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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 issuesmay 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 localeWarning in grep(lines, pattern = "VignetteEngine") :
input string 11 is invalid in this localeWarning in grep(lines, pattern = "VignetteEngine") :
input string 10 is invalid in this localeLoading required package: emoWarning 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 symbol1: 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.
The text was updated successfully, but these errors were encountered:
I manage project libraries using
renv
, including for package development.Some
renv
files ultimately crashBiocCheck
, while also raising some warnings.See below
I have worked n a branch that I will submit as PR shortly.
The text was updated successfully, but these errors were encountered: