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install.log
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Installing Dependencies
Install Zlib
/home/murraycadzow/Repo/selectionTools/zlib-1.2.8
Checking for gcc...
Checking for shared library support...
Building shared library libz.so.1.2.8 with gcc.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c
gcc -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c
gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.8 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc
rm -f libz.so libz.so.1
ln -s libz.so.1.2.8 libz.so
ln -s libz.so.1.2.8 libz.so.1
cp libz.a /home/murraycadzow/Repo/selectionTools/lib
chmod 644 /home/murraycadzow/Repo/selectionTools/lib/libz.a
cp libz.so.1.2.8 /home/murraycadzow/Repo/selectionTools/lib
chmod 755 /home/murraycadzow/Repo/selectionTools/lib/libz.so.1.2.8
cp zlib.3 /home/murraycadzow/Repo/selectionTools/share/man/man3
chmod 644 /home/murraycadzow/Repo/selectionTools/share/man/man3/zlib.3
cp zlib.pc /home/murraycadzow/Repo/selectionTools/lib/pkgconfig
chmod 644 /home/murraycadzow/Repo/selectionTools/lib/pkgconfig/zlib.pc
cp zlib.h zconf.h /home/murraycadzow/Repo/selectionTools/include
chmod 644 /home/murraycadzow/Repo/selectionTools/include/zlib.h /home/murraycadzow/Repo/selectionTools/include/zconf.h
Installing VCF tools
make[1]: Entering directory `/home/murraycadzow/Repo/selectionTools/vcftools_0.1.11/cpp'
g++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_entry_setters.cpp -o vcf_entry_setters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_entry_setters.cpp > vcf_entry_setters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_entry_setters.cpp -o bcf_entry_setters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_entry_setters.cpp > bcf_entry_setters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_filters.cpp -o variant_file_filters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_filters.cpp > variant_file_filters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_output.cpp -o variant_file_output.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_output.cpp > variant_file_output.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_format_convert.cpp -o variant_file_format_convert.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_format_convert.cpp > variant_file_format_convert.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_diff.cpp -o variant_file_diff.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_diff.cpp > variant_file_diff.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 header.cpp -o header.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 header.cpp > header.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 parameters.cpp -o parameters.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 parameters.cpp > parameters.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_index.cpp -o variant_file_index.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_index.cpp > variant_file_index.d
g++ -c -O2 -D_FILE_OFFSET_BITS=64 output_log.cpp -o output_log.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 output_log.cpp > output_log.d
gcc -O2 -m64 -O2 -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
bgzf.c: In function ‘bgzf_check_EOF’:
bgzf.c:60:39: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
#define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp))
^
bgzf.c:622:2: note: in expansion of macro ‘_bgzf_read’
_bgzf_read(fp->fp, buf, 28);
^
g++ -c -O2 -D_FILE_OFFSET_BITS=64 gamma.cpp -o gamma.o
g++ -MM -O2 -D_FILE_OFFSET_BITS=64 gamma.cpp > gamma.d
g++ -O2 -D_FILE_OFFSET_BITS=64 vcftools.o bcf_file.o vcf_file.o variant_file.o bcf_entry.o vcf_entry.o entry.o entry_setters.o entry_getters.o vcf_entry_setters.o bcf_entry_setters.o variant_file_filters.o variant_file_output.o variant_file_format_convert.o variant_file_diff.o header.o parameters.o variant_file_index.o output_log.o bgzf.o gamma.o -o vcftools -lz -L/home/murraycadzow/Repo/selectionTools/lib -I/home/murraycadzow/Repo/selectionTools/include
