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LinkageIO / Camoco

Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes.
MIT License
41 stars 32 forks source link

Installation Failed #65

Closed abbycabs closed 6 years ago

abbycabs commented 6 years ago

Hi there 👋

Just ran into this problem installing on macOS Sierra 10.12.6 and Python 2.7. Sorry I have such an old version of python! I'll try with a newer version later.


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Setting up the build environment
WARNING: timestamping does nothing in combination with -O. See the manual
for details.

--2017-10-02 16:25:29--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 2400:cb00:2048:1::6810:120a, 2400:cb00:2048:1::6810:130a, 104.16.19.10, ...
Connecting to repo.continuum.io (repo.continuum.io)|2400:cb00:2048:1::6810:120a|:443... connected.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
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100%[======================================>] 54,095,554  4.87MB/s   in 9.7s   

2017-10-02 16:25:39 (5.29 MB/s) - 'miniconda.sh' saved [54095554/54095554]

PREFIX=/Users/abigail/.camoco/conda
miniconda.sh: line 311: md5sum: command not found
WARNING: md5sum mismatch of tar archive
expected: 580c4f8c1de56c990b7d3347f1beae68
     got: 
installing: python-3.6.2-hdfe5801_15 ...
miniconda.sh: line 349: /Users/abigail/.camoco/conda/pkgs/python-3.6.2-hdfe5801_15/bin/python: cannot execute binary file
Installing git-lfs for the large files in the repo
--2017-10-02 16:25:49--  https://github.com/github/git-lfs/releases/download/v1.1.0/git-lfs-linux-amd64-1.1.0.tar.gz
Resolving github.com (github.com)... 192.30.253.113, 192.30.253.112
Connecting to github.com (github.com)|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 
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Location: https://github.com/git-lfs/git-lfs/releases/download/v1.1.0/git-lfs-linux-amd64-1.1.0.tar.gz [following]```
--2017-10-02 16:25:50--  https://github.com/git-lfs/git-lfs/releases/download/v1.1.0/git-lfs-linux-amd64-1.1.0.tar.gz
Reusing existing connection to github.com:443.
HTTP request sent, awaiting response... 
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The name is too long, 451 chars total.
Trying to shorten...
New name is b214d9a0-8dea-11e5-9730-2552c77dc7b1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171002%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171002T202550Z&X-Amz-Expires=300&X-Amz-Signature=2ab4ad12565edddf5e9c3db.
The name is too long, 451 chars total.
Trying to shorten...
New name is b214d9a0-8dea-11e5-9730-2552c77dc7b1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171002%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171002T202550Z&X-Amz-Expires=300&X-Amz-Signature=2ab4ad12565edddf5e9c3db.
--2017-10-02 16:25:50--  https://github-production-release-asset-2e65be.s3.amazonaws.com/13021798/b214d9a0-8dea-11e5-9730-2552c77dc7b1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171002%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171002T202550Z&X-Amz-Expires=300&X-Amz-Signature=2ab4ad12565edddf5e9c3dbf974280007a729b3f04896a420bdf4de7609f23db&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dgit-lfs-linux-amd64-1.1.0.tar.gz&response-content-type=application%2Foctet-stream
Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.98.51
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.98.51|:443... connected.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
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Length: 3157513 (3.0M) [application/octet-stream]
Saving to: 'b214d9a0-8dea-11e5-9730-2552c77dc7b1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171002%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171002T202550Z&X-Amz-Expires=300&X-Amz-Signature=2ab4ad12565edddf5e9c3db'

100%[======================================>] 3,157,513   5.32MB/s   in 0.6s   

2017-10-02 16:25:50 (5.32 MB/s) - 'b214d9a0-8dea-11e5-9730-2552c77dc7b1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20171002%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20171002T202550Z&X-Amz-Expires=300&X-Amz-Signature=2ab4ad12565edddf5e9c3db' saved [3157513/3157513]

