIN_H 1
| #define HAVE_PMMINTRIN_H 1
| #define HAVE_XMMINTRIN_H 1
| /* end confdefs.h.  */
| #include <sys/types.h>
| 		#include <sys/param.h>
| 
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| 		 not big endian
| 		#endif
| 
|   ;
|   return 0;
| }
configure:9542: result: no
configure:9568: checking for uint8_t
configure:9599: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:9606: $? = 0
configure:9627: result: yes
configure:9645: checking for uint16_t
configure:9676: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:9683: $? = 0
configure:9704: result: yes
configure:9718: checking for uint32_t
configure:9749: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:9756: $? = 0
configure:9777: result: yes
configure:9795: checking for uint64_t
configure:9826: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:9833: $? = 0
configure:9854: result: yes
configure:9871: checking for off_t
configure:9899: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:9906: $? = 0
configure:9933: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
conftest.c: In function 'main':
conftest.c:88:20: error: expected expression before ')' token
 if (sizeof ((off_t)))
                    ^
configure:9940: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| #define PACKAGE_NAME "Infernal"
| #define PACKAGE_TARNAME "infernal"
| #define PACKAGE_VERSION "1.1.1"
| #define PACKAGE_STRING "Infernal 1.1.1"
| #define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
| #define INFERNAL_DATE "July 2014"
| #define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define INFERNAL_VERSION "1.1.1"
| #define INFERNAL_URL "http://infernal.janelia.org/"
| #define HMMER_DATE "July 2014"
| #define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
| #define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
| #define HMMER_VERSION "i1.1.1"
| #define HMMER_URL "http://hmmer.org/"
| #define EASEL_DATE "July 2014"
| #define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
| #define EASEL_LICENSE "Freely distributed under the Janelia Software License."
| #define EASEL_VERSION "i1.1.1"
| #define eslLIBRARY 1
| #define eslDEBUGLEVEL 0
| #define HMMER_THREADS 1
| #define HAVE_PTHREAD 1
| #define HAVE_SSE2_CAST 1
| #define HAVE_FLUSH_ZERO_MODE 1
| #define HAVE_SSE2 1
| #define p7_IMPL_SSE 1
| #define HAVE_GZIP 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_ENDIAN_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_NETINET_IN_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_SYS_SYSCTL_H 1
| #define HAVE_EMMINTRIN_H 1
| #define HAVE_PMMINTRIN_H 1
| #define HAVE_XMMINTRIN_H 1
| /* end confdefs.h.  */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| #  include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| #  include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((off_t)))
| 	  return 0;
|   ;
|   return 0;
| }
configure:9963: result: yes
configure:9982: checking for mkstemp
configure:10038: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10045: $? = 0
configure:10067: result: yes
configure:10083: checking for popen
configure:10139: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10146: $? = 0
configure:10168: result: yes
configure:10184: checking for strcasecmp
configure:10240: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10247: $? = 0
configure:10269: result: yes
configure:10285: checking for times
configure:10341: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10348: $? = 0
configure:10370: result: yes
configure:10386: checking for getpid
configure:10442: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10449: $? = 0
configure:10471: result: yes
configure:10487: checking for sysctl
configure:10543: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10550: $? = 0
configure:10572: result: yes
configure:10588: checking for sysconf
configure:10644: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10651: $? = 0
configure:10673: result: yes
configure:10689: checking for getcwd
configure:10745: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10752: $? = 0
configure:10774: result: yes
configure:10790: checking for stat
configure:10846: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10853: $? = 0
configure:10875: result: yes
configure:10891: checking for fstat
configure:10947: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:10954: $? = 0
configure:10976: result: yes
configure:10993: checking for ntohs
configure:11049: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:11056: $? = 0
configure:11078: result: yes
configure:11170: checking for ntohl
configure:11226: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:11233: $? = 0
configure:11255: result: yes
configure:11347: checking for htons
configure:11403: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:11410: $? = 0
configure:11432: result: yes
configure:11524: checking for htonl
configure:11580: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:11587: $? = 0
configure:11609: result: yes
configure:11697: checking for _LARGEFILE_SOURCE value needed for large files
configure:11726: /usr/bin/gcc -std=gnu99 -o conftest -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include -L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib conftest.c  >&5
configure:11733: $? = 0
configure:11806: result: no
configure:11840: checking for special C compiler options needed for large files
configure:11935: result: no
configure:11941: checking for _FILE_OFFSET_BITS value needed for large files
configure:11976: /usr/bin/gcc -std=gnu99 -c -Os -w -pipe -march=core2 -isystem/home/linuxbrew/include conftest.c >&5
configure:11983: $? = 0
configure:12052: result: no
configure:12375: creating ./config.status

## ---------------------- ##
## Running config.status. ##
## ---------------------- ##

This file was extended by Infernal config.status 1.1.1, which was
generated by GNU Autoconf 2.63.  Invocation command line was

