Use gcc package on linux.

[johanneskoester]

In the effort to come up with a common build environment, as far as we know, bioconda and conda-forge agreed to use the gcc package for building stuff on linux. This PR adds gcc to the build requirements for perl, which is used heavily by bioconda packages. The current way of building this with the system gcc on conda-forge/linux-anvil causes problems because it is a different version with different features than the gcc package that is used to build perl packages on bioconda.

@jerowe, @nsoranzo, @bgruening

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

[jakirkham]

When/where was this agreed to or even discussed?

[johanneskoester]

There was a conda-forge meeting that me and @bgruening attended. It was decided that @msarahan would make a poll, and if I remember correctly we agreed to stick to whatever comes out of that poll. Our collective memory at bioconda tells us that the result was to use the gcc package. We did exactly that since then. @bgruening, am I right?

[msarahan]

I think we agreed to work towards this, but it was in the context of a new GCC package, not the current one.

By including all compilers in one package, the current one causes issues, especially on Mac. Please wait. @mingwandroid and I are close to new packages. They'll need to be tested and approved before conda forge should adopt them, but I'm hopeful that they'll greatly improve the ecosystem.

On Thu, Feb 23, 2017, 07:45 jakirkham notifications@github.com wrote:

When/where was this agreed to or even discussed?

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[ocefpaf]

@mingwandroid and I are close to new

packages. They'll need to be tested and approved before conda forge should adopt them, but I'm hopeful that they'll greatly improve the ecosystem.

Mike, I thought this idea was dead. It is good to know that you guys did not gave up!

I agree that this will be an awesome additions to the ecosystem! Looking forward to test it.

[johanneskoester]

That's good news. In that case, we might have misunderstood the result. Am I right that conda-forge recently switched to gcc 4.9 in the linux-anvil container?

[jakirkham]

We have not changed the compiler version in the docker image. It has remained the same for nearly a year.

[nsoranzo]

The gcc in the Docker image is 4.8.2 20140120 (Red Hat 4.8.2-15). The problem is that it contains a backport of -fstack-protector-strong which causes this issue in Bioconda: https://github.com/bioconda/bioconda-recipes/pull/3839

[johanneskoester]

Thanks @nsoranzo for clarifying. Sorry, I should have read that thread more carefully.

[msarahan]

@ocefpaf never dead, just taking a lot longer than any of us would like. =(

Soon...

[ocefpaf]

@ocefpaf https://github.com/ocefpaf never dead, just taking a lot longer than any of us would like. =(

No pressure. I'd love to help more but for now all I can do is to help test it.

Thanks you both for this effort!

[bgruening]

These are fantastic news @msarahan and @mingwandroid! @johanneskoester for us this means we can remove the explicit gcc requirement from perl-gcc packages for the time being if we don't get this PR through.

[johanneskoester]

Yes, that is what I thought as well.

[ocefpaf]

if we don't get this PR through.

Let's discussion this further about the pros and cons of this PR before we dismiss it entirely.

[jerowe]

While I am really excited about any and all improvements to conda, this whole perl thing is beginning to seriously cramp my style. What do you guys recommend? Just remove the conda gcc as a requirement from any and all perl packages?

[bgruening]

@jerowe yes remove the GCC for the time being and hope the best that we get quickly a new GCC conda package.

[jerowe]

If I fire up the conda-forge/linux-anvil image, then if I run which gcc, I get nothing. How does gcc get pulled in the conda-forge image?

[jakirkham]

How are you starting up the image?

[jerowe]

docker run --rm -t -i -v pwd:/conda-recipes:Z --entrypoint /bin/bash condaforge/linux-anvil

[jakirkham]

Changing the entrypoint is causing the issue. We configure the compiler in the entrypoint script. We also set the default command to /bin/bash so that is not necessary, but you can add another command if you want.

[jerowe]

@johanneskoester @bgruening , are we using the conda-forge entry point (and getting the conda-forge gcc) or no?

[jakirkham]

IIUC the builds with the new compilers ( https://github.com/conda-forge/perl-feedstock/pull/27 ) resolve this issue.

Should we close or am I missing something?

[bgruening]

Yes this can be closed.