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gclib: update to new version and unblacklist #12416

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bernt-matthias
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@bernt-matthias bernt-matthias commented Nov 29, 2018

  • 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).

Needed to get gffcompare running #12407 (I will remove the gclib changes from the other RP)

Test did not run locally for me since g++ was not found. But compiler is in build requirements.

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LGTM. I'd just like some comments in the patch files. Not sure why the change in namespace was necessary?

Also - PR upstream to fix these things possible?

recipes/gclib/chrono.patch Show resolved Hide resolved
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bernt-matthias commented Nov 29, 2018

I reported upstream: gpertea/gclib#3

The problem was that gclib has an implementation of chrono and ratio which are now available in the std namespace (http://www.cplusplus.com/reference/chrono/). So, the compiler reported an ambiguous namespace.

I will add comments to the patches.

I will also ask upstream if it is possible to ship the gclib Makefile such that gffcompare can easily be build (the necessary libraries are not build by default).

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bernt-matthias commented Nov 30, 2018

I added the comments. But @gpertea suggested to build gffcompare differently and NOT to distribute gclib as library: gpertea/gclib#4

I will give it a try. Maybe we leave the PR open until this is done.

On the other hand ... this way is still working.

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Superseded by #12407

@bernt-matthias bernt-matthias deleted the topic/gclib-update branch January 30, 2019 11:32
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