variant_file_format_convert.o: In function `variant_file::output_as_012_matrix(std::string const&)':
variant_file_format_convert.cpp:(.text+0x4208): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
cp /home/murraycadzow/Repo/selectionTools/vcftools_0.1.11/cpp/vcftools /home/murraycadzow/Repo/selectionTools/vcftools_0.1.11//bin/vcftools
make[1]: Leaving directory `/home/murraycadzow/Repo/selectionTools/vcftools_0.1.11/cpp'
make[1]: Entering directory `/home/murraycadzow/Repo/selectionTools/vcftools_0.1.11/perl'
make[1]: Leaving directory `/home/murraycadzow/Repo/selectionTools/vcftools_0.1.11/perl'
Installing QCTool
Installing PLINK
Archive: src/plink-1.07-x86_64.zip
creating: plink-1.07-x86_64/
inflating: plink-1.07-x86_64/plink
inflating: plink-1.07-x86_64/COPYING.txt
inflating: plink-1.07-x86_64/test.map
inflating: plink-1.07-x86_64/test.ped
inflating: plink-1.07-x86_64/gPLINK.jar
inflating: plink-1.07-x86_64/README.txt
Installing shapeit
Installing Impute2
Installing Tabix
make[1]: Entering directory `/home/murraycadzow/Repo/selectionTools/tabix-0.2.6'
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:435:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
int ret, count, block_length;
^
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE knetfile.c -o knetfile.o
In file included from knetfile.c:49:0:
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.h:9:37: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
knetfile.c:239:2: note: in expansion of macro ‘netwrite’
netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
^
knetfile.c: In function ‘khttp_connect_file’:
knetfile.h:9:37: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
#define netwrite(fd, ptr, len) write(fd, ptr, len)
^
knetfile.c:418:2: note: in expansion of macro ‘netwrite’
netwrite(fp->fd, buf, l);
^
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE index.c -o index.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bedidx.c -o bedidx.o
ar -csru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE main.c -o main.o
gcc -g -Wall -O2 -fPIC -o tabix main.o -L. -ltabix -lm -lz
gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzip.c -o bgzip.o
bgzip.c: In function ‘main’:
bgzip.c:198:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(f_dst, buffer, c);
^
bgzip.c: In function ‘write_open’:
bgzip.c:57:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
scanf("%c", &c);
^
gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
make[1]: Leaving directory `/home/murraycadzow/Repo/selectionTools/tabix-0.2.6'
Installing Variscan
I am going to run ./configure with no arguments - if you wish
to pass any to it, please specify them on the autogen.sh command line.
processing .
Running aclocal ...
aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Running automake --gnu ...
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
configure.in:3: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.in:3: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
configure.in:3: installing './install-sh'
configure.in:3: installing './missing'
src/Makefile.am: installing './depcomp'
automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
src/Makefile.am:47: warning: 'CFLAGS' is a user variable, you should not override it;
src/Makefile.am:47: use 'AM_CFLAGS' instead
Running autoconf ...
Running ./configure ...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: executing depfiles commands
Now type `make' to compile variscan
Making all in src
make[1]: Entering directory `/home/murraycadzow/Repo/selectionTools/variscan-2.0.3/src'
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT variscan.o -MD -MP -MF .deps/variscan.Tpo -c -o variscan.o variscan.c
variscan.c: In function ‘variscan’:
