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Ignore 'renv' files in relevant checks #106

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kevinrue opened this issue Oct 19, 2020 · 0 comments
Open

Ignore 'renv' files in relevant checks #106

kevinrue opened this issue Oct 19, 2020 · 0 comments

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@kevinrue
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I manage project libraries using renv, including for package development.

Some renv files ultimately crash BiocCheck, while also raising some warnings.
See below

> BiocCheck::BiocCheck()
This is BiocCheck version 1.24.0. BiocCheck is a work in progress. Output and severity of issues
may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking version number...
* Checking version number validity...
    Package version 0.0.1; pre-release
* Checking R Version dependency...
* Checking package size...
        Skipped... only checked on source tarball
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'renv/library/R-4.0/x86_64-apple-darwin17.0/stringi/libs/icudt61l.dat
      renv/library/R-4.0/x86_64-apple-darwin17.0/stringi/libs/stringi.so'
* Checking biocViews...
* Checking that biocViews are present...
    * ERROR: No biocViews terms found.
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking vignette directory...
    This is an unknown type of package
    * ERROR: No 'vignettes' directory.
* Checking library calls...
* Checking for library/require of BiocPackageSofwareTemplate...
* Checking coding practice...
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/BiocCheck/testpackages/testpkg0/R/baddeps.R'
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/BiocCheck/testpackages/testpkg0/R/morebadcode.R'
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/BiocCheck/testpackages/testpkg0/R/morecode.R'
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/BiocCheck/testpackages/testpkg0/R/parseme.R'
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/BiocCheck/testpackages/testpkg0/R/requireme.R'
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/RBGL/unitTests/test_segfault.R'
Warning in readLines(infile) :
  incomplete final line found on '/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/whisker/specs/convert.R'
Warning in grep(lines, pattern = "VignetteEngine") :
  input string 8 is invalid in this locale
Warning in grep(lines, pattern = "VignetteEngine") :
  input string 11 is invalid in this locale
Warning in grep(lines, pattern = "VignetteEngine") :
  input string 10 is invalid in this locale
Loading required package: emo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'emo'
Quitting from lines 9-15 (/Users/kevin/github/kevinrue/BiocPackageSofwareTemplate/renv/library/R-4.0/x86_64-apple-darwin17.0/markdown/doc/markdown-examples.Rmd) 
Error in parse(text = code, keep.source = FALSE) : 
  <text>:2:1: unexpected symbol
1: read_chunk(system.file('examples', 'markdownExtensions.R', package = 'markdown')
2: read_chunk
   ^

I have worked n a branch that I will submit as PR shortly.

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