tar: Error opening archive: Failed to open 'git-lfs-linux-amd64-1.1.0.tar.gz'
./install.sh: line 104: cd: git-lfs-1.1.0/: No such file or directory
mv: rename git-lfs to /Users/abigail/.camoco/bin/git-lfs: No such file or directory
WARNING: You called a Git command named 'lfs', which does not exist.
Continuing under the assumption that you meant 'log'
in 0.1 seconds automatically...
fatal: Not a git repository (or any of the parent directories): .git
WARNING: You called a Git command named 'lfs', which does not exist.
Continuing under the assumption that you meant 'log'
in 0.1 seconds automatically...
fatal: Not a git repository (or any of the parent directories): .git
Installing a local version of the icu library
--2017-10-02 16:25:51--  http://archive.ubuntu.com/ubuntu/pool/main/i/icu/icu_4.8.1.1.orig.tar.gz
Resolving archive.ubuntu.com (archive.ubuntu.com)... 2001:67c:1360:8001::21, 2001:67c:1560:8001::14, 2001:67c:1360:8001::17, ...
Connecting to archive.ubuntu.com (archive.ubuntu.com)|2001:67c:1360:8001::21|:80... connected.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
  Date: Mon, 02 Oct 2017 20:25:51 GMT
  Server: Apache/2.4.18 (Ubuntu)
  Last-Modified: Sun, 20 Nov 2011 14:04:12 GMT
  ETag: "11cf845-4b22b0b6eef00"
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  Keep-Alive: timeout=5, max=100
  Connection: Keep-Alive
  Content-Type: application/x-gzip
Length: 18675781 (18M) [application/x-gzip]
Saving to: 'icu_4.8.1.1.orig.tar.gz'

100%[======================================>] 18,675,781   820KB/s   in 22s    

2017-10-02 16:26:13 (826 KB/s) - 'icu_4.8.1.1.orig.tar.gz' saved [18675781/18675781]

Extracting the tarball
checking for ICU version numbers... release 4.8.1.1, library 48.1.1, unicode version 6.0
checking build system type... i386-apple-darwin16.7.0
checking host system type... i386-apple-darwin16.7.0
checking target system type... i386-apple-darwin16.7.0
checking whether to build debug libraries... no
checking whether to build release libraries... yes
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/Users/abigail/.camoco/icu/source':
configure: error: C compiler cannot create executables
See `config.log' for more details

Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

Installing a local version of the qhull library
--2017-10-02 16:26:16--  http://www.qhull.org/download/qhull-2012.1-src.tgz
Resolving www.qhull.org (www.qhull.org)... 64.71.34.21
Connecting to www.qhull.org (www.qhull.org)|64.71.34.21|:80... connected.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
  Date: Mon, 02 Oct 2017 20:26:17 GMT
  Server: Apache
  Last-Modified: Wed, 22 Feb 2012 04:00:05 GMT
  ETag: "aef79-4b9859006db40"
  Accept-Ranges: bytes
  Content-Length: 716665
  Keep-Alive: timeout=5, max=256
  Connection: Keep-Alive
  Content-Type: application/x-gzip
Length: 716665 (700K) [application/x-gzip]
Saving to: 'qhull-2012.1-src.tgz'

100%[======================================>] 716,665     1.64MB/s   in 0.4s   

2017-10-02 16:26:17 (1.64 MB/s) - 'qhull-2012.1-src.tgz' saved [716665/716665]

Extracting the tarball

Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

mv: rename bin/* to /Users/abigail/.camoco/bin/*: No such file or directory
mv: rename lib/* to /Users/abigail/.camoco/lib/*: No such file or directory
Installing mcl locally
--2017-10-02 16:26:17--  http://micans.org/mcl/src/mcl-latest.tar.gz
Resolving micans.org (micans.org)... 2001:888:0:18::117:80, 194.109.6.98
Connecting to micans.org (micans.org)|2001:888:0:18::117:80|:80... connected.
HTTP request sent, awaiting response... 
  HTTP/1.1 200 OK
  Server: openresty
  Date: Mon, 02 Oct 2017 20:26:17 GMT
  Content-Type: application/x-gzip
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  Connection: keep-alive
  Last-Modified: Fri, 16 May 2014 22:20:31 GMT
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Length: 3035491 (2.9M) [application/x-gzip]
Saving to: 'mcl-latest.tar.gz'

100%[======================================>] 3,035,491    623KB/s   in 5.0s   

2017-10-02 16:26:22 (595 KB/s) - 'mcl-latest.tar.gz' saved [3035491/3035491]

Extracting the taball
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/local/bin/gmkdir -p
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... no
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... none
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/Users/abigail/.camoco/mcl-14-137':
configure: error: C compiler cannot create executables
See `config.log' for more details.

Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

Making the conda virtual environment named camoco in /Users/abigail/.camoco
./install.sh: line 181: conda: command not found
./install.sh: line 182: conda: command not found
./install.sh: line 183: conda: command not found
./install.sh: line 184: conda: command not found
./install.sh: line 185: conda: command not found
activating camoco
./install.sh: line 197: /Users/abigail/.camoco/conda/bin/activate: No such file or directory
checking python
/usr/bin/python
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named powerlaw
Collecting powerlaw
  Downloading powerlaw-1.4.3.tar.gz
Building wheels for collected packages: powerlaw
  Running setup.py bdist_wheel for powerlaw ... done
  Stored in directory: /Users/abigail/Library/Caches/pip/wheels/0f/3a/65/ef4d039991b4e047000baf4c735e572a90409c31a1772f04d2
Successfully built powerlaw
Installing collected packages: powerlaw
Successfully installed powerlaw-1.4.3
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named bcolz
Collecting bcolz
  Downloading bcolz-1.1.2.tar.gz (1.3MB)
    100% |████████████████████████████████| 1.3MB 735kB/s 
    Complete output from command python setup.py egg_info:
    Unable to find pgen, not compiling formal grammar.
    SSE2 detected
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Plex/Scanners.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Plex/Actions.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Pythran.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Lexicon.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Scanning.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Parsing.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Visitor.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/FlowControl.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Code.py because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Runtime/refnanny.pyx because it changed.
    Compiling /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Tempita/_tempita.py because it changed.
    [ 1/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Code.py
    [ 2/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/FlowControl.py
    [ 3/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Lexicon.py
    [ 4/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Parsing.py
    [ 5/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Pythran.py
    [ 6/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Scanning.py
    [ 7/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Compiler/Visitor.py
    [ 8/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Plex/Actions.py
    [ 9/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Plex/Scanners.py
    [10/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Runtime/refnanny.pyx
    [11/11] Cythonizing /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/easy_install-IcEQti/Cython-0.27.1/Cython/Tempita/_tempita.py
    warning: no files found matching '2to3-fixers.txt'
    warning: no files found matching 'Doc/*'
    warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
    warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
    warning: no files found matching '*.pxd' under directory 'Cython/Utility'

    Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-uamD26/bcolz/setup.py", line 234, in <module>
        cmdclass=LazyCommandClass(),
      File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 111, in setup
        _setup_distribution = dist = klass(attrs)
      File "/usr/local/lib/python2.7/site-packages/setuptools/dist.py", line 316, in __init__
        self.fetch_build_eggs(attrs['setup_requires'])
      File "/usr/local/lib/python2.7/site-packages/setuptools/dist.py", line 371, in fetch_build_eggs
        replace_conflicting=True,
      File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 846, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1118, in best_match
        return self.obtain(req, installer)
      File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1130, in obtain
        return installer(requirement)
      File "/usr/local/lib/python2.7/site-packages/setuptools/dist.py", line 439, in fetch_build_egg
        return cmd.easy_install(req)
      File "/usr/local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 665, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/usr/local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 695, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/usr/local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 876, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/usr/local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1115, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/usr/local/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1103, in run_setup
        raise DistutilsError("Setup script exited with %s" % (v.args[0],))
    distutils.errors.DistutilsError: Setup script exited with error: command 'clang' failed with exit status 69

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-uamD26/bcolz/
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named GeneWordSearch
Collecting GeneWordSearch
  Downloading GeneWordSearch-2.5.1.tar.gz (11.6MB)
    100% |████████████████████████████████| 11.6MB 87kB/s 
Requirement already satisfied: numpy in /usr/local/lib/python2.7/site-packages (from GeneWordSearch)
Collecting scipy (from GeneWordSearch)
  Downloading scipy-0.19.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.2MB)
    100% |████████████████████████████████| 16.2MB 49kB/s 
Building wheels for collected packages: GeneWordSearch
  Running setup.py bdist_wheel for GeneWordSearch ... error
  Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/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 /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/tmpc6MVTfpip-wheel- --python-tag cp27:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib
  creating build/lib/genewordsearch
  copying genewordsearch/__init__.py -> build/lib/genewordsearch
  copying genewordsearch/Classes.py -> build/lib/genewordsearch
  copying genewordsearch/DBBuilder.py -> build/lib/genewordsearch
  copying genewordsearch/GeneWordSearch.py -> build/lib/genewordsearch
  creating build/lib/webapp
  copying webapp/__init__.py -> build/lib/webapp
  copying webapp/guniConfig.py -> build/lib/webapp
  copying webapp/views.py -> build/lib/webapp
  creating build/lib/genewordsearch/databases
  copying genewordsearch/databases/__init__.py -> build/lib/genewordsearch/databases
  running build_scripts
  creating build/scripts-2.7
  copying and adjusting bin/gws -> build/scripts-2.7
  changing mode of build/scripts-2.7/gws from 644 to 755
  installing to build/bdist.macosx-10.12-x86_64/wheel
  running install
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/setup.py", line 42, in <module>
      install_requires=['numpy','scipy'])
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup
      dist.run_commands()
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
      self.run_command(cmd)
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/usr/local/lib/python2.7/site-packages/wheel/bdist_wheel.py", line 215, in run
      self.run_command('install')
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command
      self.distribution.run_command(command)
    File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
      cmd_obj.run()
    File "/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/setup.py", line 19, in run
      os.makedirs(zmDir, exist_ok=True)
  TypeError: makedirs() got an unexpected keyword argument 'exist_ok'

