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nanoporetech / pomoxis

Analysis components from Oxford Nanopore Research
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Installation problems #16

Closed weedcentipede closed 6 years ago

weedcentipede commented 6 years ago

Hi, Running Pomoxis installation I've get the three following error, in different situations, but never it installed: root@biocomp04:~/pomoxis# make install In file included from submodules/scrappie/src/decode.h:4:0, from pomoxis/pyscrap/pyscrap.c:15: submodules/scrappie/src/fast5_interface.h:4:18: fatal error: hdf5.h: No such file or directory compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 Makefile:57: recipe for target 'install' failed make: *** [install] Error 1

(venv) root@biocomp04:~/pomoxis# python setup.py install running install running bdist_egg running egg_info writing requirements to pomoxis.egg-info/requires.txt writing pomoxis.egg-info/PKG-INFO writing top-level names to pomoxis.egg-info/top_level.txt writing dependency_links to pomoxis.egg-info/dependency_links.txt writing entry points to pomoxis.egg-info/entry_points.txt reading manifest file 'pomoxis.egg-info/SOURCES.txt' writing manifest file 'pomoxis.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py running build_ext building 'pyscrap' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Isubmodules/scrappie/src -I/usr/include/python2.7 -c pomoxis/pyscrap/pyscrap.c -o build/temp.linux-x86_64-2.7/pomoxis/pyscrap/pyscrap.o -pedantic -Wall -std=c99 -march=native -ffast-math -DUSE_SSE2 -DNDEBUG In file included from submodules/scrappie/src/decode.h:4:0, from pomoxis/pyscrap/pyscrap.c:15: submodules/scrappie/src/fast5_interface.h:4:18: fatal error: hdf5.h: No such file or directory compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

bio@biocomp04:~/pomoxis$ make install ... writing requirements to pomoxis.egg-info/requires.txt error: [Errno 13] Permission denied: 'pomoxis.egg-info/requires.txt' Makefile:57: recipe for target 'install' failed make: *** [install] Error 1

Could you please help me? gcc version: gcc (Ubuntu 5.4.0-6ubuntu1~16.04.5) 5.4.0 20160609 Ubuntu version: 16.04

cjw85 commented 6 years ago

Several libraries are required to compile some of pomoxis's dependencies (and the pyscrap python extension). These are now listed for Ubuntu 14.04 in the readme. Issue #12 has a few more details for Ubuntu 16.04.