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Bioconductor / MatrixGenerics

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
https://bioconductor.org/packages/MatrixGenerics
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Build Report Warning: File link 'rowRanges' in package 'SummarizedExperiment' does not exist #19

Closed const-ae closed 3 years ago

const-ae commented 3 years ago

I just checked the build report and noticed that there is a WARNING on windows concerning the documentation of rowRanges

Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpolctSY/R.INSTALLea848f42b6d/MatrixGenerics/man/rowRanges.Rd:62: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpolctSY/R.INSTALLea848f42b6d/MatrixGenerics/man/rowRanges.Rd:63: file link 'rowRanges' in package 'SummarizedExperiment' does not exist and so has been treated as a topic

As the deadline is tomorrow, does anyone have capacity to fix the issue today? I assume the problem was introduced here by @hpages's commit to make rowRanges compatible with SummarizedExperiment (https://github.com/Bioconductor/MatrixGenerics/commit/8b10d19bdf33c572d99767eae90fa500f1b40ae4#diff-d387fdcf206554302df9d454f50dd59442df365e2899b5afb221307fb21a6e10R25).

hpages commented 3 years ago

I tend to ignore these "treated as a topic" warnings on Windows as the whole thing makes little sense. Anyways I agree that the warnings don't make MatrixGenerics look good so I'll look into it. Don't worry too much about tomorrow's deadline.

mtmorgan commented 3 years ago

I think that R-devel (to be used in the Bioconductor 3.13 builds) addresses this so that it is not a NOTE... From the NEWS.Rd:

     \item For HTML help (both dynamic and static), Rd file links to
      help pages in external packages are now treated as references to
      topics rather than file names, and falls back to a file link only
      if the topic is not found in the target package. The earlier rule
      which prioritized file names over topics can be restored by
      setting the environment variable \env{_R_HELP_LINKS_TO_TOPICS_} to
      a false value.
hpages commented 3 years ago

Finally! Great news

hpages commented 3 years ago

I don't understand why that would even be a NOTE but it's a day to celebrate not to complain ;-)

LiNk-NY commented 3 years ago

This looks to have been resolved...