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DoaneAS / rseqc

Automatically exported from code.google.com/p/rseqc
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Error during installation #3

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
> sudo python setup.py install
running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to support .pth 
files
running bdist_egg
running egg_info
writing lib/RSeQC.egg-info/PKG-INFO
writing top-level names to lib/RSeQC.egg-info/top_level.txt
writing dependency_links to lib/RSeQC.egg-info/dependency_links.txt
writing lib/RSeQC.egg-info/PKG-INFO
writing top-level names to lib/RSeQC.egg-info/top_level.txt
writing dependency_links to lib/RSeQC.egg-info/dependency_links.txt
reading manifest file 'lib/RSeQC.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'lib/RSeQC.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
skipping 'lib/bx/bitset.c' Cython extension (up-to-date)
skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date)
skipping 'lib/bx/align/_core.c' Cython extension (up-to-date)
skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date)
skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date)
skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date)
skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date)
skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date)
skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date)
skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date)
skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date)
skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date)
skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date)
skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date)
skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date)
skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date)
skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date)
cythoning lib/bx/arrays/wiggle.pyx to lib/bx/arrays/wiggle.c

Error compiling Cython file:
------------------------------------------------------------
...
        self.file = file
        self.current_chrom = None
        self.current_pos = -1
        self.current_step = -1
        self.current_span = -1
        self.mode = MODE_BED
                           ^
------------------------------------------------------------

bx/arrays/wiggle.pyx:32:28: undeclared name not builtin: MODE_BED

Error compiling Cython file:
------------------------------------------------------------
...
                    self.current_step = -1
                    if 'span' in header:
                        self.current_span = int( header['span'] )
                    else:
                        self.current_span = 1
                    self.mode = MODE_VARIABLE
                                            ^
------------------------------------------------------------

bx/arrays/wiggle.pyx:58:45: undeclared name not builtin: MODE_VARIABLE

Error compiling Cython file:
------------------------------------------------------------
...
                    self.current_step = int( header['step'] )
                    if 'span' in header:
                        self.current_span = int( header['span'] )
                    else:
                        self.current_span = 1
                    self.mode = MODE_FIXED
                                         ^
------------------------------------------------------------

bx/arrays/wiggle.pyx:69:42: undeclared name not builtin: MODE_FIXED

Error compiling Cython file:
------------------------------------------------------------
...
                        self.current_span = int( header['span'] )
                    else:
                        self.current_span = 1
                    self.mode = MODE_FIXED
                    continue
            elif self.mode == MODE_BED:
                                     ^
------------------------------------------------------------

bx/arrays/wiggle.pyx:71:38: undeclared name not builtin: MODE_BED

Error compiling Cython file:
------------------------------------------------------------
...
                if len( fields ) > 3:
                    if len( fields ) > 5:
                        return fields[0], int( fields[1] ), int( fields[2] ), fields[5], float( fields[3] )
                    else:
                        return fields[0], int( fields[1] ), int( fields[2] ), "+", float( fields[3] )
            elif self.mode == MODE_VARIABLE: 
                                          ^
------------------------------------------------------------

bx/arrays/wiggle.pyx:78:43: undeclared name not builtin: MODE_VARIABLE

Error compiling Cython file:
------------------------------------------------------------
...
                    pos = int( fields[0] ) - 1
                    val = float( fields[1] )
                except ValueError:
                    continue
                return self.current_chrom, pos, pos + self.current_span, "+", val
            elif self.mode == MODE_FIXED:
                                       ^
------------------------------------------------------------

bx/arrays/wiggle.pyx:86:40: undeclared name not builtin: MODE_FIXED
building 'bx.arrays.wiggle' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall 
-Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c lib/bx/arrays/wiggle.c -o 
build/temp.linux-x86_64-2.7/lib/bx/arrays/wiggle.o
lib/bx/arrays/wiggle.c:1:2: 错误： #error Do not use this file, it is the 
result of a failed Cython compilation.
error: command 'gcc' failed with exit status 1

Please help.
Thanks you!

Original issue reported on code.google.com by realzh...@gmail.com on 21 Apr 2012 at 4:16

GoogleCodeExporter commented 9 years ago 
Try this version to see if it works.

http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/source/RSeQC-2.1.tar.gz

Please completely remove previous version.

Thanks for feed backs.

-Liguo

Original comment by wangligu...@gmail.com on 24 Apr 2012 at 7:09

GoogleCodeExporter commented 9 years ago 
I think his error can be solved by installing python-dev

Original comment by geyecha0...@gmail.com on 16 Aug 2012 at 2:15

GoogleCodeExporter commented 9 years ago 
Thanks. v2.3.1 solved this problem without installing python-dev.

Original comment by realzh...@gmail.com on 17 Aug 2012 at 5:35