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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
16 stars 7 forks source link

libtool required for install #29

Closed chuckpr closed 8 years ago

chuckpr commented 8 years ago

Just installed on Ubuntu 14.04 and had to install libtool in addition to other packages noted in the installation manual.

root@master:/home/ubuntu/BamM# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 14.04.3 LTS
Release:    14.04
Codename:   trusty
root@master:/home/ubuntu/BamM# uname -a
Linux master 3.13.0-61-generic #100-Ubuntu SMP Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

...just FYI, otherwise installation went very smoothly.

chuckpr commented 8 years ago

Actually, nosetests are failing.

root@master:/home/ubuntu# git clone https://github.com/Ecogenomics/BamM.git
Cloning into 'BamM'...
remote: Counting objects: 1860, done.
remote: Total 1860 (delta 0), reused 0 (delta 0), pack-reused 1860
Receiving objects: 100% (1860/1860), 88.89 MiB | 5.62 MiB/s, done.
Resolving deltas: 100% (1101/1101), done.
Checking connectivity... done.
root@master:/home/ubuntu# cd BamM/
root@master:/home/ubuntu/BamM# python setup.py install
Preparing the BamM build system...please wait

Found GNU Autoconf version 2.69
Found GNU Automake version 1.14.1
Found GNU Libtool version 2.4.2

