ea-utils (homebrew/science/ea-utils) on x86_64-linux - Homebrew build logs

# ea-utils - 2016-01-17_17-55-48.txt

Homebrew build logs for homebrew/science/ea-utils on x86_64-linux
Build date: 2016-01-17 17:55:48

00.config.out

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: 2ec1334dec2af1192f572d8c2a8bc8687dc6cb28
Last commit: 3 days ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_REPOSITORY: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: 2.7.8 => /usr
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.10/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: openjdk version "1.8.0_65"

00.doctor.out

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: Some installed formula are missing dependencies.
You should `brew install` the missing dependencies:

    brew install libuuid

Run `brew missing` for more details.

00.tap.out

Formula: ea-utils
Tap: homebrew/science
Path: /bio/linuxbrew/Library/Taps/homebrew/homebrew-science/ea-utils.rb

01.make

2016-01-17 17:55:48 +1100

make
install
PREFIX=/bio/linuxbrew/Cellar/ea-utils/1.1.2-806

cd sparsehash-2.0.2; ./configure; make
cd samtools && make libbam.a
mkdir -p /bio/linuxbrew/Cellar/ea-utils/1.1.2-806/bin
make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[1]: Entering directory '/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/samtools'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
cp fastx-graph /bio/linuxbrew/Cellar/ea-utils/1.1.2-806/bin/fastx-graph
cp determine-phred /bio/linuxbrew/Cellar/ea-utils/1.1.2-806/bin/determine-phred
cp randomFQ /bio/linuxbrew/Cellar/ea-utils/1.1.2-806/bin/randomFQ
cp alc /bio/linuxbrew/Cellar/ea-utils/1.1.2-806/bin/alc
bgzf.c: In function 'worker_aux':
bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  int i, tmp, stop = 0;
         ^
bgzf.c: In function 'bgzf_close':
bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
checking for a BSD-compatible install... /bio/linuxbrew/bin/ginstall -c
checking whether build environment is sane... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
yes
checking for a thread-safe mkdir -p... /bio/linuxbrew/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /bio/linuxbrew/bin/g++-5 accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of /bio/linuxbrew/bin/g++-5... gcc3
checking for gcc... g++
checking whether we are using the GNU C compiler... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
yes
checking whether g++ accepts -g... yes
checking for g++ option to accept ISO C89... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
unsupported
checking dependency style of g++... gcc3
checking how to run the C preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for memcpy... yes
checking for memmove... 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... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
yes
checking for uint16_t... bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
  int k, is_head = 0;
         ^
yes
checking for u_int16_t... yes
checking for __uint16... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
no
checking for long long... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for unistd.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking how to run the C++ preprocessor... /bio/linuxbrew/bin/g++-5 -E
checking google/malloc_extension.h usability... no
checking google/malloc_extension.h presence... no
checking for google/malloc_extension.h... no
checking whether the compiler implements namespaces... yes
checking the location of hash_map... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
<tr1/unordered_map>
checking how to include hash_fun directly... <tr1/functional>
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[1]: Entering directory '/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run aclocal-1.11 -I m4
/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2/missing: line 52: aclocal-1.11: command not found
WARNING: `aclocal-1.11' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `configure.ac'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.
 cd . && /bin/sh /tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run automake-1.11 --gnu
/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2/missing: line 52: automake-1.11: command not found
WARNING: `automake-1.11' is missing on your system.  You should only need it if
         you modified `Makefile.am', `acinclude.m4' or `configure.ac'.
         You might want to install the `Automake' and `Perl' packages.
         Grab them from any GNU archive site.
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run autoconf
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
aclocal.m4:16: warning: this file was generated for autoconf 2.68.
You have another version of autoconf.  It may work, but is not guaranteed to.
If you have problems, you may need to regenerate the build system entirely.
To do so, use the procedure documented by the package, typically `autoreconf'.
/bin/sh ./config.status --recheck
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
running CONFIG_SHELL=/bin/sh /bin/sh ./configure CXX=/bio/linuxbrew/bin/g++-5 CXXFLAGS=-Os -w -pipe -march=core2 LDFLAGS=-L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib CPPFLAGS=-isystem/bio/linuxbrew/include CC=g++ CFLAGS=-Os -w -pipe -march=core2 --no-create --no-recursion
checking for a BSD-compatible install... /bio/linuxbrew/bin/ginstall -c
checking whether build environment is sane... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
In file included from bam_sort.c:9:0:
bam_sort.c:363:26: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
 KSORT_INIT(sort, bam1_p, bam1_lt)
                          ^
ksort.h:148:25: note: in definition of macro 'KSORT_INIT'
    for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {   \
                         ^
bam_sort.c:57:27: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static
 KSORT_INIT(heap, heap1_t, heap_lt)
                           ^
ksort.h:148:25: note: in definition of macro 'KSORT_INIT'
    for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {   \
                         ^
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
bam_reheader.c: In function 'bam_reheader':
bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
  bam_header_t *old;
                ^
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
yes
checking for a thread-safe mkdir -p... /bio/linuxbrew/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o