variscan.c:41:25: warning: variable ‘vpa’ set but not used [-Wunused-but-set-variable]
struct vscanPolyArray *vpa;
^
variscan.c: In function ‘vscanFileFormatAndNumSeq’:
variscan.c:286:17: warning: ISO C90 forbids mixed declarations and code [-Wpedantic]
long numsites = intExp(words[1]);
^
variscan.c: In function ‘createNumOfSeqsvscanSeq’:
variscan.c:626:19: warning: variable ‘vs’ set but not used [-Wunused-but-set-variable]
struct vscanSeq *vs;
^
variscan.c: In function ‘loadBlockDataFile’:
variscan.c:1530:13: warning: variable ‘wordCount’ set but not used [-Wunused-but-set-variable]
int wordCount;
^
mv -f .deps/variscan.Tpo .deps/variscan.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT statistics.o -MD -MP -MF .deps/statistics.Tpo -c -o statistics.o statistics.c
statistics.c: In function ‘calcRunMode11Stats’:
statistics.c:420:16: warning: variable ‘avgNumSeq’ set but not used [-Wunused-but-set-variable]
double avgNumSeq;
^
statistics.c: In function ‘comparePairwise’:
statistics.c:1411:41: warning: value computed is not used [-Wunused-value]
*zerocount--;
^
mv -f .deps/statistics.Tpo .deps/statistics.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.c
common.c: In function ‘firstWordInFile’:
common.c:1207:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(wordBuf, wordBufSize, f);
^
mv -f .deps/common.Tpo .deps/common.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT linefile.o -MD -MP -MF .deps/linefile.Tpo -c -o linefile.o linefile.c
mv -f .deps/linefile.Tpo .deps/linefile.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT memalloc.o -MD -MP -MF .deps/memalloc.Tpo -c -o memalloc.o memalloc.c
mv -f .deps/memalloc.Tpo .deps/memalloc.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT dlist.o -MD -MP -MF .deps/dlist.Tpo -c -o dlist.o dlist.c
mv -f .deps/dlist.Tpo .deps/dlist.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT errabort.o -MD -MP -MF .deps/errabort.Tpo -c -o errabort.o errabort.c
mv -f .deps/errabort.Tpo .deps/errabort.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT dystring.o -MD -MP -MF .deps/dystring.Tpo -c -o dystring.o dystring.c
mv -f .deps/dystring.Tpo .deps/dystring.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT intExp.o -MD -MP -MF .deps/intExp.Tpo -c -o intExp.o intExp.c
mv -f .deps/intExp.Tpo .deps/intExp.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT kxTok.o -MD -MP -MF .deps/kxTok.Tpo -c -o kxTok.o kxTok.c
mv -f .deps/kxTok.Tpo .deps/kxTok.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT pop.o -MD -MP -MF .deps/pop.Tpo -c -o pop.o pop.c
pop.c: In function ‘chooseSequences’:
pop.c:136:24: warning: variable ‘chosenVs_node’ set but not used [-Wunused-but-set-variable]
struct dlNode *chosenVs_node;
^
mv -f .deps/pop.Tpo .deps/pop.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT window.o -MD -MP -MF .deps/window.Tpo -c -o window.o window.c
mv -f .deps/window.Tpo .deps/window.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT free.o -MD -MP -MF .deps/free.Tpo -c -o free.o free.c
mv -f .deps/free.Tpo .deps/free.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT output.o -MD -MP -MF .deps/output.Tpo -c -o output.o output.c
mv -f .deps/output.Tpo .deps/output.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readphylip.o -MD -MP -MF .deps/readphylip.Tpo -c -o readphylip.o readphylip.c
readphylip.c: In function ‘phylipFirstStretch’:
readphylip.c:36:19: warning: variable ‘vs’ set but not used [-Wunused-but-set-variable]
struct vscanSeq *vs;
^
readphylip.c: In function ‘phylipNextStretch’:
readphylip.c:119:19: warning: variable ‘vs’ set but not used [-Wunused-but-set-variable]
struct vscanSeq *vs;
^
mv -f .deps/readphylip.Tpo .deps/readphylip.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readaxt.o -MD -MP -MF .deps/readaxt.Tpo -c -o readaxt.o readaxt.c
readaxt.c: In function ‘axtNextStretch’:
readaxt.c:33:26: warning: variable ‘vs’ set but not used [-Wunused-but-set-variable]
struct vscanSeq *vs;
^
readaxt.c:26:13: warning: variable ‘wordCount’ set but not used [-Wunused-but-set-variable]
int wordCount;
^
mv -f .deps/readaxt.Tpo .deps/readaxt.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readmga.o -MD -MP -MF .deps/readmga.Tpo -c -o readmga.o readmga.c
readmga.c: In function ‘mgaNextSegment’:
readmga.c:104:33: warning: value computed is not used [-Wunused-value]
*(initwords[1])++;
^
readmga.c:143:33: warning: value computed is not used [-Wunused-value]
*(start)++;
^
readmga.c:44:13: warning: variable ‘wordCount’ set but not used [-Wunused-but-set-variable]
int wordCount;
^
readmga.c:40:13: warning: variable ‘initCount’ set but not used [-Wunused-but-set-variable]
int initCount;
^
readmga.c: In function ‘readMgaAli’:
readmga.c:203:13: warning: variable ‘wordCount’ set but not used [-Wunused-but-set-variable]
int wordCount;
^
readmga.c: In function ‘annotateMgaGap’:
readmga.c:271:17: warning: value computed is not used [-Wunused-value]
*(c)++;
^
readmga.c:282:17: warning: value computed is not used [-Wunused-value]
*(c)++;
^
readmga.c:286:17: warning: value computed is not used [-Wunused-value]
*(c)++;
^
mv -f .deps/readmga.Tpo .deps/readmga.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readmaf.o -MD -MP -MF .deps/readmaf.Tpo -c -o readmaf.o readmaf.c
mv -f .deps/readmaf.Tpo .deps/readmaf.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readhapmap.o -MD -MP -MF .deps/readhapmap.Tpo -c -o readhapmap.o readhapmap.c
mv -f .deps/readhapmap.Tpo .deps/readhapmap.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readxmfa.o -MD -MP -MF .deps/readxmfa.Tpo -c -o readxmfa.o readxmfa.c
mv -f .deps/readxmfa.Tpo .deps/readxmfa.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT readmav.o -MD -MP -MF .deps/readmav.Tpo -c -o readmav.o readmav.c
readmav.c: In function ‘mavNextStretch’:
readmav.c:28:13: warning: variable ‘wordCount’ set but not used [-Wunused-but-set-variable]
int wordCount=0;
^
mv -f .deps/readmav.Tpo .deps/readmav.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT ran1.o -MD -MP -MF .deps/ran1.Tpo -c -o ran1.o ran1.c
mv -f .deps/ran1.Tpo .deps/ran1.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT swcolumn.o -MD -MP -MF .deps/swcolumn.Tpo -c -o swcolumn.o swcolumn.c
mv -f .deps/swcolumn.Tpo .deps/swcolumn.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT swnet.o -MD -MP -MF .deps/swnet.Tpo -c -o swnet.o swnet.c
mv -f .deps/swnet.Tpo .deps/swnet.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT swpoly.o -MD -MP -MF .deps/swpoly.Tpo -c -o swpoly.o swpoly.c
mv -f .deps/swpoly.Tpo .deps/swpoly.Po
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"variscan\" -DVERSION=\"1.0.1\" -I. -DVARISCAN -DNDEBUG -O3 -W -Wall -ansi -pedantic -MT swref.o -MD -MP -MF .deps/swref.Tpo -c -o swref.o swref.c
mv -f .deps/swref.Tpo .deps/swref.Po
gcc -DNDEBUG -O3 -W -Wall -ansi -pedantic -o variscan variscan.o statistics.o common.o linefile.o memalloc.o dlist.o errabort.o dystring.o intExp.o kxTok.o pop.o window.o free.o output.o readphylip.o readaxt.o readmga.o readmaf.o readhapmap.o readxmfa.o readmav.o ran1.o swcolumn.o swnet.o swpoly.o swref.o -lm
make[1]: Leaving directory `/home/murraycadzow/Repo/selectionTools/variscan-2.0.3/src'
make[1]: Entering directory `/home/murraycadzow/Repo/selectionTools/variscan-2.0.3'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/murraycadzow/Repo/selectionTools/variscan-2.0.3'
mv: cannot stat ‘variscan-2.0.3/src/variscan’: No such file or directory
Installing getopt
[1] "getopt"
Installing package into ‘/home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/getopt_1.20.0.tar.gz'
Content type 'application/x-gzip' length 16473 bytes (16 Kb)
opened URL
==================================================
downloaded 16 Kb
* installing *source* package ‘getopt’ ...
