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lixin6135 / pysam

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Trouble installing pysam (gcc-related error) #62

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Download and extract pysam-0.4.1
2. From the pysam-0.4.1 directory, type sudo python2.6 setup.py install

Here's the output I get:
/usr/lib/python2.6/dist-packages/Pyrex/Compiler/Errors.py:17: 
DeprecationWarning: BaseException.message has been deprecated as of Python 2.6
  self.message = message
running install
Checking .pth file support in /usr/local/lib/python2.6/dist-packages/
/usr/bin/python2.6 -E -c pass
TEST PASSED: /usr/local/lib/python2.6/dist-packages/ appears to support .pth 
files
running bdist_egg
running egg_info
writing requirements to pysam.egg-info/requires.txt
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pysam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
building 'csamtools' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall 
-Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools 
-Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o 
build/temp.linux-x86_64-2.6/pysam/csamtools.o
In file included from /usr/include/python2.6/unicodeobject.h:57,
                 from /usr/include/python2.6/Python.h:85,
                 from pysam/csamtools.c:4:
/usr/include/python2.6/ctype.h: In function ‘stringlib_isspace’:
/usr/include/python2.6/ctype.h:9: warning: implicit declaration of function 
‘STRINGLIB_STR’
/usr/include/python2.6/ctype.h:9: warning: implicit declaration of function 
‘STRINGLIB_LEN’
/usr/include/python2.6/ctype.h:9: warning: passing argument 1 of 
‘_Py_bytes_isspace’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_isalpha’:
/usr/include/python2.6/ctype.h:15: warning: passing argument 1 of 
‘_Py_bytes_isalpha’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_isalnum’:
/usr/include/python2.6/ctype.h:21: warning: passing argument 1 of 
‘_Py_bytes_isalnum’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_isdigit’:
/usr/include/python2.6/ctype.h:27: warning: passing argument 1 of 
‘_Py_bytes_isdigit’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_islower’:
/usr/include/python2.6/ctype.h:33: warning: passing argument 1 of 
‘_Py_bytes_islower’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_isupper’:
/usr/include/python2.6/ctype.h:39: warning: passing argument 1 of 
‘_Py_bytes_isupper’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_istitle’:
/usr/include/python2.6/ctype.h:45: warning: passing argument 1 of 
‘_Py_bytes_istitle’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_lower’:
/usr/include/python2.6/ctype.h:55: warning: implicit declaration of function 
‘STRINGLIB_NEW’
/usr/include/python2.6/ctype.h:55: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:59: warning: passing argument 1 of 
‘_Py_bytes_lower’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:59: warning: passing argument 2 of 
‘_Py_bytes_lower’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_upper’:
/usr/include/python2.6/ctype.h:67: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:71: warning: passing argument 1 of 
‘_Py_bytes_upper’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:71: warning: passing argument 2 of 
‘_Py_bytes_upper’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_title’:
/usr/include/python2.6/ctype.h:79: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:83: warning: passing argument 1 of 
‘_Py_bytes_title’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:83: warning: passing argument 2 of 
‘_Py_bytes_title’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_capitalize’:
/usr/include/python2.6/ctype.h:91: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:95: warning: passing argument 1 of 
‘_Py_bytes_capitalize’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:95: warning: passing argument 2 of 
‘_Py_bytes_capitalize’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: In function ‘stringlib_swapcase’:
/usr/include/python2.6/ctype.h:103: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:107: warning: passing argument 1 of 
‘_Py_bytes_swapcase’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:107: warning: passing argument 2 of 
‘_Py_bytes_swapcase’ makes pointer from integer without a cast
In file included from pysam/csamtools.c:203:
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:7: error: redefinition of ‘stringlib_isspace’
/usr/include/python2.6/ctype.h:8: error: previous definition of 
‘stringlib_isspace’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_isspace’:
/usr/include/python2.6/ctype.h:9: warning: passing argument 1 of 
‘_Py_bytes_isspace’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:13: error: redefinition of 
‘stringlib_isalpha’
/usr/include/python2.6/ctype.h:14: error: previous definition of 
‘stringlib_isalpha’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_isalpha’:
/usr/include/python2.6/ctype.h:15: warning: passing argument 1 of 
‘_Py_bytes_isalpha’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:19: error: redefinition of 
‘stringlib_isalnum’
/usr/include/python2.6/ctype.h:20: error: previous definition of 
‘stringlib_isalnum’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_isalnum’:
/usr/include/python2.6/ctype.h:21: warning: passing argument 1 of 
‘_Py_bytes_isalnum’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:25: error: redefinition of 
‘stringlib_isdigit’
/usr/include/python2.6/ctype.h:26: error: previous definition of 
‘stringlib_isdigit’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_isdigit’:
/usr/include/python2.6/ctype.h:27: warning: passing argument 1 of 
‘_Py_bytes_isdigit’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:31: error: redefinition of 
‘stringlib_islower’
/usr/include/python2.6/ctype.h:32: error: previous definition of 