checking whether we are cross compiling... ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
make[1]: Leaving directory '/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/samtools'
no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /bio/linuxbrew/bin/g++-5 accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of /bio/linuxbrew/bin/g++-5... gcc3
checking for gcc... g++
checking whether we are using the GNU C compiler... yes
checking whether g++ accepts -g... yes
checking for g++ option to accept ISO C89... unsupported
checking dependency style of g++... gcc3
checking how to run the C preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for memcpy... yes
checking for memmove... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for uint16_t... yes
checking for u_int16_t... yes
checking for __uint16... no
checking for long long... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for unistd.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking how to run the C++ preprocessor... /bio/linuxbrew/bin/g++-5 -E
checking google/malloc_extension.h usability... no
checking google/malloc_extension.h presence... no
checking for google/malloc_extension.h... no
checking whether the compiler implements namespaces... yes
checking the location of hash_map... <tr1/unordered_map>
checking how to include hash_fun directly... <tr1/functional>
configure: creating ./config.status
 /bin/sh ./config.status
config.status: creating Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2/missing --run autoheader)
rm -f src/stamp-h1
touch src/config.h.in
cd . && /bin/sh ./config.status src/config.h
config.status: creating src/config.h
config.status: src/config.h is unchanged
make  all-am
make[2]: Entering directory '/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2'
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT template_util_unittest.o -MD -MP -MF .deps/template_util_unittest.Tpo -c -o template_util_unittest.o `test -f 'src/template_util_unittest.cc' || echo './'`src/template_util_unittest.cc
mv -f .deps/template_util_unittest.Tpo .deps/template_util_unittest.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o template_util_unittest template_util_unittest.o   
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT type_traits_unittest.o -MD -MP -MF .deps/type_traits_unittest.Tpo -c -o type_traits_unittest.o `test -f 'src/type_traits_unittest.cc' || echo './'`src/type_traits_unittest.cc
mv -f .deps/type_traits_unittest.Tpo .deps/type_traits_unittest.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o type_traits_unittest type_traits_unittest.o    
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT libc_allocator_with_realloc_test.o -MD -MP -MF .deps/libc_allocator_with_realloc_test.Tpo -c -o libc_allocator_with_realloc_test.o `test -f 'src/libc_allocator_with_realloc_test.cc' || echo './'`src/libc_allocator_with_realloc_test.cc
mv -f .deps/libc_allocator_with_realloc_test.Tpo .deps/libc_allocator_with_realloc_test.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o libc_allocator_with_realloc_test libc_allocator_with_realloc_test.o   
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT sparsetable_unittest.o -MD -MP -MF .deps/sparsetable_unittest.Tpo -c -o sparsetable_unittest.o `test -f 'src/sparsetable_unittest.cc' || echo './'`src/sparsetable_unittest.cc
mv -f .deps/sparsetable_unittest.Tpo .deps/sparsetable_unittest.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o sparsetable_unittest sparsetable_unittest.o    
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT hashtable_test.o -MD -MP -MF .deps/hashtable_test.Tpo -c -o hashtable_test.o `test -f 'src/hashtable_test.cc' || echo './'`src/hashtable_test.cc
mv -f .deps/hashtable_test.Tpo .deps/hashtable_test.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o hashtable_test hashtable_test.o     
