singularity v2.5.0

[regro-cf-autotick-bot]

This PR was created by the cf-regro-autotick-bot.

The cf-regro-autotick-bot is a service to automatically track the dependency graph and propose package version updates for conda-forge. It is very likely that the current package version for this feedstock is out of date.

Notes and instructions for merging this PR:

1. Please check that the dependencies have not changed.
2. Please merge the PR only after the tests have passed.
3. Feel free to push to the bot's branch to update this PR if needed.
4. The bot will almost always only open one PR per version.

If you would like a local version of this bot, you might consider using rever. Rever is a tool for automating software releases and forms the backbone of the bot's conda-forge PRing capability. Rever is both conda (conda install -c conda-forge rever) and pip (pip install re-ver) installable.

Finally, feel free to drop us a line if there are any issues!

[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.

[conda-forge-linter]

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

I wanted to let you know that I linted all conda-recipes in your PR (recipe) and found some lint.

Here's what I've got...

For recipe:

• Failed to even lint the recipe, probably because of a conda-smithy bug 😢. This likely indicates a problem in your meta.yaml, though. To get a traceback to help figure out what's going on, install conda-smithy and run conda smithy recipe-lint . from the recipe directory.

[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]

I think we need libarchive in host as well.

[bgruening]

@jakirkham if we ust host, do we need runtime dependency then. Assuming libarchive would had a run_export?

[jakirkham]

Nothing has been built with run_exports yet. Though that is the plan. So we still need it in run for now.

[jakirkham]

Currently failing as it thinks this host does not support the NO_NEW_PRIVS prctl functions. Though CentOS 6 should actually support this according to Red Hat and Singularity (in the release notes for 2.5.0). Think some is getting fouled up in how configure is checking for these things. Will try to look again later unless someone beats me to it.

ref: https://circleci.com/gh/conda-forge/singularity-feedstock/14
ref: https://access.redhat.com/errata/RHSA-2015:0864
ref: https://github.com/singularityware/singularity/releases/tag/2.5.0
ref: apptainer/singularity@3d878d8

[jakirkham]

On a different note, am I using the compiler portion correctly @isuruf? Doesn't look like it is picking up toolchain.

[isuruf]

@jakirkham, you need to rerender with the dev version of conda-forge-pinning

[jakirkham]

Oops. 😬 Yep, that makes sense. Thanks @isuruf.

[jakirkham]

Thanks again @isuruf. Turns out that fixed both issues. 🎉

Worth noting then that the Anaconda gcc compiler was unable to pick up system headers. @mingwandroid, have you seen this before? FTR am referring to commit ( f91d903 ) and this build. Is there some way that you typically solve these sorts of things?

Could you please review when you have a chance @bgruening? Should add that this pulls in libgcc as a run requirement thanks to @isuruf's changes in PR ( conda-forge/toolchain-feedstock#34 ).

[bgruening]

Looks good to me, I just realized I need to learn a lot about the new system :)

[mingwandroid]

I don't know without investigating. The compilers provide their own system headers for glibc the kernel and the compiler runtimes though to isolate it from the build machine.

At a guess (not on a computer to check) this package requires a kernel feature that CentOS6 doesn't provide.

[jakirkham]

So CentOS 6 does provide the required features. Though that might not seem obvious at first. Have outlined the info regarding the NO_NEW_PRIVS prctl functions in this comment. These are confirmed present in CentOS 6.7+ (we are on CentOS 6.9) by both Red Hat and Singularity.

The header it is looking for is sys/prctl.h, which also requires linux/prctl.h. These are present in /usr/include in the Docker image if you are interested in taking a closer look.