‘stringlib_islower’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_islower’:
/usr/include/python2.6/ctype.h:33: warning: passing argument 1 of 
‘_Py_bytes_islower’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:37: error: redefinition of 
‘stringlib_isupper’
/usr/include/python2.6/ctype.h:38: error: previous definition of 
‘stringlib_isupper’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_isupper’:
/usr/include/python2.6/ctype.h:39: warning: passing argument 1 of 
‘_Py_bytes_isupper’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:43: error: redefinition of 
‘stringlib_istitle’
/usr/include/python2.6/ctype.h:44: error: previous definition of 
‘stringlib_istitle’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_istitle’:
/usr/include/python2.6/ctype.h:45: warning: passing argument 1 of 
‘_Py_bytes_istitle’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:52: error: redefinition of ‘stringlib_lower’
/usr/include/python2.6/ctype.h:53: error: previous definition of 
‘stringlib_lower’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_lower’:
/usr/include/python2.6/ctype.h:55: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:59: warning: passing argument 1 of 
‘_Py_bytes_lower’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:59: warning: passing argument 2 of 
‘_Py_bytes_lower’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:64: error: redefinition of ‘stringlib_upper’
/usr/include/python2.6/ctype.h:65: error: previous definition of 
‘stringlib_upper’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_upper’:
/usr/include/python2.6/ctype.h:67: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:71: warning: passing argument 1 of 
‘_Py_bytes_upper’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:71: warning: passing argument 2 of 
‘_Py_bytes_upper’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:76: error: redefinition of ‘stringlib_title’
/usr/include/python2.6/ctype.h:77: error: previous definition of 
‘stringlib_title’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_title’:
/usr/include/python2.6/ctype.h:79: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:83: warning: passing argument 1 of 
‘_Py_bytes_title’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:83: warning: passing argument 2 of 
‘_Py_bytes_title’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:88: error: redefinition of 
‘stringlib_capitalize’
/usr/include/python2.6/ctype.h:89: error: previous definition of 
‘stringlib_capitalize’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_capitalize’:
/usr/include/python2.6/ctype.h:91: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:95: warning: passing argument 1 of 
‘_Py_bytes_capitalize’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:95: warning: passing argument 2 of 
‘_Py_bytes_capitalize’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h: At top level:
/usr/include/python2.6/ctype.h:100: error: redefinition of 
‘stringlib_swapcase’
/usr/include/python2.6/ctype.h:101: error: previous definition of 
‘stringlib_swapcase’ was here
/usr/include/python2.6/ctype.h: In function ‘stringlib_swapcase’:
/usr/include/python2.6/ctype.h:103: warning: assignment makes pointer from 
integer without a cast
/usr/include/python2.6/ctype.h:107: warning: passing argument 1 of 
‘_Py_bytes_swapcase’ makes pointer from integer without a cast
/usr/include/python2.6/ctype.h:107: warning: passing argument 2 of 
‘_Py_bytes_swapcase’ makes pointer from integer without a cast
In file included from pysam/csamtools.c:208:
samtools/bam.h: At top level:
samtools/bam.h:354: warning: function declaration isn’t a prototype
samtools/bam.h:369: warning: function declaration isn’t a prototype
In file included from pysam/csamtools.c:210:
samtools/glf.h:43: warning: function declaration isn’t a prototype
In file included from pysam/csamtools.c:211:
samtools/bam_maqcns.h:44: warning: function declaration isn’t a prototype
samtools/bam_maqcns.h:52: warning: function declaration isn’t a prototype
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_fetch’:
pysam/csamtools.c:7771: warning: passing argument 7 of ‘bam_fetch’ from 
incompatible pointer type
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_mate’:
pysam/csamtools.c:8168: warning: passing argument 7 of ‘bam_fetch’ from 
incompatible pointer type
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_count’:
pysam/csamtools.c:8685: warning: passing argument 7 of ‘bam_fetch’ from 
incompatible pointer type
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_pileup’:
pysam/csamtools.c:9146: warning: passing argument 7 of ‘bam_fetch’ from 
incompatible pointer type
pysam/csamtools.c: In function ‘__pyx_f_9csamtools___advance_snpcalls’:
pysam/csamtools.c:13721: warning: implicit declaration of function 
‘bam_prob_realn’
pysam/csamtools.c:13749: warning: implicit declaration of function 
‘bam_cap_mapQ’
pysam/csamtools.c: In function ‘__pyx_f_9csamtools_13SNPCallerBase___dump’:
pysam/csamtools.c:25100: warning: format not a string literal and no format 
arguments
pysam/csamtools.c: In function 
‘__pyx_pf_9csamtools_15IndelCallerBase__call’:
pysam/csamtools.c:27457: warning: assignment discards qualifiers from pointer 
target type
pysam/csamtools.c: In function ‘__Pyx_Print’:
pysam/csamtools.c:35136: warning: implicit declaration of function 
‘undefined_isspace’
error: command 'gcc' failed with exit status 1

I'm running Ubuntu 9.04.

Any suggestions would be greatly appreciated!

Thanks,
Kevin Kocot

Original issue reported on code.google.com by kmko...@gmail.com on 13 May 2011 at 6:45

GoogleCodeExporter commented 8 years ago 
Thanks for your report.

Unfortunately I have no system to really test this.

I have not seen the ctype.h related errors before - is your python installation
in order?

Bw,
Andreas

Original comment by andreas....@gmail.com on 4 Jun 2011 at 8:43