Automatically preparing build ... done

The BamM build system is now prepared. To build here, run:
 ./configure
 make
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 g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for lgamma,log,exp in -lm... yes
libcfu location not specified - building from local version
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 build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for pthread_mutex_init... yes
checking for ANSI C header files... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for gettimeofday... yes
checking for memset... yes
checking for strcasecmp... yes
checking for strncasecmp... yes
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
config.status: executing libtool commands
Making clean in src
make[1]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
rm -f *.o
rm -f ../lib/libcfu.a
make[1]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
make[1]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03'
rm -rf .libs _libs
rm -f *.lo
make[1]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03'
Making all in src
make[1]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfuhash.o -MD -MP -MF .deps/cfuhash.Tpo -c -o cfuhash.o cfuhash.c
mv -f .deps/cfuhash.Tpo .deps/cfuhash.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfutime.o -MD -MP -MF .deps/cfutime.Tpo -c -o cfutime.o cfutime.c
mv -f .deps/cfutime.Tpo .deps/cfutime.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfustring.o -MD -MP -MF .deps/cfustring.Tpo -c -o cfustring.o cfustring.c
mv -f .deps/cfustring.Tpo .deps/cfustring.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfulist.o -MD -MP -MF .deps/cfulist.Tpo -c -o cfulist.o cfulist.c
mv -f .deps/cfulist.Tpo .deps/cfulist.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfuconf.o -MD -MP -MF .deps/cfuconf.Tpo -c -o cfuconf.o cfuconf.c
mv -f .deps/cfuconf.Tpo .deps/cfuconf.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfuthread_queue.o -MD -MP -MF .deps/cfuthread_queue.Tpo -c -o cfuthread_queue.o cfuthread_queue.c
mv -f .deps/cfuthread_queue.Tpo .deps/cfuthread_queue.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfu.o -MD -MP -MF .deps/cfu.Tpo -c -o cfu.o cfu.c
mv -f .deps/cfu.Tpo .deps/cfu.Po
gcc -DPACKAGE_NAME=\"libcfu\" -DPACKAGE_TARNAME=\"libcfu\" -DPACKAGE_VERSION=\"0.03\" -DPACKAGE_STRING=\"libcfu\ 0.03\" -DPACKAGE_BUGREPORT=\"mike@mikeimelfort.com\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libcfu\" -DVERSION=\"0.03\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_TIME_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_STRCASECMP=1 -DHAVE_STRNCASECMP=1 -I.  -I../include  -I../include -std=gnu99 -W -pthread -g -fPIC -pthread -O2 -Wall -Wno-unused-but-set-variable -Wno-unused-function -pthread -g -O2 -MT cfuopt.o -MD -MP -MF .deps/cfuopt.Tpo -c -o cfuopt.o cfuopt.c
mv -f .deps/cfuopt.Tpo .deps/cfuopt.Po
rm -f libcfu.a
ar cru libcfu.a cfuhash.o cfutime.o cfustring.o cfulist.o cfuconf.o cfuthread_queue.o cfu.o cfuopt.o 
ranlib libcfu.a
make[1]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
make[1]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03'
Making install in src
make[1]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
make[2]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '../lib'
 /usr/bin/install -c -m 644  libcfu.a '../lib'
 ( cd '../lib' && ranlib libcfu.a )
make[2]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
make[1]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03/src'
make[1]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03'
make[2]: Entering directory `/home/ubuntu/BamM/c/libcfu-0.03'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03'
make[1]: Leaving directory `/home/ubuntu/BamM/c/libcfu-0.03'
checking for libcfu headers in /home/ubuntu/BamM/c/libcfu-0.03/include... found
checking for libcfu libraries in /home/ubuntu/BamM/c/libcfu-0.03/lib... found
htslib location not specified - building from local version
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 ranlib... ranlib
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
rm -f test/*.tmp test/*.tmp.*
rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
rm -f libhts.so libhts.so.*
rm -f libhts.a bgzip htsfile tabix test/fieldarith test/hfile test/sam test/test-regidx test/test_view test/test-vcf-api test/test-vcf-sweep
gcc -g -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -O2 -I. -c -o kstring.o kstring.c
gcc -g -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -O2 -I. -c -o faidx.o faidx.c
gcc -g -O2 -I. -c -o hfile.o hfile.c
gcc -g -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.2.1"' > version.h
gcc -g -O2 -I. -c -o hts.o hts.c
gcc -g -O2 -I. -c -o regidx.o regidx.c
gcc -g -O2 -I. -c -o sam.o sam.c
gcc -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -I. -c -o tbx.o tbx.c
gcc -g -O2 -I. -c -o vcf.o vcf.c
gcc -g -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -I. -c -o cram/files.o cram/files.c
gcc -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -I. -c -o cram/md5.o cram/md5.c
gcc -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -O2 -I. -c -o cram/vlen.o cram/vlen.c
gcc -g -O2 -I. -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gcc -g -O2 -I. -fpic -c -o kfunc.pico kfunc.c
gcc -g -O2 -I. -fpic -c -o knetfile.pico knetfile.c
gcc -g -O2 -I. -fpic -c -o kstring.pico kstring.c
gcc -g -O2 -I. -fpic -c -o bgzf.pico bgzf.c
gcc -g -O2 -I. -fpic -c -o faidx.pico faidx.c
gcc -g -O2 -I. -fpic -c -o hfile.pico hfile.c
gcc -g -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -I. -fpic -c -o hts.pico hts.c
gcc -g -O2 -I. -fpic -c -o regidx.pico regidx.c
gcc -g -O2 -I. -fpic -c -o sam.pico sam.c
gcc -g -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -I. -fpic -c -o tbx.pico tbx.c
gcc -g -O2 -I. -fpic -c -o vcf.pico vcf.c
gcc -g -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -I. -fpic -c -o cram/files.pico cram/files.c
gcc -g -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -I. -fpic -c -o cram/md5.pico cram/md5.c
gcc -g -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -I. -fpic -c -o cram/thread_pool.pico cram/thread_pool.c
gcc -g -O2 -I. -fpic -c -o cram/vlen.pico cram/vlen.c
gcc -g -O2 -I. -fpic -c -o cram/zfio.pico cram/zfio.c
gcc -shared -Wl,-soname,libhts.so.1 -pthread  -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/md5.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico  -lz -lm
ln -sf libhts.so libhts.so.1
gcc -g -O2 -I. -c -o bgzip.o bgzip.c
gcc -pthread  -o bgzip bgzip.o libhts.a  -lz
gcc -g -O2 -I. -c -o htsfile.o htsfile.c
gcc -pthread  -o htsfile htsfile.o libhts.a  -lz
gcc -g -O2 -I. -c -o tabix.o tabix.c
gcc -pthread  -o tabix tabix.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -pthread  -o test/fieldarith test/fieldarith.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/hfile.o test/hfile.c
gcc  -o test/hfile test/hfile.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/sam.o test/sam.c
gcc -pthread  -o test/sam test/sam.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -pthread  -o test/test-regidx test/test-regidx.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/test_view.o test/test_view.c
gcc -pthread  -o test/test_view test/test_view.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -pthread  -o test/test-vcf-api test/test-vcf-api.o libhts.a  -lz
gcc -g -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -pthread  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a  -lz
checking for libhts headers in /home/ubuntu/BamM/c/htslib-1.2.1/htslib... found
checking for libhts libraries in /home/ubuntu/BamM/c/htslib-1.2.1... found
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
