pip version of pysam 0.15.1 seemingly not supported in Mac OS about binder

[alimanfoo]

@amakunin might also be worth checking if you can install pysam on your mac from current github master, should at least confirm that the problem is fixed and just a release is needed.

[tnguyensanger]

@AndreasHeger @alimanfoo @amakunin @podpearson pip install of pysam==0.15.2 works for me. Many thanks!

[alimanfoo]

Hi @amakunin, I think we just need to beg @AndreasHeger to cut a new release of pysam, looks like a fix was merged into master a couple of weeks ago (pysam-developers/pysam#729).

[amakunin]

Installing from repo is failing in an unusual place, as expected for Mac OS. Will try to dig into this.

In the meanwhile, conda and pip remain the only options for seamless installation of pysam on Mac. So, I will also investigate pysam versioning in conda. For me, installation of 0.15.1 yields 0.13, while tarball for 0.15.1 contains version 0.15.0

[tnguyensanger]

@amakunin I'm running into this too. Is the workaround to manually edit /binder/environment.yml to use pysam=0.13 ?

[alimanfoo]

Given that pysam/pysamstats is not normally needed for most interactive tasks, we could remove it from the malariagen/binder environment until this is resolved. This just means that if anyone wants to use pysam or pysamstats they need to install it manually. Btw I never fully understood why this works on Travis under osx but doesn't work on a mac machine. @amakunin did you get to the bottom of that?

…

On Thu, 10 Jan 2019 at 17:01, tnguyensanger ***@***.***> wrote: @amakunin <https://github.com/amakunin> I'm running into this too. Is the workaround to manually edit /binder/environment.yml to use pysam=0.13 ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAq8Qs7UQKgJz2UTk9MNVr2KE32VvS4nks5vB3HrgaJpZM4Zd-sZ> .

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[AndreasHeger]

I am releasing pysam 0.15.2 with the fix (#729). I really apologize for the delay, I started to fix a couple of other issues, but then got bogged down and times were very busy.

[AndreasHeger]

It would be great if somebody could confirm it works. I can't test locally.

[alimanfoo]

@AndreasHeger thank you!

@amakunin / @tnguyensanger / @podpearson can you confirm if pip install pysam==0.15.2 works ok on your mac?

[podpearson]

I've just tried to do a fresh install of binder on my Mac, using the the instructions at https://github.com/malariagen/binder/blob/master/README.md#add-binder-as-a-submodule. This is giving me the following error for pysam:

      gcc: error: @loader_path: No such file or directory
      gcc: error: unrecognized command line option '-rpath'
      error: command 'gcc' failed with exit status 1
  
      ----------------------------------------
  Command "/Users/rpearson/src/github/malariagen/SIMS/binder/deps/conda/envs/SIMS/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-install-nn5n9d69/pysam/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/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-record-gkrbueq3/install-record.txt --single-version-externally-managed --prefix /private/var/folders/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-build-env-grpioma4 --compile" failed with error code 1 in /private/var/folders/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-install-nn5n9d69/pysam/
  
  ----------------------------------------
Command "/Users/rpearson/src/github/malariagen/SIMS/binder/deps/conda/envs/SIMS/bin/python -m pip install --ignore-installed --no-user --prefix /private/var/folders/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-build-env-grpioma4 --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel "pysam (<0.16)"" failed with error code 1 in None

CondaValueError: pip returned an error

I also tried installing directly using binder/deps/conda/bin/pip install pysam==0.15.2 and got:

    gcc: error: @loader_path: No such file or directory
    gcc: error: unrecognized command line option '-rpath'
    error: command 'gcc' failed with exit status 1
    
    ----------------------------------------
Command "/Users/rpearson/src/github/malariagen/SIMS/binder/deps/conda/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-install-fz68an38/pysam/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/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-record-ebza1u0u/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/v6/nyyqw2bx3wlfyxvy334mxwyh0000gn/T/pip-install-fz68an38/pysam/

Has anyone else managed to successfully install pysam 0.15.2 on a Mac? Any suggestions of where I should go next?