update andi to 0.13

[pmenzel]

Describe your pull request here

update andi to 0.13

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[pmenzel]

@bioconda/core in this PR I intend to update andi to 0.13, and at the same time maybe fix a dependency issue, that I get with other packages. For example, I get

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package gsl conflicts for:
bioconda::mash=2.2.2 -> gsl[version='>=2.5,<2.6.0a0']
bioconda::andi=0.12 -> gsl[version='2.2.*|>=2.2.1,<2.3.0a0']
...

So it seems that andi 0.12 can have gsl not above 2.3.0. I am not sure where these version requirements for gsl are stored, I didn't see it in meta.yaml.

Now I added gsl >=2.2 as a dependency in the hopes that it will also accept higher versions, resolving the conflict.

[BiocondaBot]

Reposting to enable pings (courtesy of the BiocondaBot):

@bioconda/core: in this PR I intend to update andi to 0.13, and at the same time maybe fix a dependency issue, that I get with other packages. For example, I get

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package gsl conflicts for:
bioconda::mash=2.2.2 -> gsl[version='>=2.5,<2.6.0a0']
bioconda::andi=0.12 -> gsl[version='2.2.*|>=2.2.1,<2.3.0a0']
...

So it seems that andi 0.12 can have gsl not above 2.3.0. I am not sure where these version requirements for gsl are stored, I didn't see it in meta.yaml.

Now I added gsl >=2.2 as a dependency in the hopes that it will also accept higher versions, resolving the conflict.

[dpryan79]

@bioconda-bot please fetch artifacts

@pmenzel Thanks, the GSL restriction comes from a global pinning file. I'm surprised the old version didn't get rebuilt when we updated the GSL pinning.

[BiocondaBot]

No artifacts found on the most recent CircleCI build. Either the build failed or the recipe was blacklisted/skipped.

[dpryan79]

Ah, I bet the recipe is blacklisted due to compilation issues. That'd explain things.

[pmenzel]

Thanks for looking into it, Devon.
The compiler error message is

17:34:49 BIOCONDA INFO (OUT) pfasta.c:39:10: fatal error: threads.h: No such file or directory
17:34:49 BIOCONDA INFO (OUT)  #include <threads.h>

Maybe the used gcc is too old not have C11 threads?

[dpryan79]

It's gcc 7. I'm guess that we need to pass std=c11.

[dpryan79]

Actually, glibc only added support in 2018 or so, so that'd be after the version we're using (HPCs don't exactly update frequently, we're building basically with centos 6).

[pmenzel]

would it be helpful to ask the author for statically linked binaries, that could instead be used?

[dpryan79]

That'd be one option

[kloetzl]

Hi all,

andi (or to be precise, its FASTA parser pasta) can be compiled without threads.h. Newer C version set __STDC_NO_THREADS__ to indicate it is not available. Apparently, the converse is not true. Can you try to build with export CFLAGS="$CFLAGS -D__STDC_NO_THREADS__=1"?

Hope this helps,
Fabian

[pmenzel]

hurray, it seems to have worked!

[kloetzl]

Thanks for your effort, I will look for a patch upstream and integrate it in both andi and phylonium (the successor to andi). So the next time things should be easier again. 😄

[pmenzel]

Thanks for your fast fix! :)

quick question: Would you recommend to use phylonium (once it is available in bioconda) over andi when only having a handful of genomes? My understanding was that phylonium is "just" faster, but not more accurate.

[kloetzl]

One could say that phylonium is andi, but faster. As long as your genomes are closely related you should not see a big difference in the estimated substitution rates. Note that “faster” means 2× for small data sets and minutes instead of hours for thousands of bacterial genomes.

[pmenzel]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[BiocondaBot]

Sorry, this PR cannot be merged at this time.

[dpryan79]

@bioconda-bot please fetch artifacts

[BiocondaBot]

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
linux-64	andi-0.13-h1e169f7_0.tar.bz2	repodata.json
osx-64	andi-0.13-h0d51cb5_0.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages on linux-64:

conda install -c https://104738-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

• For packages on osx-64:

conda install -c https://104739-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	Install with docker
andi	0.13--h1e169f7_0	show curl "https://104738-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/andi%3A0.13--h1e169f7_0.tar.gz" | gzip -dc | docker load

[dpryan79]

@bioconda-bot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[kloetzl]

Thanks everyone for your work!