[miso-users] Problem with Install

Tue Jul 10 11:39:04 EDT 2012

Hi Gabe,

Are you installing from GitHub? If so, did you run "make Pythonpackage" prior to running "python setup.py install"?  

Also, if you want to install it locally, you should pass the --prefix= option to setup.py, e.g.:

$ make Pythonpackage
$ python setup.py install --prefix=/my/homedir/pylibs/

Best, --Yarden

On Jul 10, 2012, at 11:21 AM, Gabriel Otte wrote:

> Hi.  I'm currently trying to install MISO onto a cluster (without admin) locally in my home folder.  I've installed all the dependencies but the install fails with the following:
> 
> ~/python/epd-7.3-1-rh5-x86_64/bin/python setup.py install
> /gpfs/fs121/h/gotte/python/epd-7.3-1-rh5-x86_64/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/misopy
> copying misopy/Gene.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/__init__.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/as_events.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/cluster_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/credible_intervals.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/exon_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/filter_events.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/gff_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/hypothesis_test.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/index_gff.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/json_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/kde_subclass.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/miso_sampler.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/miso_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/module_availability.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/parse_csv.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/parse_gene.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/pe_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/pickle_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/py2c_gene.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/read_simulator.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/reads_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/run_events_analysis.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/run_miso.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/sam_rpkm.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/sam_to_bam.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/sam_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/samples_utils.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/settings.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/test_cluster.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/test_miso.py -> build/lib.linux-x86_64-2.7/misopy
> copying misopy/test_pysplicing.py -> build/lib.linux-x86_64-2.7/misopy
> creating build/lib.linux-x86_64-2.7/misopy/sashimi_plot
> copying misopy/sashimi_plot/Sashimi.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot
> copying misopy/sashimi_plot/__init__.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot
> copying misopy/sashimi_plot/plot.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot
> creating build/lib.linux-x86_64-2.7/misopy/sashimi_plot/plot_utils
> copying misopy/sashimi_plot/plot_utils/__init__.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot/plot_utils
> copying misopy/sashimi_plot/plot_utils/plot_gene.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot/plot_utils
> copying misopy/sashimi_plot/plot_utils/plot_settings.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot/plot_utils
> copying misopy/sashimi_plot/plot_utils/plotting.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot/plot_utils
> copying misopy/sashimi_plot/plot_utils/samples_plotter.py -> build/lib.linux-x86_64-2.7/misopy/sashimi_plot/plot_utils
> creating build/lib.linux-x86_64-2.7/pysplicing
> copying pysplicing/pysplicing/__init__.py -> build/lib.linux-x86_64-2.7/pysplicing
> running build_ext
> building 'pysplicing.pysplicing' extension
> creating build/temp.linux-x86_64-2.7
> creating build/temp.linux-x86_64-2.7/pysplicing
> creating build/temp.linux-x86_64-2.7/pysplicing/src
> creating build/temp.linux-x86_64-2.7/pysplicing/src/lapack
> creating build/temp.linux-x86_64-2.7/pysplicing/src/f2c
> gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/gpfs/fs121/h/gotte/python/epd-7.3-1-rh5-x86_64/include/python2.7 -c pysplicing/src/pyconvert.c -o build/temp.linux-x86_64-2.7/pysplicing/src/pyconvert.o
> In file included from pysplicing/src/pyconvert.c:2:
> pysplicing/include/pysplicing.h:7:22: error: splicing.h: No such file or directory
> In file included from pysplicing/src/pyconvert.c:2:
> pysplicing/include/pysplicing.h:9: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:10: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_t’
> pysplicing/include/pysplicing.h:11: error: expected declaration specifiers or ‘...’ before ‘splicing_strvector_t’
> pysplicing/include/pysplicing.h:12: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:13: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:15: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:16: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:17: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:18: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:19: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:21: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:4: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_vector_int’:
> pysplicing/src/pyconvert.c:13: error: ‘v’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c:13: error: (Each undeclared identifier is reported only once
> pysplicing/src/pyconvert.c:13: error: for each function it appears in.)
> pysplicing/src/pyconvert.c:16: error: subscripted value is neither array nor pointer
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:22: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_vector’:
> pysplicing/src/pyconvert.c:31: error: ‘v’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c:34: error: subscripted value is neither array nor pointer
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:40: error: expected declaration specifiers or ‘...’ before ‘splicing_strvector_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_strvector’:
> pysplicing/src/pyconvert.c:49: error: ‘v’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:59: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_exons’:
> pysplicing/src/pyconvert.c:61: error: ‘ex’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c:64: error: subscripted value is neither array nor pointer
> pysplicing/src/pyconvert.c:65: error: subscripted value is neither array nor pointer
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:70: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_isoforms’:
> pysplicing/src/pyconvert.c:77: error: ‘iso’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c:83: error: subscripted value is neither array nor pointer
> pysplicing/src/pyconvert.c:85: error: subscripted value is neither array nor pointer
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:91: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:101: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:118: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:135: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:146: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:156: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:174: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> error: command 'gcc' failed with exit status 1
> 
> 
> Any thoughts?
> 
> Best,
> 
> Gabe
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