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT simple_test.o -MD -MP -MF .deps/simple_test.Tpo -c -o simple_test.o `test -f 'src/simple_test.cc' || echo './'`src/simple_test.cc
mv -f .deps/simple_test.Tpo .deps/simple_test.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o simple_test simple_test.o    
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT simple_compat_test.o -MD -MP -MF .deps/simple_compat_test.Tpo -c -o simple_compat_test.o `test -f 'src/simple_compat_test.cc' || echo './'`src/simple_compat_test.cc
mv -f .deps/simple_compat_test.Tpo .deps/simple_compat_test.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o simple_compat_test simple_compat_test.o      
/bio/linuxbrew/bin/g++-5 -DHAVE_CONFIG_H -I. -I./src  -I./src -isystem/bio/linuxbrew/include -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2 -MT time_hash_map-time_hash_map.o -MD -MP -MF .deps/time_hash_map-time_hash_map.Tpo -c -o time_hash_map-time_hash_map.o `test -f 'src/time_hash_map.cc' || echo './'`src/time_hash_map.cc
mv -f .deps/time_hash_map-time_hash_map.Tpo .deps/time_hash_map-time_hash_map.Po
/bio/linuxbrew/bin/g++-5 -Wall -W -Wwrite-strings -Woverloaded-virtual -Wshadow -Os -w -pipe -march=core2  -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib -o time_hash_map time_hash_map-time_hash_map.o     
echo 'prefix=/usr/local' > "libsparsehash.pc".tmp
echo 'exec_prefix='`echo '/usr/local' | sed 's@^/usr/local@${prefix}@'` >> "libsparsehash.pc".tmp
echo 'libdir='`echo '/usr/local/lib' | sed 's@^/usr/local@${exec_prefix}@'` >> "libsparsehash.pc".tmp
echo 'includedir='`echo '/usr/local/include' | sed 's@^/usr/local@${prefix}@'` >> "libsparsehash.pc".tmp
echo '' >> "libsparsehash.pc".tmp
echo 'Name: sparsehash' >> "libsparsehash.pc".tmp
echo 'Version: 2.0.2' >> "libsparsehash.pc".tmp
grep '^Summary:' ./packages/rpm/rpm.spec | sed s/^Summary:/Description:/ | head -n1 >> "libsparsehash.pc".tmp
grep '^URL: ' ./packages/rpm/rpm.spec >> "libsparsehash.pc".tmp
echo 'Requires:' >> "libsparsehash.pc".tmp
echo 'Libs:' >> "libsparsehash.pc".tmp
echo 'Cflags: -I${includedir}' >> "libsparsehash.pc".tmp
mv -f "libsparsehash.pc".tmp "libsparsehash.pc"
make[2]: Leaving directory '/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2'
make[1]: Leaving directory '/tmp/ea-utils20160117-10881-uu8mzd/ea-utils.1.1.2-806/sparsehash-2.0.2'
mkdir sparsehash
cp -r sparsehash-2.0.2/src/sparsehash/* sparsehash/
g++ -Os -w -pipe -march=core2 fastq-mcf.cpp fastq-lib.cpp -o fastq-mcf
g++ -Os -w -pipe -march=core2 fastq-multx.cpp fastq-lib.cpp -o fastq-multx
g++ -Os -w -pipe -march=core2 fastq-join.cpp fastq-lib.cpp -o fastq-join
g++ -Os -w -pipe -march=core2 fastq-lib.cpp gcModel.cpp -o fastq-stats fastq-stats.cpp
g++ -Os -w -pipe -march=core2 fastq-clipper.cpp fastq-lib.cpp -o fastq-clipper
g++ -Os -w -pipe -march=core2 samtools/*.o -lz -lpthread fastq-lib.cpp sam-stats.cpp -o sam-stats
g++ -Os -w -pipe -march=core2 fastq-lib.cpp tidx/tidx-lib.cpp -o varcall varcall.cpp -lgsl -lgslcblas
fastq-mcf.cpp:29:81: fatal error: sparsehash/sparse_hash_map: No such file or directory
compilation terminated.
Makefile:71: recipe for target 'fastq-mcf' failed
make: *** [fastq-mcf] Error 1
make: *** Waiting for unfinished jobs....
tidx/tidx-lib.cpp:12:37: fatal error: sparsehash/dense_hash_map: No such file or directory
compilation terminated.
sam-stats.cpp:37:81: fatal error: sparsehash/sparse_hash_map: No such file or directory
compilation terminated.
Makefile:83: recipe for target 'sam-stats' failed
make: *** [sam-stats] Error 1
varcall.cpp:33:29: fatal error: gsl/gsl_randist.h: No such file or directory
compilation terminated.
Makefile:96: recipe for target 'varcall' failed
make: *** [varcall] Error 1
fastq-stats.cpp:78:81: fatal error: sparsehash/sparse_hash_map: No such file or directory
compilation terminated.
Makefile:100: recipe for target 'fastq-stats' failed
make: *** [fastq-stats] Error 1

HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/linuxbrew
HEAD: 2ec1334dec2af1192f572d8c2a8bc8687dc6cb28
Last commit: 3 days ago
HOMEBREW_PREFIX: /bio/linuxbrew
HOMEBREW_REPOSITORY: /bio/linuxbrew
HOMEBREW_CELLAR: /bio/linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 72-core 64-bit haswell
OS X: 0-x86_64
Xcode: N/A
CLT: N/A
Clang: N/A
X11: 2.7.8 => /usr
System Ruby: 2.2.2 => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Perl: /usr/bin/perl
Python: /bio/linuxbrew/bin/python => /bio/linuxbrew/Cellar/python/2.7.10/bin/python2.7
Ruby: /bio/linuxbrew/bin/ruby => /bio/linuxbrew/Cellar/ruby/2.2.2/bin/ruby
Java: openjdk version "1.8.0_65"

CC: /bio/linuxbrew/bin/gcc-5 => /bio/linuxbrew/Cellar/gcc/5.3.0/bin/gcc-5
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OBJC: /bio/linuxbrew/bin/gcc-5
OBJCXX: /bio/linuxbrew/bin/g++-5
CFLAGS: -Os -w -pipe -march=core2
CXXFLAGS: -Os -w -pipe -march=core2
CPPFLAGS: -isystem/bio/linuxbrew/include
LDFLAGS: -L/bio/linuxbrew/lib -Wl,-rpath,/bio/linuxbrew/lib
MAKEFLAGS: -j72
CMAKE_PREFIX_PATH: /bio/linuxbrew
PKG_CONFIG_LIBDIR: /bio/linuxbrew/lib/pkgconfig:/bio/linuxbrew/share/pkgconfig
PATH: /home/tseemann/perl5/bin:/bio/perl5/bin:/bio/linuxbrew/bin:/bio/linuxbrew/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/home/agoncalves/bin:/bio/sw/hierBAPS:/bio/sw/brat:/bio/sw/mauve:/bio/sw/splitstree4:/bio/sw/vbc/fqa-tools:/bio/sw/vbc/misc:/bio/sw/MUMmer:/bio/sw/tablet:/home/tseemann/git/wombac/bin:/home/tseemann/git/snippy/bin:/home/tseemann/git/barrnap/bin:/home/tseemann/git/nullarbor/bin:/home/tseemann/git/prokka/bin:/home/tseemann/git/mlst/bin:/home/tseemann/git/abricate/bin:/home/tseemann/git/mdu-tools/bin:/usr/local/sbin:/usr/sbin:/home/tseemann/.local/bin:/home/tseemann/bin:/bio/linuxbrew/Library/ENV/scm