hemantgujar
commented
3 years ago ok figured it out somehow i was not using the wright curl directory.
Closed hemantgujar closed 3 years ago
hemantgujar
commented
3 years ago ok figured it out somehow i was not using the wright curl directory.
keh218
commented
3 years ago I have this problem now too- how did you correct it if you remember? thanks :)
dpryan79
commented
3 years ago @keh218 I suggest installing with conda.
I have also gone through https://github.com/deeptools/pyBigWig/issues/9 however could not resolve issue ..
Collecting pyBigWig Using cached pyBigWig-0.3.17.tar.gz (64 kB) Building wheels for collected packages: pyBigWig Building wheel for pyBigWig (setup.py) ... error ERROR: Command errored out with exit status 1: command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/setup.py'"'"'; file='"'"'/tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-pyuxs3vi cwd: /tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/ Complete output (71 lines): /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/pyBigWigTest copying pyBigWigTest/init.py -> build/lib.linux-x86_64-3.7/pyBigWigTest copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.7/pyBigWigTest running egg_info writing pyBigWig.egg-info/PKG-INFO writing dependency_links to pyBigWig.egg-info/dependency_links.txt writing requirements to pyBigWig.egg-info/requires.txt writing top-level names to pyBigWig.egg-info/top_level.txt reading manifest file 'pyBigWig.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pyBigWig.egg-info/SOURCES.txt' copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.7/pyBigWigTest copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.7/pyBigWigTest running build_ext building 'pyBigWig' extension Warning: Can't read registry to find the necessary compiler setting Make sure that Python modules winreg, win32api or win32con are installed. C compiler: /spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC
creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/libBigWig compile options: '-DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/include/python3.7m -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/lib/python3.7/site-packages/numpy/core/include -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/include/python3.7m -c' gcc: libBigWig/bwRead.cgcc: libBigWig/io.c
gcc: libBigWig/bwStats.c gcc: libBigWig/bwWrite.c gcc: libBigWig/bwValues.c gcc: pyBigWig.c libBigWig/io.c:2:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
compilation terminated. In file included from libBigWig/bigWig.h:1, from libBigWig/bwRead.c:1: libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
compilation terminated. In file included from libBigWig/bigWig.h:1, from libBigWig/bwStats.c:1: libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
compilation terminated. In file included from libBigWig/bigWig.h:1, from libBigWig/bwValues.c:1: libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
compilation terminated. In file included from libBigWig/bigWig.h:1, from libBigWig/bwWrite.c:6: libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
compilation terminated. In file included from libBigWig/bigWig.h:1, from pyBigWig.h:3, from pyBigWig.c:3: libBigWig/bigWigIO.h:2:10: fatal error: curl/curl.h: No such file or directory
include <curl/curl.h>
compilation terminated. error: Command "/spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC -DWITHNUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -IlibBigWig -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/include/python3.7m -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/lib/python3.7/site-packages/numpy/core/include -I/spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/include/python3.7m -c libBigWig/bwRead.c -o build/temp.linux-x86_64-3.7/libBigWig/bwRead.o" failed with exit status 1
ERROR: Failed building wheel for pyBigWig Running setup.py clean for pyBigWig Failed to build pyBigWig Installing collected packages: pyBigWig Running setup.py install for pyBigWig ... error ERROR: Command errored out with exit status 1: command: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/setup.py'"'"'; file='"'"'/tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-4do25bze/install-record.txt --single-version-externally-managed --home /tmp/pip-target-i_35toe3 --compile --install-headers /tmp/pip-target-i_35toe3/include/python/pyBigWig cwd: /tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/ Complete output (71 lines): /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/pyBigWigTest copying pyBigWigTest/init.py -> build/lib.linux-x86_64-3.7/pyBigWigTest copying pyBigWigTest/test.py -> build/lib.linux-x86_64-3.7/pyBigWigTest running egg_info writing pyBigWig.egg-info/PKG-INFO writing dependency_links to pyBigWig.egg-info/dependency_links.txt writing requirements to pyBigWig.egg-info/requires.txt writing top-level names to pyBigWig.egg-info/top_level.txt reading manifest file 'pyBigWig.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pyBigWig.egg-info/SOURCES.txt' copying pyBigWigTest/test.bigBed -> build/lib.linux-x86_64-3.7/pyBigWigTest copying pyBigWigTest/test.bw -> build/lib.linux-x86_64-3.7/pyBigWigTest running build_ext building 'pyBigWig' extension Warning: Can't read registry to find the necessary compiler setting Make sure that Python modules winreg, win32api or win32con are installed. C compiler: /spack/apps/gcc/8.3.0/bin/gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -fPIC
ERROR: Command errored out with exit status 1: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/python-3.7.6-dd2am3dyvlpovhd4rizwfzc45wnsajxf/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/setup.py'"'"'; file='"'"'/tmp/pip-install-47iztnjk/pybigwig_fa75be7a7938497198624c64806dd224/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-4do25bze/install-record.txt --single-version-externally-managed --home /tmp/pip-target-i_35toe3 --compile --install-headers /tmp/pip-target-i_35toe3/include/python/pyBigWig Check the logs for full command output.