Open linsalrob opened 9 years ago
Here is the sysinfo
Numpy version: 1.9.2
Location: /usr/local/lib/python2.7/site-packages/numpy/__init__.pyc
Linux 2.6.32-504.12.2.el6.x86_64
2.7.9 (default, Mar 31 2015, 16:20:45)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
['/root/bamm/BamM/bamm/tests', '/usr/local/lib/python2.7/site-packages/setuptools-1.4.2-py2.7.egg', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']
Here is the output of setup.py.out as well
Preparing the BamM build system...please wait
Found GNU Autoconf version 2.63
Found GNU Automake version 1.11.1
Found GNU Libtool version 2.2.6b
Automatically preparing build ... Warning: autoreconf failed
Attempting to run the preparation steps individually
Preparing build ... ERROR: aclocal failed
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether 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
checking for libcfu headers in /usr/local/include... found
checking for libcfu libraries in /usr/local/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 /root/bamm/BamM/c/htslib-1.2.1/htslib... found
checking for libhts libraries in /root/bamm/BamM/c/htslib-1.2.1... found
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
=== configuring in libcfu-0.03 (/root/bamm/BamM/c/libcfu-0.03)
configure: running /bin/sh ./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 $(MAKE)... yes
checking whether make supports nested variables... yes
rm -f *.o
rm -f libBamM.a
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamParser.o bamParser.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamRead.o bamRead.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o stats.o stats.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/root/bamm/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/root/bamm/BamM/c/htslib-1.2.1 -o libBamM.a bamExtractor.c bamParser.c pairedLink.c bamRead.c coverageEstimators.c stats.c -lm -L/usr/local/lib -lcfu -L/root/bamm/BamM/c/htslib-1.2.1 -lhts
As far as the CentOS stuff goes, the problem starts here:
configure: error: cannot run /bin/sh ./config.sub
This is almost definitely an issue with my knowledge on the build system on CentOS. I'll keep looking into it.
I think the first issue is that lines 1042-47 of c/autogen.sh include:
for file in config.guess config.sub ltmain.sh ; do
if test -f "${_aux_dir}/${file}" ; then
$VERBOSE_ECHO "mv -f \"${_aux_dir}/${file}\" \"${_aux_dir}/${file}.backup\""
mv -f "${_aux_dir}/${file}" "${_aux_dir}/${file}.backup"
fi
done
If I comment out those lines, and also restore those files:
cd libcfu-0.03/
cp config.guess.backup config.guess; cp config.sub.backup config.sub; cp ltmain.sh.backup ltmain.sh
you can ./configure the files in that directory but now you get a missing aclocal error. That can be resolved with
touch configure.ac aclocal.m4 configure Makefile.am Makefile.in
which now allows you to ./configure && make
in the c/libcfu-0.03 directory
This allows me to run
/usr/bin/python setup.py install --with-libhts-lib /usr/local/lib/libhts.a --with-libhts-inc /usr/local/include/htslib
the bamm command runs just fine:
# bamm
...::: BamM :::...
Working with the BAM, not against it...
-------------------------------------------------------------------------
version: 1.4.1
-------------------------------------------------------------------------
bamm make -> Make BAM/TAM files (sorted + indexed)
bamm parse -> Get coverage profiles / linking reads / insert types
bamm extract -> Extract reads / headers from BAM files
USE: bamm OPTION -h to see detailed options
but the nosetests faill:
# cd bamm
# nosetests
.********************************************************************************
ERROR:
Problem importing the BamM c library. This typically means that BamM is not installed correctly.
Please check the installation logs for more details.
If you don't have the installation logs then please try to reinstall BamM and look at the output.
Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a
********************************************************************************
********************************************************************************
ERROR:
Problem importing the BamM c library. This typically means that BamM is not installed correctly.
Please check the installation logs for more details.
If you don't have the installation logs then please try to reinstall BamM and look at the output.
Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a
********************************************************************************
********************************************************************************
ERROR:
Problem importing the BamM c library. This typically means that BamM is not installed correctly.
Please check the installation logs for more details.
If you don't have the installation logs then please try to reinstall BamM and look at the output.
Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a
********************************************************************************
Process Process-4:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/python2.6/site-packages/bamm/bamParser.py", line 92, in externalParseWrapper
CW = CWrapper()
File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 461, in __init__
self.libPMBam = c.cdll.LoadLibrary(c_lib)
File "/usr/lib64/python2.6/ctypes/__init__.py", line 431, in LoadLibrary
return self._dlltype(name)
File "/usr/lib64/python2.6/ctypes/__init__.py", line 353, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libhts.so.1: cannot open shared object file: No such file or directory
Process Process-3:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/python2.6/site-packages/bamm/bamParser.py", line 92, in externalParseWrapper
CW = CWrapper()
File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 461, in __init__
self.libPMBam = c.cdll.LoadLibrary(c_lib)
File "/usr/lib64/python2.6/ctypes/__init__.py", line 431, in LoadLibrary
return self._dlltype(name)
File "/usr/lib64/python2.6/ctypes/__init__.py", line 353, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libhts.so.1: cannot open shared object file: No such file or directory
Process Process-2:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/python2.6/site-packages/bamm/bamParser.py", line 92, in externalParseWrapper
CW = CWrapper()
File "/usr/lib/python2.6/site-packages/bamm/cWrapper.py", line 461, in __init__
self.libPMBam = c.cdll.LoadLibrary(c_lib)
File "/usr/lib64/python2.6/ctypes/__init__.py", line 431, in LoadLibrary
return self._dlltype(name)
File "/usr/lib64/python2.6/ctypes/__init__.py", line 353, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libhts.so.1: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/usr/bin/bamm", line 584, in <module>
doWork(args)
File "/usr/bin/bamm", line 216, in doWork
except BAMFileNotFoundException as e:
NameError: global name 'BAMFileNotFoundException' is not defined
Exception in thread QueueFeederThread (most likely raised during interpreter shutdown):
Traceback (most recent call last):
File "/usr/lib64/python2.6/threading.py", line 532, in __bootstrap_inner
File "/usr/lib64/python2.6/threading.py", line 484, in run
File "/usr/lib64/python2.6/multiprocessing/queues.py", line 233, in _feed
<type 'exceptions.TypeError'>: 'NoneType' object is not callable
E********************************************************************************
ERROR:
Problem importing the BamM c library. This typically means that BamM is not installed correctly.
