Import error after installing Pysam

[DavyK]

Hi all,
I now there are a couple of threads asking about installing pysam already, and I tried the solutions posted there to no avail.

I am trying in install pysam on my MAC running OSX 10.7 with python 2.7.3.

I have downloaded and appear to have successfully installed samtools and added it to my path. When I type samtools into the command line I get the nice help message that one expects to see if you don't give anything to do.

So after downloading, unpacking and entering into the directory of the latest version of pysam, when I run 'python setup.py build' there are many warnings, but the script doesn't exit, so I tried installing it after build anyway. The install seems to go fine, but when I start up IDLE and try to import pysam I get the following error:

Traceback (most recent call last):

File "<pyshell#0>", line 1, in <module>
import pysam
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysam-0.6-py2.7-macosx-10.6-intel.egg/pysam/init.py", line 1, in <module>
from csamtools import
ImportError?: dlopen(/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysam-0.6-py2.7-macosx-10.6-intel.egg/csamtools.so, 2): Symbol not found: ks_insertsort_heap
Referenced from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysam-0.6-py2.7-macosx-10.6-intel.egg/csamtools.so Expected in: flat namespace
in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysam-0.6-py2.7-macosx-10.6-intel.egg/csamtools.so

the output of the setup.py build command is too large to post here but some of the out if helps is:

running build running build_py creating build creating build/lib.macosx-10.6-intel-2.7 creating build/lib.macosx-10.6-intel-2.7/pysam copying pysam/init.py -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/Pileup.py -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/namedtuple.py -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/version.py -> build/lib.macosx-10.6-intel-2.7/pysam running build_ext gcc-4.2 not found, using clang instead building 'csamtools' extension creating build/temp.macosx-10.6-intel-2.7 creating build/temp.macosx-10.6-intel-2.7/pysam creating build/temp.macosx-10.6-intel-2.7/samtools creating build/temp.macosx-10.6-intel-2.7/samtools/bcftools creating build/temp.macosx-10.6-intel-2.7/samtools/misc clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/csamtools.c -o build/temp.macosx-10.6-intel-2.7/pysam/csamtools.o pysam/csamtools.c:8432:249: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter

of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...pyx_v_rstart, pyx_v_rend, ((void )pyx_v_callback), pyx_f_9csamtools_fetch_callback)); if ...
^
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:8840:427: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...+ 1), ((void )(&pyx_v_mate_data)), pyx_f_9csamtools_mate_callback);
^~
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:9327:222: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...pyx_v_rstart, pyx_v_rend, ((void )(&pyx_v_counter)), pyx_f_9csamtools_count_callback);
^
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:9764:207: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...pyx_v_rtid, pyx_v_rstart, pyx_v_rend, pyx_v_buf, pyx_f_9csamtools_pileup_fetch_callback);
^~
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:15344:7: warning: implicit declaration of function 'bam_prob_realn' is invalid in C99
[-Wimplicit-function-declaration] bam_prob_realn(pyx_v_b, pyx_v_d->seq); ^
pysam/csamtools.c:15372:19: warning: implicit declaration of function 'bam_cap_mapQ' is invalid in C99
[-Wimplicit-function-declaration] pyx_v_q = bam_cap_mapQ(pyx_v_b, pyx_v_d->seq, pyx_v_capQ_thres);
^
6 warnings generated. pysam/csamtools.c:8432:249: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...pyx_v_rstart, pyx_v_rend, ((void )pyx_v_callback), pyx_f_9csamtools_fetch_callback)); if ...
^
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:8840:427: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...+ 1), ((void )(&pyx_v_mate_data)), pyx_f_9csamtools_mate_callback);
^~
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:9327:222: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...pyx_v_rstart, pyx_v_rend, ((void )(&pyx_v_counter)), pyx_f_9csamtools_count_callback);
^
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:9764:207: warning: incompatible pointer types passing 'int (bam1_t , void )' to parameter
of type 'bam_fetch_f' (aka 'int ()(const bam1_t , void )') [-Wincompatible-pointer-types]
...pyx_v_rtid, pyx_v_rstart, pyx_v_rend, pyx_v_buf, pyx_f_9csamtools_pileup_fetch_callback);
^~
samtools/bam.h:626:103: note: passing argument to parameter 'func' here
...bam_fetch(bamFile fp, const bam_index_t idx, int tid, int beg, int end, void data, bam_fetch_f func);
^
pysam/csamtools.c:15344:7: warning: implicit declaration of function 'bam_prob_realn' is invalid in C99
[-Wimplicit-function-declaration] bam_prob_realn(pyx_v_b, pyx_v_d->seq); ^
pysam/csamtools.c:15372:19: warning: implicit declaration of function 'bam_cap_mapQ' is invalid in C99
[-Wimplicit-function-declaration] pyx_v_q = bam_cap_mapQ(pyx_v_b, pyx_v_d->seq, pyx_v_capQ_thres);

I noticed that it says gcc-4.2 is not found. but when I type gcc at the command prompt It says: i686-apple-darwin11-llvm-gcc-4.2: no input files So I think that means it's installed.

Any help is appreciated, Cheers, Davy

[Dogetorenk]

i think maybe the version which you have installed of PYSAM is not supporting your mac os so i would prefer you to contact the moderator of the site and to look up for the version which is suitable for your mac os.