=== configuring in libcfu-0.03 (/home/ubuntu/BamM/c/libcfu-0.03)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
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 build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
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 whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for pthread_mutex_init... yes
checking for ANSI C header files... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for gettimeofday... yes
checking for memset... yes
checking for strcasecmp... yes
checking for strncasecmp... yes
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
config.status: executing libtool commands
=== configuring in htslib-1.2.1 (/home/ubuntu/BamM/c/htslib-1.2.1)
configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
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 ranlib... ranlib
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
rm -f *.o
rm -f libBamM.a
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o bamExtractor.o bamExtractor.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o bamParser.o bamParser.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o pairedLink.o pairedLink.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o bamRead.o bamRead.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o coverageEstimators.o coverageEstimators.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o stats.o stats.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include  -c -o bamFilter.o bamFilter.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/home/ubuntu/BamM/c/htslib-1.2.1/htslib -I/home/ubuntu/BamM/c/libcfu-0.03/include -static-libgcc -shared -Wl,-rpath,/home/ubuntu/BamM/c/htslib-1.2.1 -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c bamFilter.c -lm -L/home/ubuntu/BamM/c/libcfu-0.03/lib -lcfu -L/home/ubuntu/BamM/c/htslib-1.2.1 -lhts
Building BamM library
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
  warnings.warn(msg)
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/bamm
copying bamm/bammExceptions.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamFile.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamLink.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamRead.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamParser.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamFilter.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/cWrapper.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/version.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/__init__.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamMaker.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/bamExtractor.py -> build/lib.linux-x86_64-2.7/bamm
copying bamm/libBamM.a -> build/lib.linux-x86_64-2.7/bamm
running build_scripts
creating build/scripts-2.7
copying and adjusting bin/bamm -> build/scripts-2.7
copying and adjusting bin/bamFlags -> build/scripts-2.7
changing mode of build/scripts-2.7/bamm from 644 to 755
changing mode of build/scripts-2.7/bamFlags from 644 to 755
running install_lib
copying build/lib.linux-x86_64-2.7/bamm/bammExceptions.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamFile.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamLink.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamRead.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamParser.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamFilter.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/cWrapper.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/version.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/__init__.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamMaker.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/bamExtractor.py -> /usr/local/lib/python2.7/dist-packages/bamm
copying build/lib.linux-x86_64-2.7/bamm/libBamM.a -> /usr/local/lib/python2.7/dist-packages/bamm
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bammExceptions.py to bammExceptions.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamFile.py to bamFile.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamLink.py to bamLink.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamRead.py to bamRead.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamParser.py to bamParser.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamFilter.py to bamFilter.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/cWrapper.py to cWrapper.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/version.py to version.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/__init__.py to __init__.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py to bamMaker.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/bamm/bamExtractor.py to bamExtractor.pyc
running install_scripts
copying build/scripts-2.7/bamm -> /usr/local/bin
copying build/scripts-2.7/bamFlags -> /usr/local/bin
changing mode of /usr/local/bin/bamm to 755
changing mode of /usr/local/bin/bamFlags to 755
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/BamM-1.5.1.egg-info
Writing /usr/local/lib/python2.7/dist-packages/BamM-1.5.1.egg-info
root@master:/home/ubuntu/BamM# nosetests
ETraceback (most recent call last):
  File "/usr/local/bin/bamm", line 655, in <module>
    doWork(args)
  File "/usr/local/bin/bamm", line 153, in doWork
    BS.makeBams()
  File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 292, in makeBams
    BM.makeBam()
  File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 620, in makeBam
    self.mem_to_sorted_indexed_bam()
  File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 842, in mem_to_sorted_indexed_bam
    self.samtoolsIndex(self.outFileName)
  File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 921, in samtoolsIndex
    self._run_cmd(cmd)
  File "/usr/local/lib/python2.7/dist-packages/bamm/bamMaker.py", line 669, in _run_cmd
    subprocess.check_call(cmd, shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'samtools index /home/ubuntu/BamM/bamm/tests/modeling/contigs.pe.1.bam 2> /dev/null' returned non-zero exit status 1
ETraceback (most recent call last):
  File "/usr/local/bin/bamm", line 655, in <module>
    doWork(args)
  File "/usr/local/bin/bamm", line 220, in doWork
    verbose=args.verbose)
  File "/usr/local/lib/python2.7/dist-packages/bamm/bamParser.py", line 351, in parseBams
    ("%s.bai" % bam))
bamm.bammExceptions.BAMIndexNotFoundException: Index file /home/ubuntu/BamM/bamm/tests/modeling/contigs.pe.1.bam.bai not found
EERROR: Random retrieval only works for indexed files.
[E::hts_open] fail to open file '/home/ubuntu/BamM/bamm/tests/modeling/contigs.mp.bam'
ERROR: Failed to open "/home/ubuntu/BamM/bamm/tests/modeling/contigs.mp.bam" for reading.
[E::hts_open] fail to open file '/home/ubuntu/BamM/bamm/tests/modeling/contigs.up.bam'
ERROR: Failed to open "/home/ubuntu/BamM/bamm/tests/modeling/contigs.up.bam" for reading.
FNo file: /home/ubuntu/BamM/bamm/tests/modeling/contigs.pe.1.bam.bai
No file: /home/ubuntu/BamM/bamm/tests/modeling/contigs.mp.bam
No file: /home/ubuntu/BamM/bamm/tests/modeling/contigs.mp.bam.bai
No file: /home/ubuntu/BamM/bamm/tests/modeling/contigs.up.bam
No file: /home/ubuntu/BamM/bamm/tests/modeling/contigs.up.bam.bai
No file: /home/ubuntu/BamM/bamm/tests/modeling/covs
No file: /home/ubuntu/BamM/bamm/tests/modeling/links
.............................................
======================================================================
ERROR: Failure: ImportError (No module named pysam)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/ubuntu/BamM/bamm/tests/test_bamFilter.py", line 32, in <module>
    import pysam
ImportError: No module named pysam

