Failed installation

[Aoi W.]

Hello!

I'm currently having issues installing majiq. I've attached the full output in the .txt file. I have python 3.8.1 installed and upgraded pip to the current version (21.3.1). I am fairly new to computational work so any basic advice is much appreciated.

Thanks!

Aoi

[Paul Jewell]

Hello Aoi,

The issue stems from the final error message at the bottom of the report:

"clang: error: unsupported option '-fopenmp'"

You will need to use the c/c++ compiler 'gcc'/'g++' instead of 'clang' because 'clang' does not support the multithreading option 'openmp'

You can do this by installing gcc/g++ , and then exporting the following variables:

$ export CC=/path/to/where/gcc/is/installed

$ export CXX=/path/to/where/g++/is/installed

Then try running the same installation command once again.

Thanks.

[Aoi Wakabayashi]

Hi Paul,

Thanks for your response! I tried installing gcc/g++ and exporting, but still get the error "clang: error: unsupported option '-fopenmp'"

I thought I had gcc/g++ installed. When checking the version I get:

Aois-iMac:~ aoiwakabayashi$ gcc --version

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 11.0.3 (clang-1103.0.32.62)

Target: x86_64-apple-darwin21.1.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

(env) Aois-iMac:~ aoiwakabayashi$ g++ --version

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 11.0.3 (clang-1103.0.32.62)

Target: x86_64-apple-darwin21.1.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

I tried reinstalling with brew install gcc and it just updated it. Is there something else I need to do? I attached the full output to this message.

Thanks!

-Aoi

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[Joseph Aicher]

Dear Aoi,

I think you're almost there. There is one last thing you need to do:

• MacOS ships with a version of gcc/g++ that isn't actually gcc/g++ (it's clang) for whatever reason
• When you install gcc/g++ in Homebrew, it doesn't actually replace the default gcc/g++ commands on OSX
• Instead, it typically is gcc-{major version}. On my laptop, it's gcc-11.
• It's probably already on your path, so you can probably find it by typing "gcc-" and then hitting tab to autocomplete
• Otherwise, you can probably also find it in /usr/local/bin (the MacOS default non-gcc gcc is in /usr/bin)
• Once you know what the command/path you should use, you can run the commands that Paul said above
• In my case, with "gcc-11", I would run `export CC=gcc-11; export CXX=g++-11` (you can expand out the path if tab-complete didn't work for you, which means it isn't on your PATH)
• Then in the same session, you can try the pip install again.

Hope this helps and let us know if this does/doesn't work or if you have any other questions!

Best,

Joseph

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Joseph Aicher

MD/PhD Candidate, GS6

Perelman School of Medicine

Genomics and Computational Biology Graduate Group

[Aoi Wakabayashi]

Hey Joseph,

Thanks for the note! So I found the path I should use and ran:

(env) Aois-iMac:~ aoiwakabayashi$ export CC=/usr/local/bin/gcc-11 

(env) Aois-iMac:~ aoiwakabayashi$ export CXX=/usr/local/bin/g++-11 

(env) Aois-iMac:~ aoiwakabayashi$ pip install git+https://bitbucket.org/biociphers/majiq_academic.git

This time I get a different error:

/usr/local/bin/gcc-11 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/Users/aoiwakabayashi/env/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-install-d8e2rhia/cython_db2f8dc6e74241ad9fd5781a0d6e29a6/Cython/Plex/Scanners.c -o build/temp.macosx-10.9-x86_64-3.8/private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-install-d8e2rhia/cython_db2f8dc6e74241ad9fd5781a0d6e29a6/Cython/Plex/Scanners.o

      In file included from /usr/local/Cellar/gcc/11.2.0_2/lib/gcc/11/gcc/x86_64-apple-darwin21/11/include-fixed/syslimits.h:7,

                       from /usr/local/Cellar/gcc/11.2.0_2/lib/gcc/11/gcc/x86_64-apple-darwin21/11/include-fixed/limits.h:34,

                       from /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/Python.h:11,

                       from /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-install-d8e2rhia/cython_db2f8dc6e74241ad9fd5781a0d6e29a6/Cython/Plex/Scanners.c:19:

      /usr/local/Cellar/gcc/11.2.0_2/lib/gcc/11/gcc/x86_64-apple-darwin21/11/include-fixed/limits.h:203:75: error: no include path in which to search for limits.h

        203 | #include_next <limits.h>                /* recurse down to the real one */

            |                                                                           ^

      In file included from /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/Python.h:25,

                       from /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-install-d8e2rhia/cython_db2f8dc6e74241ad9fd5781a0d6e29a6/Cython/Plex/Scanners.c:19:

      /usr/local/Cellar/gcc/11.2.0_2/lib/gcc/11/gcc/x86_64-apple-darwin21/11/include-fixed/stdio.h:78:10: fatal error: _stdio.h: No such file or directory

         78 | #include <_stdio.h>

            |          ^~~~~~~~~~

      compilation terminated.

      error: command '/usr/local/bin/gcc-11' failed with exit status 1

      ----------------------------------------

  ERROR: Command errored out with exit status 1: /Users/aoiwakabayashi/env/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-install-d8e2rhia/cython_db2f8dc6e74241ad9fd5781a0d6e29a6/setup.py'"'"'; __file__='"'"'/private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-install-d8e2rhia/cython_db2f8dc6e74241ad9fd5781a0d6e29a6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-record-rg37rafz/install-record.txt --single-version-externally-managed --prefix /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-build-env-c1py4rbx/overlay --compile --install-headers /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-build-env-c1py4rbx/overlay/include/site/python3.8/Cython Check the logs for full command output.

  ----------------------------------------

WARNING: Discarding file://localhost/private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-req-build-5n94iek2/majiq/. Command errored out with exit status 1: /Users/aoiwakabayashi/env/bin/python3 /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-standalone-pip-1_15n8yq/__env_pip__.zip/pip install --ignore-installed --no-user --prefix /private/var/folders/bp/ptvbfd216l573f6c7vt7xyg40000gn/T/pip-build-env-c1py4rbx/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=45' wheel Cython==0.29.14 'numpy>=1.18.1' 'setuptools_scm>=6.2' Check the logs for full command output.

ERROR: Could not find a version that satisfies the requirement rna-majiq (unavailable) (from rna-majiq-meta) (from versions: 0.0.1)

ERROR: No matching distribution found for rna-majiq (unavailable)

Full output is attached. Thanks a lot for all of your help Joseph and Paul! I really appreciate it!

-Aoi

[Paul Jewell]

Hi Aoi,

This seems to still be a mac specific issue relating to xcode or search paths. I don't have a mac machine to reproduce this on currently, have you tried the suggestions for this specific error ( fatal error: _stdio.h: No such file or directory ) in these locations?

https://trac.macports.org/ticket/57937

https://nkaushik.com/mac/mac-c-compilation-error/

?