  CONFIG_FILES    = 
  CONFIG_HEADERS  = 
  CONFIG_LINKS    = 
  CONFIG_COMMANDS = 
  $ ./config.status 

on 526080-s598782

config.status:853: creating src/Makefile
config.status:853: creating src/impl_sse/Makefile
config.status:853: creating testsuite/Makefile
config.status:853: creating rmark/Makefile
config.status:853: creating documentation/Makefile
config.status:853: creating documentation/manpages/Makefile
config.status:853: creating documentation/userguide/Makefile
config.status:853: creating hmmer/documentation/Makefile
config.status:853: creating hmmer/documentation/man/Makefile
config.status:853: creating hmmer/documentation/userguide/Makefile
config.status:853: creating hmmer/src/Makefile
config.status:853: creating hmmer/testsuite/Makefile
config.status:853: creating hmmer/profmark/Makefile
config.status:853: creating hmmer/src/impl_sse/Makefile
config.status:853: creating hmmer/libdivsufsort/Makefile
config.status:853: creating hmmer/Makefile
config.status:853: creating easel/miniapps/Makefile
config.status:853: creating easel/testsuite/Makefile
config.status:853: creating easel/Makefile
config.status:853: creating easel/documentation/Makefile
config.status:853: creating Makefile
config.status:853: creating src/config.h
config.status:853: creating hmmer/src/p7_config.h
config.status:853: creating hmmer/libdivsufsort/divsufsort.h
config.status:853: creating easel/esl_config.h
config.status:1099: linking hmmer/src/impl_sse to hmmer/src/impl

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_uint16_t=yes
ac_cv_c_uint32_t=yes
ac_cv_c_uint64_t=yes
ac_cv_c_uint8_t=yes
ac_cv_env_CC_set=set
ac_cv_env_CC_value=/usr/bin/gcc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-Os -w -pipe -march=core2'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-isystem/home/linuxbrew/include
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib'
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_MPICC_set=
ac_cv_env_MPICC_value=
ac_cv_env_PIC_FLAGS_set=
ac_cv_env_PIC_FLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func_fstat=yes
ac_cv_func_getcwd=yes
ac_cv_func_getpid=yes
ac_cv_func_htonl=yes
ac_cv_func_htons=yes
ac_cv_func_mkstemp=yes
ac_cv_func_ntohl=yes
ac_cv_func_ntohs=yes
ac_cv_func_popen=yes
ac_cv_func_stat=yes
ac_cv_func_strcasecmp=yes
ac_cv_func_sysconf=yes
ac_cv_func_sysctl=yes
ac_cv_func_times=yes
ac_cv_header_emmintrin_h=yes
ac_cv_header_endian_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_netinet_in_h=yes
ac_cv_header_pmmintrin_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_param_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_sysctl_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_header_xmmintrin_h=yes
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_objext=o
ac_cv_path_AR=/bin/ar
ac_cv_path_EGREP='/bin/grep -E'
ac_cv_path_GREP=/bin/grep
ac_cv_path_HAVE_GZIP=/bin/gzip
ac_cv_path_install='/bin/install -c'
ac_cv_prog_CPP='/usr/bin/gcc -E'
ac_cv_prog_PTHREAD_CC=/usr/bin/gcc
ac_cv_prog_ac_ct_CC=/usr/bin/gcc
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_c99=-std=gnu99
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=-std=gnu99
ac_cv_sys_file_offset_bits=no
ac_cv_sys_largefile_CC=no
ac_cv_sys_largefile_source=no
ac_cv_type_off_t=yes
ax_cv_c_compiler_vendor=gnu
ax_cv_c_flags__msse2=yes
ax_cv_c_flags__msse2__msse3=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

