Dashing

[SilasK]

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• I have read the guidelines for bioconda recipes.
• This PR adds a new recipe.
• AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
• This PR updates an existing recipe.
• This PR does something else (explain below).

[SilasK]

@dnbaker here we go, probably it won't pass the checks in the first time

[dnbaker]

Thanks! I don't full understand how bioconda works, but I'll try installing via conda on my personal machine in the interim.

[dnbaker]

https://github.com/dnbaker/bioconda-recipes/tree/dash

I have some changes, including requiring libomp. But it breaks when I try to install it, for what seems to be a fundamental compiler issue:

ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd
Undefined symbols for architecture x86_64:
  "___bzero", referenced from:
      _deflateReset in libz.a(deflate.o)
      _deflateSetDictionary in libz.a(deflate.o)
      _fill_window in libz.a(deflate.o)
      _deflateParams in libz.a(deflate.o)
      _deflate in libz.a(deflate.o)
      _gz_write in libz.a(gzwrite.o)
      _gzputc in libz.a(gzwrite.o)
      ...
  "___sprintf_chk", referenced from:
      _gzdopen in libz.a(gzlib.o)

Maybe my libSystem is too new or too old?

[SilasK]

@dnbaker Sorry I didn't use your fork. I'm working from https://github.com/bioconda/bioconda-recipes/tree/dash

I copied your recipe because I don't have access to it. I added the c++ compiler:
{{ compiler('cxx') }}

See if it passes the checks.

[SilasK]

Do you have a list of requirements for the building process?

• You were talking about omplib and libSystem?
• They should have new compilers, as I understand it.

[SilasK]

Relevant section from the docs: https://bioconda.github.io/contributor/guidelines.html#c-c

[dnbaker]

The biggest issue here is that bioconda seems to want to use clang on OSX, but it doesn't come with omp baked in. (In the README, I recommend building with g++.) But I'm hoping that requiring libomp somehow helps.

There may have been an issue with clang compatibility in 0.3.6, so I've patched that and bumped to 0.4.0. I'll work on this today, but that's what I've been trying to figure out.

[dnbaker]

dnbaker@696c9eb

I've made changes; a number of these dependencies only exist on github. I've used git as a package manager previously. I believe this will cause it to build, unless the omp problem remains. (I would definitely have preferred a recursive clone, as all modules would be loaded with correct versions already), but I've added releases to a variety of these. I'll test later, but I wanted to report on these changes.

[dnbaker]

The current bug I'm experiencing is here: ContinuumIO/anaconda-issues#9096

But perhaps I should be testing on linux instead.

[SilasK]

release instead of git

Ideally the submodules should be included in the release, but this is not yet the case on github.

build on linux

We can always skip the osx build for now and get it out on linux.

I merged your commits #18857

They are tested automatically on linux. see the checks

https://app.circleci.com/jobs/github/bioconda/bioconda-recipes/83605

[SilasK]

circle ci fails on linux with gcc: Command not found

https://bioconda.github.io/contributor/troubleshooting.html#id8

[dnbaker]

Maybe try adding {{ compiler('c') }}? gcc is needed for zlib, whereas the rest of the codebase needs g++.

[dpryan79]

This build on Linux now.

[SilasK]

Do you know a way to get the g++ 5 on macOS ?

Should we just skip the osx build ?

[dpryan79]

GCC isn't used on OSX, so if you require that rather than clang you'll need to skip OSX.

[SilasK]

If I see it correctly it passes the compilation macOS. But then the tests dashing --help doesn't work.

[dpryan79]

@bioconda-bot please fetch artifacts

[BiocondaBot]

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

Arch	Package	Repodata
linux-64	dashing-0.4.0-hfc8b89e_0.tar.bz2	repodata.json
osx-64	dashing-0.4.0-h2f51686_0.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages on linux-64:

conda install -c https://84445-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

• For packages on osx-64:

conda install -c https://84452-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	Install with docker
dashing	0.4.0--hfc8b89e_0	show curl "https://84445-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/dashing%3A0.4.0--hfc8b89e_0.tar.gz" | gzip -dc | docker load

[dpryan79]

I think the problem is that it both compiles in libzstd.a but also links to it with -lzstd. GCC seems to ignore libzstd.so, but clang appears not to.

[dpryan79]

That fixed it

[dpryan79]

@bioconda-bot please merge

[BiocondaBot]

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