** package ‘getopt’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (getopt)
The downloaded source packages are in
‘/tmp/RtmpqhPGUy/downloaded_packages’
Installing R Multicore
[1] "multicore"
Installing package into ‘/home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/multicore_0.1-7.tar.gz'
Content type 'application/x-gzip' length 25300 bytes (24 Kb)
opened URL
==================================================
downloaded 24 Kb
* installing *source* package ‘multicore’ ...
** package ‘multicore’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c fork.c -o fork.o
fork.c: In function ‘mc_exit’:
fork.c:633:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
write(master_fd, &len, sizeof(len));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c forknt.c -o forknt.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c perf.c -o perf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c winfix.c -o winfix.o
gcc -std=gnu99 -shared -o multicore.so fork.o forknt.o perf.o winfix.o -L/usr/lib/R/lib -lR
installing to /home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0/multicore/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (multicore)
The downloaded source packages are in
‘/tmp/RtmpTGDqUk/downloaded_packages’
Installing old rehh
[1] "rehh"
Installing package into ‘/home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/rehh_1.11.tar.gz'
Content type 'application/x-gzip' length 2204723 bytes (2.1 Mb)
opened URL
==================================================
downloaded 2.1 Mb
* installing *source* package ‘rehh’ ...
** package ‘rehh’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c ehh_utils.c -o ehh_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c r_ehh.c -o r_ehh.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c r_ehhs.c -o r_ehhs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c r_scan_hh.c -o r_scan_hh.o
gcc -std=gnu99 -shared -o rehh.so ehh_utils.o r_ehh.o r_ehhs.o r_scan_hh.o -L/usr/lib/R/lib -lR
installing to /home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0/rehh/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rehh)
The downloaded source packages are in
‘/tmp/RtmpEBRsUt/downloaded_packages’
Install rehh
* installing to library ‘/home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0’
* installing *source* package ‘rehh’ ...
files ‘DESCRIPTION’, ‘R/ies2rsb.R’, ‘R/ihh2ihs.R’, ‘R/ihsplot.R’, ‘R/scan_hh.R’, ‘src/ehh_utils.c’, ‘src/ehh_utils.h’, ‘src/r_scan_hh.c’ have the wrong MD5 checksums
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c ehh_utils.c -o ehh_utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c r_scan_hh.c -o r_scan_hh.o
gcc -std=gnu99 -shared -o rehh.so ehh_utils.o r_ehh.o r_ehhs.o r_scan_hh.o -L/usr/lib/R/lib -lR
installing to /home/murraycadzow/R/x86_64-pc-linux-gnu-library/3.0/rehh/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rehh)
Updating submodules
Generating Default Config File
Installing PyFasta
running install
running bdist_egg
running egg_info
writing pyfasta.egg-info/PKG-INFO
writing top-level names to pyfasta.egg-info/top_level.txt
writing dependency_links to pyfasta.egg-info/dependency_links.txt
writing entry points to pyfasta.egg-info/entry_points.txt
reading manifest file 'pyfasta.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pyfasta.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pyfasta
copying build/lib.linux-x86_64-2.7/pyfasta/split_fasta.py -> build/bdist.linux-x86_64/egg/pyfasta
copying build/lib.linux-x86_64-2.7/pyfasta/fasta.py -> build/bdist.linux-x86_64/egg/pyfasta
copying build/lib.linux-x86_64-2.7/pyfasta/records.py -> build/bdist.linux-x86_64/egg/pyfasta
copying build/lib.linux-x86_64-2.7/pyfasta/__init__.py -> build/bdist.linux-x86_64/egg/pyfasta
byte-compiling build/bdist.linux-x86_64/egg/pyfasta/split_fasta.py to split_fasta.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyfasta/fasta.py to fasta.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyfasta/records.py to records.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyfasta/__init__.py to __init__.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying pyfasta.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyfasta.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyfasta.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyfasta.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyfasta.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyfasta.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/pyfasta-0.5.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pyfasta-0.5.0-py2.7.egg
removing '/home/murraycadzow/.local/lib/python2.7/site-packages/pyfasta-0.5.0-py2.7.egg' (and everything under it)
creating /home/murraycadzow/.local/lib/python2.7/site-packages/pyfasta-0.5.0-py2.7.egg
Extracting pyfasta-0.5.0-py2.7.egg to /home/murraycadzow/.local/lib/python2.7/site-packages