======================================================================
ERROR: test_bamParser.TestBamParser.test_A_make
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/ubuntu/BamM/bamm/tests/test_bamParser.py", line 131, in test_A_make
    subprocess.check_call(cmd, shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command 'bamm make --silent -d /home/ubuntu/BamM/bamm/tests/modeling/contigs.fa -i /home/ubuntu/BamM/bamm/tests/modeling/mp.fa -c /home/ubuntu/BamM/bamm/tests/modeling/pe.1.fa /home/ubuntu/BamM/bamm/tests/modeling/pe.2.fa -s /home/ubuntu/BamM/bamm/tests/modeling/up.fa -o /home/ubuntu/BamM/bamm/tests/modeling' returned non-zero exit status 1

======================================================================
ERROR: test_bamParser.TestBamParser.test_B_parse
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/ubuntu/BamM/bamm/tests/test_bamParser.py", line 166, in test_B_parse
    with open(covs_file) as c_fh:
IOError: [Errno 2] No such file or directory: '/home/ubuntu/BamM/bamm/tests/modeling/covs'

======================================================================
FAIL: test_bamParser.TestBamParser.test_C_extract
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/ubuntu/BamM/bamm/tests/test_bamParser.py", line 240, in test_C_extract
    assert_true(os.path.exists(full_path))
AssertionError: False is not true

----------------------------------------------------------------------
Ran 49 tests in 1.439s

FAILED (errors=3, failures=1)
root@master:/home/ubuntu/BamM#
chuckpr commented 8 years ago 
root@master:/home/ubuntu/BamM# samtools --version
samtools 1.2-189-g2bd7837
Using htslib 1.2.1-192-ge7e2b3d
Copyright (C) 2015 Genome Research Ltd.
root@master:/home/ubuntu/BamM# bwa 

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.12-r1044
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.
chuckpr commented 8 years ago

Ok, had to install an older version of samtools (v1.2) from http://sourceforge.net/projects/samtools/files/samtools/1.2/ and pysam. Now the nosetests are passing.

root@master:/home/ubuntu/BamM# nosetests
.................................................
----------------------------------------------------------------------
Ran 49 tests in 27.543s

OK

The manual does specify version 1.2 for samtools but the samtools link points to the samtools github repo where 1.2.1 is found by default.

wwood commented 8 years ago

Thanks for tracking all that down.

I've added a reference to libtool and pysam and updated the samtools URL in the manual. Thanks.

(the issue with pysam is that setup.py doesn't recognize install_requires - there is a warning buried in up there). We are working on an easier install procedure in general though.

If there is anything else feel free to reopen this issue.