AR='/bin/ar'
CC='/usr/bin/gcc -std=gnu99'
CFLAGS='-Os -w -pipe -march=core2'
CPP='/usr/bin/gcc -E'
CPPFLAGS='-isystem/home/linuxbrew/include'
DEFS='-DHAVE_CONFIG_H'
EASEL_COPYRIGHT='Copyright (C) 2014 HHMI Janelia Farm Research Campus'
EASEL_DATE='July 2014'
EASEL_LICENSE='Freely distributed under the Janelia Software License.'
EASEL_URL='http://bioeasel.org/'
EASEL_VERSION='i1.1.1'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/bin/grep -E'
EXEC_DEPENDENCY='%: %.o'
EXEEXT=''
GREP='/bin/grep'
GROUPHMMERLIBS='-Wl,--start-group -lhmmer -lhmmerimpl -Wl,--end-group'
HAVE_GZIP='/bin/gzip'
HMMERIMPLLIB='impl_sse/libhmmerimpl.a'
HMMER_COPYRIGHT='Copyright (C) 2014 Howard Hughes Medical Institute.'
HMMER_DATE='July 2014'
HMMER_ESLDIR='../easel'
HMMER_LICENSE='Freely distributed under the GNU General Public License (GPLv3).'
HMMER_SADIR='libdivsufsort'
HMMER_URL='http://hmmer.org/'
HMMER_VERSION='i1.1.1'
IMPL_CHOICE='sse'
INFERNAL_COPYRIGHT='Copyright (C) 2014 Howard Hughes Medical Institute.'
INFERNAL_DATE='July 2014'
INFERNAL_ESLDIR='easel'
INFERNAL_HMMERDIR='hmmer'
INFERNAL_IMPLDIR='impl_sse'
INFERNAL_LICENSE='Freely distributed under the GNU General Public License (GPLv3).'
INFERNAL_SADIR='hmmer/libdivsufsort'
INFERNAL_URL='http://infernal.janelia.org/'
INFERNAL_VERSION='1.1.1'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
LDFLAGS='-L/home/linuxbrew/lib -Wl,-rpath,/home/linuxbrew/lib'
LIBGSL=''
LIBOBJS=''
LIBS=''
LN_S='ln -s'
LTLIBOBJS=''
MPICC=''
MPILIBS=''
MPI_BENCHMARKS=''
MPI_UTESTS=''
OBJEXT='o'
PACKAGE_BUGREPORT='nawrockie@janelia.hhmi.org'
PACKAGE_NAME='Infernal'
PACKAGE_STRING='Infernal 1.1.1'
PACKAGE_TARNAME='infernal'
PACKAGE_VERSION='1.1.1'
PATH_SEPARATOR=':'
PIC_FLAGS='-fPIC'
PRTDIAG=''
PTHREAD_CC='/usr/bin/gcc'
PTHREAD_CFLAGS='-pthread'
PTHREAD_LIBS=''
RANLIB='ranlib'
SHELL='/bin/sh'
SIMD_CFLAGS='-msse2 -msse3'
ac_ct_CC='/usr/bin/gcc'
acx_pthread_config=''
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/home/linuxbrew/Cellar/infernal/1.1.1'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_NAME "Infernal"
#define PACKAGE_TARNAME "infernal"
#define PACKAGE_VERSION "1.1.1"
#define PACKAGE_STRING "Infernal 1.1.1"
#define PACKAGE_BUGREPORT "nawrockie@janelia.hhmi.org"
#define INFERNAL_DATE "July 2014"
#define INFERNAL_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
#define INFERNAL_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
#define INFERNAL_VERSION "1.1.1"
#define INFERNAL_URL "http://infernal.janelia.org/"
#define HMMER_DATE "July 2014"
#define HMMER_COPYRIGHT "Copyright (C) 2014 Howard Hughes Medical Institute."
#define HMMER_LICENSE "Freely distributed under the GNU General Public License (GPLv3)."
#define HMMER_VERSION "i1.1.1"
#define HMMER_URL "http://hmmer.org/"
#define EASEL_DATE "July 2014"
#define EASEL_COPYRIGHT "Copyright (C) 2014 HHMI Janelia Farm Research Campus"
#define EASEL_LICENSE "Freely distributed under the Janelia Software License."
#define EASEL_VERSION "i1.1.1"
#define eslLIBRARY 1
#define eslDEBUGLEVEL 0
#define HMMER_THREADS 1
#define HAVE_PTHREAD 1
#define HAVE_SSE2_CAST 1
#define HAVE_FLUSH_ZERO_MODE 1
#define HAVE_SSE2 1
#define p7_IMPL_SSE 1
#define HAVE_GZIP 1
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_ENDIAN_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_NETINET_IN_H 1
#define HAVE_SYS_PARAM_H 1
#define HAVE_SYS_SYSCTL_H 1
#define HAVE_EMMINTRIN_H 1
#define HAVE_PMMINTRIN_H 1
#define HAVE_XMMINTRIN_H 1
#define HAVE_MKSTEMP 1
#define HAVE_POPEN 1
#define HAVE_STRCASECMP 1
#define HAVE_TIMES 1
#define HAVE_GETPID 1
#define HAVE_SYSCTL 1
#define HAVE_SYSCONF 1
#define HAVE_GETCWD 1
#define HAVE_STAT 1
#define HAVE_FSTAT 1
#define HAVE_NTOHS 1
#define HAVE_NTOHL 1
#define HAVE_HTONS 1
#define HAVE_HTONL 1
#define HAVE_FSEEKO 1

configure: exit 0

config.out

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew.git
HEAD: 325f1adf2ad6c24b624c36b50455fbe152e6a46e
Last commit: 33 hours ago
HOMEBREW_PREFIX: /home/linuxbrew
HOMEBREW_CELLAR: /home/linuxbrew/Cellar
CPU: 72-core 64-bit 6
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: N/A
System Ruby: 2.0.0-p598 => /usr/bin/ruby
Perl: /bin/perl => /usr/bin/perl
Python: /bin/python => /usr/bin/python2.7
Ruby: /bin/ruby => /usr/bin/ruby
Java: 1.7.0_75

doctor.out

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:

  /bin/pkg-config
  /bin/rarian-sk-config
  /bin/scrollkeeper-config
  /bin/ncurses5-config
  /bin/brltty-config
  /bin/firewall-config
  /bin/xml2-config
  /bin/freetype-config
  /bin/libpng-config
  /bin/libpng15-config
  /bin/icu-config
  /bin/curl-config
  /bin/ncursesw5-config
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:

    google-sparsehash

tap.out

Formula: infernal
Tap: homebrew/homebrew-science
Path: /home/linuxbrew/Library/Taps/homebrew/homebrew-science/infernal.rb