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r-probmetab - fix conda getting stuck on solving environment #15519

Merged
merged 12 commits into from
May 24, 2019
Merged

r-probmetab - fix conda getting stuck on solving environment #15519

merged 12 commits into from
May 24, 2019

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Tomnl
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@Tomnl Tomnl commented May 21, 2019

conda getting stuck on solving environment - hopefully specifying camera version will solve this

  • 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).

Tomnl added 4 commits May 21, 2019 17:11
@Tomnl
specifying bioconductor-camera version
11c0944 
conda getting stuck on solving environment - hopefully specifying camera version will solve this
@Tomnl
update based on linting
25cb62b
@Tomnl
removed from blacklist
8996ab8
@Tomnl
fixed r-base rather than camera
87714b6
@Tomnl Tomnl changed the title specifying bioconductor-camera version r-probmetab - fix conda getting stuck on solving environment May 22, 2019
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Tomnl commented May 22, 2019 •
edited

Hi @lecorguille, I have been having trouble installing r-probmetab with Galaxy and conda recently and the following command will just hang on the solving environment stage

conda install r-probmetab -c bioconda

I have made some updates in this pull request that will hopefully fix the problem.

I just wanted to check if these updates are OK with you (and W4M) and if you have been experiencing any problems with r-probmetab

Note that the linting is currently failing but the bioconda-test is passing. It is not clear to me why the lint would fail but I have asked on gitter for some help with it.

FYI: @RJMW

@Tomnl Tomnl mentioned this pull request May 23, 2019
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@npavlovikj
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@BiocondaBot recheck

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biocondabot bot commented May 23, 2019

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

Arch Package Repodata
linux-64 r-probmetab-1.0-r341hf484d3e_2.tar.bz2 repodata.json
linux-64 r-probmetab-1.1-r341hf484d3e_3.tar.bz2 repodata.json

You may alsu use conda to install these:

  • For packages in linux-64: 
    conda install -c https://58529-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
r-probmetab 1.0--r341hf484d3e_2
showcurl "https://58529-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/r-probmetab%3A1.0--r341hf484d3e_2.tar.gz" | gzip -dc | docker load
r-probmetab 1.1--r341hf484d3e_3
showcurl "https://58529-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/r-probmetab%3A1.1--r341hf484d3e_3.tar.gz" | gzip -dc | docker load

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As of now, "Linting Recipes" is not mandatory to be green in order for you to be able to merge your recipe (as long as "bioconda-test" is green). It is work in progress, and sometimes that step gets stuck or disabled. You can try and re-trigger "Linting Recipes" by typing @BiocondaBot recheck.

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Tomnl commented May 24, 2019

@BiocondaBot recheck

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Tomnl commented May 24, 2019

Thanks for the information @npavlovikj !

@RJMW RJMW merged commit a7cb64d into bioconda:master May 24, 2019
epruesse added a commit to epruesse/bioconda-recipes that referenced this pull request May 25, 2019
@epruesse
Merge branch 'master' into colinbrislawn-patch-2
d8eda61 
* master: (336 commits)
  Rebuild libgtextutils (bioconda#14659)
  set minced=0.3 (bioconda#15575)
  Update to plantcv v3.3.0 (bioconda#15539)
  add cami-opal recipe (bioconda#15573)
  Tango (bioconda#15570)
  stacks: bump version 2.4 (bioconda#15546)
  Bump segtools build for newer python versions (bioconda#15572)
  Update blast to 2.9.0 (bioconda#15550)
  add fastqsplitter recipe (bioconda#15568)
  Update xopen (bioconda#15566)
  r-probmetab - fix conda getting stuck on solving environment (bioconda#15519)
  Change sha256 for PGCGAP (bioconda#15565)
  Update PGCGAP to v1.0.2 (bioconda#15562)
  pb-falcon-0.3.3 (bioconda#15559)
  Spoa (bioconda#15555)
  seqbuster: bump to latest version (bioconda#15558)
  update irida uploader 0.2.1 (bioconda#15557)
  Super distance (bioconda#15551)
  Fix nanoplotter (bioconda#15548)
  Pycoqc requires h5py (bioconda#15545)
  ...
kpalin pushed a commit to kpalin/bioconda-recipes that referenced this pull request Aug 7, 2019
@Tomnl @kpalin
r-probmetab - fix conda getting stuck on solving environment (biocond…
68277c8 
…a#15519)

removed from blacklist; fix versions for r-base, camera, libnetcdf, mzr and rcytoscape; update recipe for c++; add most recent release to base directory
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@Tomnl @npavlovikj @RJMW