  ----------------------------------------
  Failed building wheel for GeneWordSearch
  Running setup.py clean for GeneWordSearch
Failed to build GeneWordSearch
Installing collected packages: scipy, GeneWordSearch
  Running setup.py install for GeneWordSearch ... error
    Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-7pdUq9-record/install-record.txt --single-version-externally-managed --compile:
    running install
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/setup.py", line 42, in <module>
        install_requires=['numpy','scipy'])
      File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup
        dist.run_commands()
      File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
        cmd_obj.run()
      File "/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/setup.py", line 19, in run
        os.makedirs(zmDir, exist_ok=True)
    TypeError: makedirs() got an unexpected keyword argument 'exist_ok'

    ----------------------------------------
Command "/usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-7pdUq9-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-build-yV4GfS/GeneWordSearch/
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named apsw
Installing apsw into the conda environment
/usr/local/lib/python2.7/site-packages/pip/commands/install.py:194: UserWarning: Disabling all use of wheels due to the use of --build-options / --global-options / --install-options.
  cmdoptions.check_install_build_global(options)
Collecting https://github.com/rogerbinns/apsw/releases/download/3.15.2-r1/apsw-3.15.2-r1.zip
  Downloading https://github.com/rogerbinns/apsw/releases/download/3.15.2-r1/apsw-3.15.2-r1.zip (691kB)
    100% |████████████████████████████████| 696kB 945kB/s 
Skipping bdist_wheel for apsw, due to binaries being disabled for it.
Installing collected packages: apsw
  Running setup.py install for apsw ... error
    Complete output from command /usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-1LXnUL-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" fetch --version 3.15.2 --all build --enable-all-extensions install --record /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-29oL2d-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
    /usr/local/lib/python2.7/site-packages/setuptools/dist.py:332: UserWarning: Normalizing '3.15.2-r1' to '3.15.2.post1'
      normalized_version,
    running fetch
      Getting the SQLite amalgamation
        Fetching https://sqlite.org/2016/sqlite-autoconf-3150200.tar.gz
        Length: 2491735  SHA1: 31f52169bcfeef9efb61480d0950e928ad059552  MD5: 6b4fc0d8f7f02dd56bbde10a7c497a05
        Checksums verified
        Running configure to work out SQLite compilation flags
    configure: error: in `/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-1LXnUL-build/sqlite3':
    configure: error: C compiler cannot create executables
    See `config.log' for more details
    error: [Errno 2] No such file or directory: 'Makefile'

    ----------------------------------------
Command "/usr/local/opt/python/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-1LXnUL-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" fetch --version 3.15.2 --all build --enable-all-extensions install --record /var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-29oL2d-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /private/var/folders/fs/y0303j4n1n512jdjdvhgk7t00000gn/T/pip-1LXnUL-build/
Installing Camoco
Traceback (most recent call last):
  File "setup.py", line 4, in <module>
    from Cython.Distutils import build_ext
ImportError: No module named Cython.Distutils
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "camoco/__init__.py", line 41, in <module>
    import pyximport
ImportError: No module named pyximport
Camoco failed to install!
schae234 commented 6 years ago

Hey @acabunoc

Thats a doozy! Guess we weren't checking return codes on a lot of those dependency installs ... We will open an issue to get Camoco running on OSX 🍎 and keep you updated!

Thanks for the trace! 🥇 👍

seraco commented 6 years ago

Hello @acabunoc. I am working on this issue. The installation on MacOS is already working in my machine and TravisCI. I hope that the modifications can be merged into the original code soon 😀.

abbycabs commented 6 years ago

Amazing! Thanks @seraco 😀

On Oct 13, 2017, at 11:45 AM, seraco notifications@github.com wrote:

Hello @acabunoc. I am working on this issue. The installation on MacOS is already working in my machine and TravisCI. I hope that the modifications can be merged into the original code soon 😀.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.