Biom-format install issue on Mac OS X 10.8.5 (Cannot locate working compiler)

roserise commented 9 years ago

I have a problem in installing Biom-format.

mY mac is Mac OS X 10.8.5
Python 2.7.10
I have installed numpy through: pip install bumpy and got: Successfully installed numpy-1.9.2 then confirmed: python -c "import numpy; print numpy.version" 1.9.2
then i have a problem in installing biom-format through: pip install biom-format Collecting biom-format Downloading biom-format-2.1.4.tar.gz (435kB) 100% |████████████████████████████████| 438kB 35kB/s Requirement already satisfied (use --upgrade to upgrade): numpy>=1.3.0 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from biom-format) Collecting pyqi==0.3.2 (from biom-format) Downloading pyqi-0.3.2.tar.gz (240kB) 100% |████████████████████████████████| 241kB 74kB/s Collecting scipy>=0.13.0 (from biom-format) Downloading scipy-0.16.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (20.5MB) 100% |████████████████████████████████| 20.5MB 11kB/s Installing collected packages: pyqi, scipy, biom-format Running setup.py install for pyqi Running setup.py install for biom-format Complete output from command /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;file='/private/var/folders/33/zygxjp6d4cjg88b_ny_pq7nc0000gn/T/pip-build-ZIQRUu/biom-format/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/33/zygxjp6d4cjg88b_ny_pq7nc0000gn/T/pip-eS1MWo-record/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.macosx-10.6-intel-2.7 creating build/lib.macosx-10.6-intel-2.7/biom copying biom/init.py -> build/lib.macosx-10.6-intel-2.7/biom copying biom/err.py -> build/lib.macosx-10.6-intel-2.7/biom copying biom/exception.py -> build/lib.macosx-10.6-intel-2.7/biom copying biom/parse.py -> build/lib.macosx-10.6-intel-2.7/biom copying biom/table.py -> build/lib.macosx-10.6-intel-2.7/biom copying biom/util.py -> build/lib.macosx-10.6-intel-2.7/biom creating build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/init.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/installation_informer.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/metadata_adder.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/table_converter.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/table_normalizer.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/table_subsetter.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/table_summarizer.py -> build/lib.macosx-10.6-intel-2.7/biom/commands copying biom/commands/table_validator.py -> build/lib.macosx-10.6-intel-2.7/biom/commands creating build/lib.macosx-10.6-intel-2.7/biom/interfaces copying biom/interfaces/init.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces creating build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse copying biom/interfaces/optparse/init.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse copying biom/interfaces/optparse/input_handler.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse copying biom/interfaces/optparse/output_handler.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse creating build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/init.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/add_metadata.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/convert.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/normalize_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/show_install_info.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/subset_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/summarize_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config copying biom/interfaces/optparse/config/validate_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/optparse/config creating build/lib.macosx-10.6-intel-2.7/biom/interfaces/html copying biom/interfaces/html/init.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html copying biom/interfaces/html/input_handler.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html copying biom/interfaces/html/output_handler.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html creating build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/init.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/add_metadata.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/convert.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/normalize_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/show_install_info.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/summarize_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config copying biom/interfaces/html/config/validate_table.py -> build/lib.macosx-10.6-intel-2.7/biom/interfaces/html/config running build_ext Traceback (most recent call last): File "", line 1, in File "/private/var/folders/33/zygxjp6d4cjg88b_ny_pq7nc0000gn/T/pip-build-ZIQRUu/biom-format/setup.py", line 111, in classifiers=classifiers File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/install.py", line 61, in run return orig.install.run(self) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/install.py", line 563, in run self.run_command('build') File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build.py", line 127, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools/command/build_ext.py", line 50, in run _build_ext.run(self) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 307, in run customize_compiler(self.compiler) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/sysconfig.py", line 171, in customize_compiler _osx_support.customize_compiler(_config_vars) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.py", line 418, in customize_compiler _find_appropriate_compiler(_config_vars) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.py", line 191, in _find_appropriate_compiler "Cannot locate working compiler") SystemError: Cannot locate working compiler

Command "/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;file='/private/var/folders/33/zygxjp6d4cjg88b_ny_pq7nc0000gn/T/pip-build-ZIQRUu/biom-format/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /var/folders/33/zygxjp6d4cjg88b_ny_pq7nc0000gn/T/pip-eS1MWo-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/33/zygxjp6d4cjg88b_ny_pq7nc0000gn/T/pip-build-ZIQRUu/biom-format
How could i fix this problem???

wasade commented 9 years ago

It looks like you don't have Xcode installed? Xcode is the developer stack from Apple and it contains the necessary toolchains to compile C programs (among other languages)

roserise commented 9 years ago

Thanks a lot for your rapid reply. I found 2 versions of Xcode:

Xcode 7 beta 6
Xcode 6.4 Which one is suitable?

wasade commented 9 years ago

6.4? No need for beta

On Mon, Aug 24, 2015 at 4:50 PM, roserise notifications@github.com wrote:

Thanks a lot for your rapid reply. I found 2 versions of Xcode:

Xcode 7 beta 6

Xcode 6.4 Which one is suitable?

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/641#issuecomment-134404310 .

wasade commented 7 years ago

I'm closing this issue as I believe it was an environment problem. Please reopen if necessary.

biocore / biom-format

Biom-format install issue on Mac OS X 10.8.5 (Cannot locate working compiler) #641