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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ginmappeR_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ginmappeR ────────────────────────────────────────────────────────
✔ Package installed successfully
── ginmappeR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnwHRTm/filea6f68215068f2/ginmappeR
→ BiocVersion: 3.24
→ Package: ginmappeR
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ginmappeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpnwHRTm/filea6f68215068f2/ginmappeR
→ installDir: /tmp/RtmpnwHRTm/filea6f6827ab680b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ginmappeR ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ginmappeR.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ginmappeR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ginmappeR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/00utils.R (line 237, column 71)
    • ...
    • R/UniProtFunctions.R (line 405, column 83)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • KEGGFunctions.R (line 19, column 66)
    • ...
    • UniProtFunctions.R (line 208, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/00utils.R (line 465, column 5)
    • cat() in R/00utils.R (line 491, column 5)
    • print() in R/00utils.R (line 135, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cachedFunctions.R (line 1, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/00utils.R (line 541, column 24)
    • R/00utils.R (line 583, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/00utils.R (line 196, column 45)
    • R/00utils.R (line 197, column 47)
    • R/00utils.R (line 263, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 35 times)
  • <<- in R/00utils.R (line 386, column 30)
  • ...
  • <<- in R/00utils.R (line 515, column 26)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/00utils.R (line 156, column 20)
  • suppressMessages() in R/00utils.R (line 156, column 37)
  • suppressMessages() in R/00utils.R (line 280, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • getKEGGVersion() (R/00utils.R): 91 lines
    • ...
    • .getUniProtSimilarGenes() (R/UniProtFunctions.R): 60 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • changeCARDPath.Rd
    • ...
    • updateCARDDataBase.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 79% of man
pages use at least one of these tags.
  Found in files:
    • getCARD2KEGG.Rd
    • ...
    • getUniProtSimilarGenes.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 434 lines (10%) are > 80 characters long.
  First few lines:
    • R/00utils.R#L22 # [ACCN] means we look for an Accesi ...
    • ...
    • vignettes/ginmappeR.Rmd#L147 All the functions in ginmappeR are vecto ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 355 lines (8%) are
not.
  First few lines:
    • R/KEGGFunctions.R#L70 'protein' = .suppressOu ...
    • ...
    • vignettes/ginmappeR.Rmd#L24 class.output="bg-s ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the ginmappeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.