pyfasta 0.5.0 is already the active version in easy-install.pth
Installing pyfasta script to /home/murraycadzow/.local/bin
Installed /home/murraycadzow/.local/lib/python2.7/site-packages/pyfasta-0.5.0-py2.7.egg
Processing dependencies for pyfasta==0.5.0
Finished processing dependencies for pyfasta==0.5.0
Install PyVCF
running install
running bdist_egg
running egg_info
writing requirements to PyVCF.egg-info/requires.txt
writing PyVCF.egg-info/PKG-INFO
writing top-level names to PyVCF.egg-info/top_level.txt
writing dependency_links to PyVCF.egg-info/dependency_links.txt
writing entry points to PyVCF.egg-info/entry_points.txt
reading manifest file 'PyVCF.egg-info/SOURCES.txt'
writing manifest file 'PyVCF.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/vcf
copying build/lib.linux-x86_64-2.7/vcf/parser.py -> build/bdist.linux-x86_64/egg/vcf
copying build/lib.linux-x86_64-2.7/vcf/utils.py -> build/bdist.linux-x86_64/egg/vcf
copying build/lib.linux-x86_64-2.7/vcf/__init__.py -> build/bdist.linux-x86_64/egg/vcf
creating build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/1kg.sites.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/example-4.1-sv.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/samples-space.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/tb.vcf.gz.tbi -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/example-4.1.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/null_genotype_mono.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/example-4.1-bnd.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/issue-16.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/bcftools.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/1kg.vcf.gz -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/tb.vcf.gz -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/gatk_26_meta.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/walk_left.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/test_vcf.py -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/gatk.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/__init__.py -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/example-4.0.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/example-4.1-info-multiple-values.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/issue_49.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/prof.py -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/mixed-filtering.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/freebayes.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/gonl.chr20.release4.gtc.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/test/samtools.vcf -> build/bdist.linux-x86_64/egg/vcf/test
copying build/lib.linux-x86_64-2.7/vcf/filters.py -> build/bdist.linux-x86_64/egg/vcf
copying build/lib.linux-x86_64-2.7/vcf/model.py -> build/bdist.linux-x86_64/egg/vcf
byte-compiling build/bdist.linux-x86_64/egg/vcf/parser.py to parser.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/utils.py to utils.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/test/test_vcf.py to test_vcf.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/test/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/test/prof.py to prof.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/filters.py to filters.pyc
byte-compiling build/bdist.linux-x86_64/egg/vcf/model.py to model.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/vcf_melt -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/vcf_filter.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/vcf_melt to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/vcf_filter.py to 755
copying PyVCF.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying PyVCF.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying PyVCF.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying PyVCF.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying PyVCF.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying PyVCF.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
vcf.test.test_vcf: module references __file__
creating 'dist/PyVCF-0.6.4-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing PyVCF-0.6.4-py2.7.egg
removing '/home/murraycadzow/.local/lib/python2.7/site-packages/PyVCF-0.6.4-py2.7.egg' (and everything under it)
creating /home/murraycadzow/.local/lib/python2.7/site-packages/PyVCF-0.6.4-py2.7.egg
Extracting PyVCF-0.6.4-py2.7.egg to /home/murraycadzow/.local/lib/python2.7/site-packages
PyVCF 0.6.4 is already the active version in easy-install.pth
Installing vcf_melt script to /home/murraycadzow/.local/bin
Installing vcf_filter.py script to /home/murraycadzow/.local/bin
Installed /home/murraycadzow/.local/lib/python2.7/site-packages/PyVCF-0.6.4-py2.7.egg
Processing dependencies for PyVCF==0.6.4
Searching for distribute==0.6.35
Best match: distribute 0.6.35
Processing distribute-0.6.35-py2.7.egg
distribute 0.6.35 is already the active version in easy-install.pth
Installing easy_install script to /home/murraycadzow/.local/bin
Installing easy_install-2.7 script to /home/murraycadzow/.local/bin
Using /usr/local/lib/python2.7/dist-packages/distribute-0.6.35-py2.7.egg
Finished processing dependencies for PyVCF==0.6.4
Installing selection_pipeline
running install
running bdist_egg
running egg_info
writing selectionTools.egg-info/PKG-INFO
writing top-level names to selectionTools.egg-info/top_level.txt
writing dependency_links to selectionTools.egg-info/dependency_links.txt
writing entry points to selectionTools.egg-info/entry_points.txt
reading manifest file 'selectionTools.egg-info/SOURCES.txt'
writing manifest file 'selectionTools.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/version.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/run_pipeline.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/standard_run_utilities.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/haps_filters.py -> build/bdist.linux-x86_64/egg/selection_pipeline
creating build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/filter.haps -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/CEU_test.ids -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/one_line.haps -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/ancestor.fa -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/defaults.cfg -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/test_selection_pipeline.py -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/__init__.py -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/tests/CEU_test.vcf -> build/bdist.linux-x86_64/egg/selection_pipeline/tests
copying build/lib.linux-x86_64-2.7/selection_pipeline/environment.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/__init__.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/standard_run.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/haps_to_hapmap.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/multipipeline.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/selection_pipeline.py -> build/bdist.linux-x86_64/egg/selection_pipeline
copying build/lib.linux-x86_64-2.7/selection_pipeline/aa_annotate.py -> build/bdist.linux-x86_64/egg/selection_pipeline
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/version.py to version.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/run_pipeline.py to run_pipeline.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/standard_run_utilities.py to standard_run_utilities.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/haps_filters.py to haps_filters.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/tests/test_selection_pipeline.py to test_selection_pipeline.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/tests/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/environment.py to environment.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/standard_run.py to standard_run.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/haps_to_hapmap.py to haps_to_hapmap.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/multipipeline.py to multipipeline.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/selection_pipeline.py to selection_pipeline.pyc
byte-compiling build/bdist.linux-x86_64/egg/selection_pipeline/aa_annotate.py to aa_annotate.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying selectionTools.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying selectionTools.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying selectionTools.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying selectionTools.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying selectionTools.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying selectionTools.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/selectionTools-0.9-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing selectionTools-0.9-py2.7.egg
removing '/home/murraycadzow/.local/lib/python2.7/site-packages/selectionTools-0.9-py2.7.egg' (and everything under it)
creating /home/murraycadzow/.local/lib/python2.7/site-packages/selectionTools-0.9-py2.7.egg
Extracting selectionTools-0.9-py2.7.egg to /home/murraycadzow/.local/lib/python2.7/site-packages
selectionTools 0.9 is already the active version in easy-install.pth
Installing haps_to_hapmap script to /home/murraycadzow/.local/bin
Installing haps_filters script to /home/murraycadzow/.local/bin
Installing multi_population script to /home/murraycadzow/.local/bin
Installing ancestral_annotation script to /home/murraycadzow/.local/bin
Installing selection_pipeline script to /home/murraycadzow/.local/bin
Installed /home/murraycadzow/.local/lib/python2.7/site-packages/selectionTools-0.9-py2.7.egg
Processing dependencies for selectionTools==0.9
Finished processing dependencies for selectionTools==0.9