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Mac OS Mojave installation error - error: command 'clang' failed with exit status 1
See original GitHub issueHi,
When trying to install Velocyto on macOS 10.14.4 (Mojave) I receive the following error:
Collecting velocyto
Using cached https://files.pythonhosted.org/packages/81/66/e8fff9d3b824fd99c0f678c47c740fec058ce2d9a0cfdf11b114ea8889f2/velocyto-0.17.17.tar.gz
Requirement already satisfied: numpy in /usr/local/lib/python3.7/site-packages (from velocyto) (1.16.3)
Requirement already satisfied: scipy in /usr/local/lib/python3.7/site-packages (from velocyto) (1.2.1)
Requirement already satisfied: cython in /usr/local/lib/python3.7/site-packages (from velocyto) (0.29.7)
Requirement already satisfied: numba in /usr/local/lib/python3.7/site-packages (from velocyto) (0.43.1)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/site-packages (from velocyto) (3.0.3)
Requirement already satisfied: scikit-learn in /usr/local/lib/python3.7/site-packages (from velocyto) (0.20.3)
Requirement already satisfied: h5py in /usr/local/lib/python3.7/site-packages (from velocyto) (2.9.0)
Requirement already satisfied: loompy in /usr/local/lib/python3.7/site-packages (from velocyto) (2.0.17)
Requirement already satisfied: pysam in /usr/local/lib/python3.7/site-packages (from velocyto) (0.15.2)
Requirement already satisfied: Click in /usr/local/lib/python3.7/site-packages (from velocyto) (7.0)
Requirement already satisfied: pandas in /usr/local/lib/python3.7/site-packages (from velocyto) (0.24.2)
Requirement already satisfied: llvmlite>=0.28.0dev0 in /usr/local/lib/python3.7/site-packages (from numba->velocyto) (0.28.0)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->velocyto) (2.8.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->velocyto) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->velocyto) (1.0.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->velocyto) (2.4.0)
Requirement already satisfied: six in /usr/local/lib/python3.7/site-packages (from h5py->velocyto) (1.12.0)
Requirement already satisfied: setuptools in /usr/local/lib/python3.7/site-packages (from loompy->velocyto) (40.8.0)
Requirement already satisfied: pytz>=2011k in /usr/local/lib/python3.7/site-packages (from pandas->velocyto) (2019.1)
Building wheels for collected packages: velocyto
Building wheel for velocyto (setup.py) ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-install-gn6cymm9/velocyto/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 /private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-wheel-gyph1018 --python-tag cp37:
['-c', 'bdist_wheel', '-d', '/private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-wheel-gyph1018', '--python-tag', 'cp37']
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/transcript_model.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/diffusion.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/metadata.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/analysis.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/molitem.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/_version.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/neighbors.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/constants.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/estimation.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/feature.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/logic.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/indexes.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/utils.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/gene_info.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/r_interface.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/segment_match.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/counter.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/serialization.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/read.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
creating build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/velocyto.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run10x.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/_run.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
running build_ext
building 'velocyto.speedboosted' extension
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/velocyto
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c velocyto/speedboosted.c -o build/temp.macosx-10.14-x86_64-3.7/velocyto/speedboosted.o -fopenmp -ffast-math
velocyto/speedboosted.c:613:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
^~~~~~~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Failed building wheel for velocyto
Running setup.py clean for velocyto
Failed to build velocyto
Installing collected packages: velocyto
Running setup.py install for velocyto ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-install-gn6cymm9/velocyto/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-record-hpsa6hb2/install-record.txt --single-version-externally-managed --compile:
['-c', 'install', '--record', '/private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-record-hpsa6hb2/install-record.txt', '--single-version-externally-managed', '--compile']
running install
running build
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/transcript_model.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/diffusion.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/metadata.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/analysis.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/molitem.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/_version.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/neighbors.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/constants.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/estimation.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/feature.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/logic.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/indexes.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/utils.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/gene_info.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/r_interface.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/segment_match.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/counter.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/serialization.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
copying velocyto/read.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto
creating build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/velocyto.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/run10x.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
copying velocyto/commands/_run.py -> build/lib.macosx-10.14-x86_64-3.7/velocyto/commands
running build_ext
building 'velocyto.speedboosted' extension
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/velocyto
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c velocyto/speedboosted.c -o build/temp.macosx-10.14-x86_64-3.7/velocyto/speedboosted.o -fopenmp -ffast-math
velocyto/speedboosted.c:613:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
^~~~~~~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------
Command "/usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-install-gn6cymm9/velocyto/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-record-hpsa6hb2/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/m5/xjs7y13n2_s81sxlztjk1z7h0000gn/T/pip-install-gn6cymm9/velocyto/
I installed all dependencies using
conda install numpy scipy cython numba matplotlib scikit-learn h5py click
As well as pysam using pip and all seem to be installed correctly.
I can’t seem to find a solution in any of the other posts about installation errors.
Any help would be much appreciated.
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I’m experiencing the same exact issue on macOS Mojave (10.14.5)
Having the same problem. Running conda. Tried resolving based on similar problems elsewhere:
export CFLAGS=“-I /path/to/numpygetincl $CFLAGS”
where path/to/numpygetinc is found via numpy.get_include() in Python. Unfortunately this just kicks error down the road to:
Installing collected packages: velocyto Running setup.py install for velocyto … error Complete output from command /usr/local/opt/python/bin/python3.6 -u -c “import setuptools, tokenize;file=‘/private/var/folders/7c/cvkdt6yx031g81ncvhd2t56r0000gn/T/pip-install-pw_lg8bv/velocyto/setup.py’;f=getattr(tokenize, ‘open’, open)(file);code=f.read().replace(‘\r\n’, ‘\n’);f.close();exec(compile(code, file, ‘exec’))” install --record /private/var/folders/7c/cvkdt6yx031g81ncvhd2t56r0000gn/T/pip-record-c5bls8cc/install-record.txt --single-version-externally-managed --compile: [‘-c’, ‘install’, ‘–record’, ‘/private/var/folders/7c/cvkdt6yx031g81ncvhd2t56r0000gn/T/pip-record-c5bls8cc/install-record.txt’, ‘–single-version-externally-managed’, ‘–compile’] running install running build running build_py creating build creating build/lib.macosx-10.13-x86_64-3.6 creating build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/transcript_model.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/diffusion.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/metadata.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/analysis.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/molitem.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/_version.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/neighbors.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/constants.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/estimation.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/init.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/feature.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/logic.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/indexes.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/utils.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/gene_info.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/r_interface.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/segment_match.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/counter.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/serialization.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto copying velocyto/read.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto creating build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/velocyto.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/run.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/init.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/run10x.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands copying velocyto/commands/_run.py -> build/lib.macosx-10.13-x86_64-3.6/velocyto/commands running build_ext building ‘velocyto.speedboosted’ extension creating build/temp.macosx-10.13-x86_64-3.6 creating build/temp.macosx-10.13-x86_64-3.6/velocyto clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.6.5_1/Frameworks/Python.framework/Versions/3.6/include/python3.6m -c velocyto/speedboosted.c -o build/temp.macosx-10.13-x86_64-3.6/velocyto/speedboosted.o -fopenmp -ffast-math velocyto/speedboosted.c:633:10: fatal error: ‘numpy/arrayobject.h’ file not found #include “numpy/arrayobject.h” ^~~~~~~~~~~~~~~~~~~~~ 1 error generated. error: command ‘clang’ failed with exit status 1
Looks like a problem with compilers on latest version of Mac OS rather than a velocyto bug … but way beyond my expertise. If anyone else has resolved this come save us!