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yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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Python.h does not exist on pip install misopy #108

Open AMChalkie opened 7 years ago

AMChalkie commented 7 years ago

Hi Guys,

An installation bug for you:

virtualenv -p python3 python3_miso_environment python3_miso_environment/bin/pip install misopy

Fails...

In file included from pysplicing/src/pyrandom.c:2:0: pysplicing/include/random.h:5:20: fatal error: Python.h: No such file or directory compilation terminated.

copying misopy/sashimi_plot/plot_utils/__init__.py -> build/lib.linux-x86_64-3.5/misopy/sashimi_plot/plot_utils
creating build/lib.linux-x86_64-3.5/pysplicing
copying pysplicing/pysplicing/__init__.py -> build/lib.linux-x86_64-3.5/pysplicing
running build_ext
building 'pysplicing.pysplicing' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/pysplicing
creating build/temp.linux-x86_64-3.5/pysplicing/src
creating build/temp.linux-x86_64-3.5/pysplicing/src/lapack
creating build/temp.linux-x86_64-3.5/pysplicing/src/f2c
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/miso_paired.c -o build/temp.linux-x86_64-3.5/pysplicing/src/miso_paired.o
pysplicing/src/miso_paired.c: In function ‘splicing_score_iso_paired’:
pysplicing/src/miso_paired.c:95:8: warning: unused variable ‘isolen’ [-Wunused-variable]
   int *isolen = VECTOR(*pisolen);
        ^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/strvector.c -o build/temp.linux-x86_64-3.5/pysplicing/src/strvector.o
pysplicing/src/strvector.c: In function ‘splicing_strvector_clear’:
pysplicing/src/strvector.c:35:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/gff.c -o build/temp.linux-x86_64-3.5/pysplicing/src/gff.o
pysplicing/src/gff.c: In function ‘splicing_gff_noiso’:
pysplicing/src/gff.c:664:25: warning: variable ‘idx2’ set but not used [-Wunused-but-set-variable]
   size_t nogenes, idx1, idx2, pos=0;
                         ^
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/memory.c -o build/temp.linux-x86_64-3.5/pysplicing/src/memory.o
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/qsort.c -o build/temp.linux-x86_64-3.5/pysplicing/src/qsort.o
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/pyrandom.c -o build/temp.linux-x86_64-3.5/pysplicing/src/pyrandom.o
In file included from pysplicing/src/pyrandom.c:2:0:
pysplicing/include/random.h:5:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

----------------------------------------

Command "/mnts/stemcell-bioinfo/bin/python3_miso_environment/bin/python3 -u -c "import setuptools, tokenize;file='/mnts/stemcell-bioinfo/javatmp/pip-build-aeseq5pg/misopy/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /mnts/stemcell-bioinfo/javatmp/pip-p_b6oyid-record/install-record.txt --single-version-externally-managed --compile --install-headers /mnts/stemcell-bioinfo/bin/python3_miso_environment/include/site/python3.5/misopy" failed with error code 1 in /mnts/stemcell-bioinfo/javatmp/pip-build-aeseq5pg/misopy/

yarden commented 7 years ago

Python 3 is not supported by MISO at the moment.

On Aug 2, 2017, at 11:54 PM, Alistair Chalk notifications@github.com wrote:

Hi Guys,

An installation bug for you:

virtualenv -p python3 python3_miso_environment python3_miso_environment/bin/pip install misopy

Fails...

In file included from pysplicing/src/pyrandom.c:2:0: pysplicing/include/random.h:5:20: fatal error: Python.h: No such file or directory compilation terminated.

copying misopy/sashimi_plot/plot_utils/init.py -> build/lib.linux-x86_64-3.5/misopy/sashimi_plot/plot_utils creating build/lib.linux-x86_64-3.5/pysplicing copying pysplicing/pysplicing/init.py -> build/lib.linux-x86_64-3.5/pysplicing running build_ext building 'pysplicing.pysplicing' extension creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/pysplicing creating build/temp.linux-x86_64-3.5/pysplicing/src creating build/temp.linux-x86_64-3.5/pysplicing/src/lapack creating build/temp.linux-x86_64-3.5/pysplicing/src/f2c x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/miso_paired.c -o build/temp.linux-x86_64-3.5/pysplicing/src/miso_paired.o pysplicing/src/miso_paired.c: In function ‘splicing_score_iso_paired’: pysplicing/src/miso_paired.c:95:8: warning: unused variable ‘isolen’ [-Wunused-variable] int isolen = VECTOR(pisolen); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/strvector.c -o build/temp.linux-x86_64-3.5/pysplicing/src/strvector.o pysplicing/src/strvector.c: In function ‘splicing_strvector_clear’: pysplicing/src/strvector.c:35:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/gff.c -o build/temp.linux-x86_64-3.5/pysplicing/src/gff.o pysplicing/src/gff.c: In function ‘splicing_gff_noiso’: pysplicing/src/gff.c:664:25: warning: variable ‘idx2’ set but not used [-Wunused-but-set-variable] size_t nogenes, idx1, idx2, pos=0; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/memory.c -o build/temp.linux-x86_64-3.5/pysplicing/src/memory.o x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/qsort.c -o build/temp.linux-x86_64-3.5/pysplicing/src/qsort.o x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/usr/include/python3.5m -I/mnts/stemcell-bioinfo/bin/python3_miso_environment/include/python3.5m -c pysplicing/src/pyrandom.c -o build/temp.linux-x86_64-3.5/pysplicing/src/pyrandom.o In file included from pysplicing/src/pyrandom.c:2:0: pysplicing/include/random.h:5:20: fatal error: Python.h: No such file or directory compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Command "/mnts/stemcell-bioinfo/bin/python3_miso_environment/bin/python3 -u -c "import setuptools, tokenize;file='/mnts/stemcell-bioinfo/javatmp/pip-build-aeseq5pg/misopy/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /mnts/stemcell-bioinfo/javatmp/pip-p_b6oyid-record/install-record.txt --single-version-externally-managed --compile --install-headers /mnts/stemcell-bioinfo/bin/python3_miso_environment/include/site/python3.5/misopy" failed with error code 1 in /mnts/stemcell-bioinfo/javatmp/pip-build-aeseq5pg/misopy/

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fu commented 6 years ago

if Python.h is missing (besides Python3 is not supported) indicates that you have not installed Python-devel on your system. :)