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biocInstaller necessary if biocViews in DESCRIPTION but not a bioc Package #1254

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muschellij2 opened this issue Jul 5, 2016 · 7 comments

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commented Jul 5, 2016

This issue arose in the matrixStats package (https://github.com/HenrikBengtsson/matrixStats), with associated issue opened there @HenrikBengtsson:
HenrikBengtsson/matrixStats#88

Overall, the "issue" is that in utils https://github.com/hadley/devtools/blob/master/R/utils.r#L155:

is_bioconductor <- function(x) {
  x$package != "BiocInstaller" && !is.null(x$biocviews)
}

Implies that if biocViews exists and the package is not BiocInstaller, then the package is assumed bioconductor package. This is probably a good assumption or one of the only ways to distinguish the CRAN/bioC package distinction. Thus, though not an Imports or Suggests, BiocInstaller seems to be a hidden/implicit dependency when installing using devtools. This affects Travis builds.

This may not be an "issue" exactly, and I may just add an install of BiocInstaller to the Travis to make it work, but figured I'd bring up the point here.

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commented Jul 5, 2016

Yes this is true, however on travis there is no need to install BiocInstaller manually. You can set

use_bioc: true

To automatically install BiocInstaller, or set

r:
  - bioc-devel
  - bioc-release

To testing using the current Bioconductor devel and release branch (automatically implies use_bioc).

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commented Jul 5, 2016

Adding bioc_packages: BiocInstaller worked:
https://travis-ci.org/muschellij2/testmatrixstats/builds/142568390
as well as use_bioc: true:
https://travis-ci.org/muschellij2/testmatrixstats/builds/142569006

As I just want to check against CRAN (as these are all CRAN-based packages), I think just using use_bioc: true maybe the most appropriate. I just have never run into biocViews causing a problem with installation because it has an inherent dependency of sorts on BiocInstaller though no packages in the installation actually depend on that package or any bioC packages

This should patch the issue discussed with @HenrikBengtsson for matrixStats, but I'd like to hear your thoughts about needing to add to the non-default .travis.yml (from use_travis()) for packages that do not depend on bioC, but have bioViews in DESCRIPTION.

@muschellij2 muschellij2 closed this Jul 5, 2016

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commented Jul 6, 2016

Although this should be solved in future versions of matrixStats, this method did not seem to work for the following package based on the error:
https://travis-ci.org/emsweene/oasis/builds/142846730#L1043

@muschellij2 muschellij2 reopened this Jul 6, 2016

@jimhester

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commented Jul 6, 2016

The argument is bioc_required: true, I was going off of memory (which is faulty, sorry).

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commented Jul 6, 2016

Thanks - I'll look into and close again.

@muschellij2 muschellij2 closed this Jul 6, 2016

@benjjneb

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commented Jul 20, 2016

I just ran into this same issue after making an innocuous change to my Bioconductor package (https://github.com/benjjneb/dada2).

Adding both use_bioc: true and bioc_required: true to .travis.yml finally fixed the problem, but why did this suddenly crop up?

AlexanderPico added a commit to cytoscape/r2cytoscape that referenced this issue Dec 10, 2017

lianos added a commit to lianos/multiGSEA that referenced this issue Aug 31, 2018

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commented Sep 18, 2018

This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/

@lock lock bot locked and limited conversation to collaborators Sep 18, 2018

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