cdanielmachado
commented
5 years ago Hi, I guess this is failing because you don't have command line tools installed for mac ?
If you use pip install carveme, it will automatically install all the python library dependencies. But of course, it cannot prevent something from going wrong if any package fails to install...
The conda installer has been suggested by other users and is in our plans: https://github.com/cdanielmachado/carveme/issues/9
Hi Daniel! I tried installing carveme on MacOS Mojave and Linux Zorinos but I failed.
Suggestions: a) maybe a subcommand to check if all dependencies are installed ( prokka and other Torsten Seeman commandline tools usually have the subcommand to check if all dependencies are installed)
b) anaconda recipe (please)
Here are my error messages:
Failed building wheel for python-libsbml
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/miniconda3/include -arch x86_64 -/miniconda3/include -arch x86_64 -DBZIP2_STATIC -DHAVE_MEMMOVE -D_LIB -DUSE_EXPAT -DUSE_ZLIB -DUSE_BZ2 -DUSE_COMP -DUSE_QUAL -DUSE_FBC -DUSE_LAYOUT -DUSE_GROUPS -DUSE_MULTI -DUSE_RENDER -I./base// -I./base//sbml -I./base//sbml/compress -I./base//sbml/validator/constraints -I./base//sbml/packages/comp/validator -I./base//sbml/packages/comp/validator/constraints -I. -I/miniconda3/include/python3.6m -c ./base/libsbml_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.6/./base/libsbml_wrap.o xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command 'gcc' failed with exit status 1
Command "miniconda3/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/s1/05bh_q_s15n3tdrqnn7r0ktr0000gn/T/pip-install-zi3dhml2/python-libsbml/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/s1/05bh_q_s15n3tdrqnn7r0ktr0000gn/T/pip-record-g511jqr6/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/s1/05bh_q_s15n3tdrqnn7r0ktr0000gn/T/pip-install-zi3dhml2/python-libsbml/