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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('annotationTools_1.87.0.tar.gz','quit-with-status'=TRUE)"
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── Installing annotationTools ──────────────────────────────────────────────────
✔ Package installed successfully
── annotationTools session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnRKxx2/file551915c1b51fd/annotationTools
→ BiocVersion: 3.24
→ Package: annotationTools
→ PackageVersion: 1.87.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/annotationTools.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpnRKxx2/file551915c1b51fd/annotationTools
→ installDir: /tmp/RtmpnRKxx2/file551912f985e4e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on annotationTools ────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: GeneExpression
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* 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 (50%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • annotationTools.Rnw
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • utils
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • annotationTools.Rnw
* Checking package installation calls in R code...
* Checking for library/require of annotationTools...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getHOMOLOG.R (line 50, column 21)
    • ...
    • R/ps2ps.R (line 10, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • compactList.R (line 6, column 19)
    • ...
    • getPROBESET.R (line 17, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/getANNOTATION.R (line 9, column 28)
    • ...
    • cat() in R/ps2ps.R (line 11, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getHOMOLOG.R (line 8, column 24)
    • ...
    • R/getHOMOLOG.R (line 11, column 22)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getHOMOLOG.R (line 15, column 33)
    • R/getHOMOLOG.R (line 21, column 33)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • getHOMOLOG() (R/getHOMOLOG.R): 60 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • ps2ps.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • ps2ps.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ps2ps.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 315 lines (22%) are > 80 characters long.
  First few lines:
    • R/getANNOTATION.R#L1 getANNOTATION<-function(identifier,annot ...
    • ...
    • vignettes/annotationTools.Rnw#L360 In conclusion, such a systematic
    compari ...
ℹ NOTE: Consider 4 spaces instead of tabs; 274 lines (19%) contain tabs.
  First few lines:
    • R/compactList.R#L3 stopifnot(length(lst)==sum(l)) ...
    • ...
    • vignettes/annotationTools.Rnw#L354
    text.col=1:length(ps_human[existing_ps_ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 124 lines (9%) are
not.
  First few lines:
    • annotationTools/NAMESPACE#L5 getGENETITLE, getHOMOLOG, getMULT ...
    • ...
    • man/ps2ps.Rd#L26 \item{mappingTable}{A data.frame with ...
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 | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the annotationTools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.