Install error - pybbi fails to build

[demmerle]

Running: OSX 10.12.6; Xcode 9.2; Xcode CLT 2347; Python 3.7.1; Conda 4.6.11; Docker Engine 18.09.2.

Hi, thanks for making this. Excited to use it but I'm having an install problem. After calling pip install higlass-manage everything goes fine until....

Running setup.py bdist_wheel for pysam ... done Stored in directory: /Users/demmerle/Library/Caches/pip/wheels/34/3b/bc/f3faaba907f333632357aae7bf09a453209a8c9c3cec4cddae Running setup.py bdist_wheel for pybbi ... error Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/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/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-wheel-wum70wlg --python-tag cp37: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.7 creating build/lib.macosx-10.7-x86_64-3.7/bbi copying bbi/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/bbi running build_ext Compiling libkent... LIBRARY_PATH: /usr/local/opt/openssl/lib: C_INCLUDE_PATH: /anaconda3/include/libpng16:/anaconda3/include/openssl:/usr/local/opt/openssl/include:/usr/local/include/libpng16: cd src && /Applications/Xcode.app/Contents/Developer/usr/bin/make gcc -g -pthread -fPIC -static -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -L/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/src/x86_64 -L/usr/lib -lz -lc -lpthread -I/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/include -I/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/src -I/usr/include -o aliType.o -c aliType.c clang: warning: -lz: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lc: 'linker' input unused [-Wunused-command-line-argument] clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/src/x86_64' [-Wunused-command-line-argument] clang: warning: argument unused during compilation: '-L/usr/lib' [-Wunused-command-line-argument]

...at which point the gcc command runs repeatedly for maybe 100 iterations before installing the rest of the wheels, and then printing it's last error message ` udc.c:39:10: fatal error: 'openssl/sha.h' file not found

include <openssl/sha.h>

         ^~~~~~~~~~~~~~~
1 error generated.
make[1]: *** [udc.o] Error 1
make: *** [src/x86_64/libkent.a] Error 2
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/setup.py", line 152, in <module>
    'build_ext': build_ext
  File "/anaconda3/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup
    return distutils.core.setup(**attrs)
  File "/anaconda3/lib/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/anaconda3/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/anaconda3/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
    return orig.install.run(self)
  File "/anaconda3/lib/python3.7/distutils/command/install.py", line 545, in run
    self.run_command('build')
  File "/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/anaconda3/lib/python3.7/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/anaconda3/lib/python3.7/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/anaconda3/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/setup.py", line 86, in run
    check_call(['make', 'build-c'])
  File "/anaconda3/lib/python3.7/subprocess.py", line 341, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make', 'build-c']' returned non-zero exit status 2.`

...and ends with this... Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/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/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-record-mgajcosf/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/p_/xr0cxrx12msf6pb1xf0r07r40000gp/T/pip-install-74z1ht_7/pybbi/

I tried pre-installing setuptools 0.40.9, but that didn't make a difference. I assume it's something silly in my mac environment, but I can't figure it out and was hoping you might have some thoughts. Thanks!

[pkerpedjiev]

Hey, sorry for the delay in answering. Any chance that the resolution to this issue helps? https://github.com/nvictus/pybbi/issues/2

[kalavattam]

Hi Peter and all,

Just want to report that I encountered this error using a system with macOS 10.14.4; homebrew installation of libpng (i.e., as referenced in the nvictus link in Peter's comment) solved the issue.

Thanks! Kris

[h-mori]

Yes,

brew install libpng
export C_INCLUDE_PATH="/usr/local/lib:/usr/local/include/libpng16:/usr/local/opt/openssl/include"
export LIBRARY_PATH="/usr/local/lib:/usr/local/include/libpng:/usr/local/opt/openssl/include"
pip install pybbi
pip install higlass-manage

solved the problem. Thanks!