Please check the installation logs for more details.
If you don't have the installation logs then please try to reinstall BamM and look at the output.
Looking for the c library at: /usr/lib/python2.6/site-packages/bamm/libBamM.a
********************************************************************************
....
Thanks for keeping up with this Rob. When I install BamM on my machine, the last few lines look like this:
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 copying bamm/libBamM.a -> build/lib.linux-x86_64-2.7/bamm running build_scripts copying and adjusting bin/bamm -> build/scripts-2.7 running install_lib copying build/lib.linux-x86_64-2.7/bamm/libBamM.a -> /usr/local/lib/python2.7/dist-packages/bamm running install_scripts copying build/scripts-2.7/bamm -> /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-1.4.1.egg-info Writing /usr/local/lib/python2.7/dist-packages/BamM-1.4.1.egg-info
So I can see that the install dir is: /usr/local/lib/python2.7/dist-packages/ and then I assume there'll be a bamm tacked on the end giving:
/usr/local/lib/python2.7/dist-packages/bamm
When I ls this directory I get:
$ ls /usr/local/lib/python2.7/dist-packages/bamm/ bamExtractor.py bamFile.py bamLink.py bamMaker.py bammExceptions.py bamParser.py bamRead.py cWrapper.py init.py libBamM.a bamExtractor.pyc bamFile.pyc bamLink.pyc bamMaker.pyc bammExceptions.pyc bamParser.pyc bamRead.pyc cWrapper.pyc init.pyc
And so everything works. I suspect the same is true on your machine.
I think my useful error may be misleading because of this:
OSError: libhts.so.1: cannot open shared object file: No such file or directory
Is this a LD_LIBRARY_PATH issue for htslib?
I added BAMFileNotFoundException to the list of imports for bin/bamm so that should fix that issue (in BamM 1.4.2)
Hi, I've been trying to install BamM and got the same error as the original issue.
My system details - Linux endeavor 2.6.32-504.23.4.el6.x86_64 #1 SMP Tue Jun 9 20:57:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
I couldn't gather from the post if the issue was fully resolved or not. Could you help me out with this please?
Thanks! Chandni
Hi Chandni,
Thanks for giving BamM a go. I don't believe this error has been fixed, no. Can I ask, which issue are you talking about specifically? Also, what is the output of /usr/bin/python --version
and python --version
?
With some fresh eyes, there's a few things that might help track things down. Would you mind looking into them please @timbalam ?
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
I wonder then if making sure bamm is installed using 2.7 and then running python2.7 /path/to/bamm
might give better results?
.a
file, when only the .so
file was specified in the install procedure. Can we double check to make sure that installing using --with-hts-lib
etc actually works on non-CentOS machines at least please?Thanks, ben
Ah, you are right. /usr/bin/python --version : Python 2.6.6 python -- version : Python 2.7.9
I'm not sure how to specifically install BamM using 2.7 though. I realized I install most others using pip, and they automatically use 2.7. What do you think is the best way to go about it?
Meanwhile, here is my run log ..
Preparing the BamM build system...please wait
Found GNU Autoconf version 2.63
Found GNU Automake version 1.11.1
Found GNU Libtool version 2.2.6b
Automatically preparing build ... Warning: autoreconf failed
Attempting to run the preparation steps individually
Preparing build ... ERROR: aclocal failed
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether 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
checking for libcfu headers in /usr/local/include... found
checking for libcfu libraries in /usr/local/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 /usr/local/src/BamM/c/htslib-1.2.1/htslib... found
checking for libhts libraries in /usr/local/src/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 (/usr/local/src/BamM/c/libcfu-0.03)
configure: WARNING: no configuration information is in libcfu-0.03
=== configuring in htslib-1.2.1 (/usr/local/src/BamM/c/htslib-1.2.1)
configure: running /bin/sh ./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/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamExtractor.o bamExtractor.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamParser.o bamParser.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o pairedLink.o pairedLink.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamRead.o bamRead.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o coverageEstimators.o coverageEstimators.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o stats.o stats.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -c -o bamFilter.o bamFilter.c
gcc -std=gnu99 -g -fPIC -pthread -O2 -Wall -I/usr/local/src/BamM/c/htslib-1.2.1/htslib -I/usr/local/include -static-libgcc -shared -Wl,-rpath,/usr/local/src/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/usr/local/lib -lcfu -L/usr/local/src/BamM/c/htslib-1.2.1 -lhts
/usr/bin/ld: /usr/local/lib/libcfu.a(cfuhash.o): relocation R_X86_64_32 against `.text' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libcfu.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [libBamM.a] Error 1
Traceback (most recent call last):
File "setup.py", line 38, in <module>
rename(join('c', 'libBamM.a'), join('bamm', 'libBamM.a'))
OSError: [Errno 2] No such file or directory
Hey Mike
I downloaded BamM today and tried to install it on CentOS6.6 (with python2.7, python2.7 numpy, samtools and bwa tools):
The error that I get is:
Any thoughts?
Rob