bioconda-recipes: circleci build fails locally when testing recipes.

New version of biopet-seqstat succeeds when build with circleci: https://github.com/bioconda/bioconda-recipes/pull/9487

Unfortunately it fails locally. I have circleci installed as a snap. Issuing the command circleci build in the root of bioconda recipes gives the following error:

recipes/biopet-seqstat
 recipes/biopet-seqstat/0.1
 recipes/biopet-seqstat/1.0
11:59:20 BIOCONDA DEBUG lint recipes/biopet-seqstat
11:59:20 BIOCONDA DEBUG lint recipes/biopet-seqstat/0.1
11:59:20 BIOCONDA DEBUG lint recipes/biopet-seqstat/1.0
====>> Testing
  #!/bin/bash -eo pipefail
bioconda-utils build recipes config.yml \
--git-range master HEAD \
--prelint

usage: bioconda-utils [-h]
                      {build,dag,dependent,lint,duplicates,bioconductor-skeleton,pypi-check,clean-cran-skeleton}
                      ...
bioconda-utils: error: unrecognized arguments: --prelint
Error: Exited with code 2
Step failed
Task failed

This means the local test does not reflect the result of the remote test, which is undesirable.

About this issue

Original URL
State: closed
Created 6 years ago
Reactions: 3
Comments: 26 (26 by maintainers)

Most upvoted comments

Did you run

docker pull bioconda/bioconda-utils-build-env

? (ref: http://bioconda.github.io/contribute-a-recipe.html#circle-ci-client-method)

mbargull on Sep 14, 2018

Ok, problem solved. One fix is in PR #10920, the other in https://github.com/bioconda/bioconda-utils/pull/333.

johanneskoester on Sep 12, 2018

@mbargull I just hit this same issue again (local build on 27 July 1645 GMT). I made sure the bioconda-recipes repo is up to date and ran circleci update this morning.

====>> Linting
  #!/bin/bash -eo pipefail
bioconda-utils lint recipes config.yml \
--loglevel debug --full-report \
--git-range master HEAD

16:42:11 BIOCONDA INFO Recipes newly unblacklisted:

16:42:11 BIOCONDA INFO Recipes to consider according to git:
recipes/phyluce
16:42:11 BIOCONDA DEBUG get_recipes(recipes, package='['*']'): *
16:42:11 BIOCONDA DEBUG recipes/phyluce
16:42:11 BIOCONDA INFO Recipes to lint:
recipes/phyluce
16:42:11 BIOCONDA DEBUG lint recipes/phyluce
====>> Testing
  #!/bin/bash -eo pipefail
bioconda-utils build recipes config.yml \
--git-range master HEAD \
--prelint

usage: bioconda-utils [-h]
                      {build,dag,dependent,lint,duplicates,bioconductor-skeleton,pypi-check,clean-cran-skeleton}
                      ...
bioconda-utils: error: unrecognized arguments: --prelint
Error: Exited with code 2
Step failed
Task failed

brantfaircloth on Jul 27, 2018