[miso-users] Problem with Install

[Gabriel Otte]

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