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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ReportingTools_2.52.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ReportingTools ───────────────────────────────────────────────────
✔ Package installed successfully
── ReportingTools session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmprIJm1f/file887e074df187f/ReportingTools
→ BiocVersion: 3.23
→ Package: ReportingTools
→ PackageVersion: 2.52.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ReportingTools.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmprIJm1f/file887e074df187f/ReportingTools
→ installDir: /tmp/RtmprIJm1f/file887e05ef9080a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ReportingTools ─────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmprIJm1f/file887e074df187f/ReportingTools/man/custHeaderPanel.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing
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 that Package field matches directory/tarball name...
* 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 (41%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • utils
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • basicReportingTools.Rnw
    • ...
    • shiny.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 41 out of 45 code chunks = 91% unevaluated
ℹ 
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • rnaseqAnalysis.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • microarrayAnalysis.Rnw
    • rnaseqAnalysis.Rnw
    • shiny.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/basicReportingTools.Rnw
    • ...
    • vignettes/shiny.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ReportingTools...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/objectToHTML-methods.R (line 113, column 4)
    • require() in R/objectToHTML-methods.R (line 122, column 4)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllClasses.R (line 171, column 7)
    • ...
    • R/readReport.R (line 22, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • addReportColumns-methods.R (line 58, column 19)
    • ...
    • toReportDF-methods.R (line 163, column 30)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllOldClasses.R (line 219, column 5)
    • ...
    • cat() in R/ReportHandlers.R (line 114, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 1, column 9)
    • ...
    • R/Utilities.R (line 5, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/addReportColumns-methods.R (line 19, column 32)
    • ...
    • R/objectToHTML-methods.R (line 192, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/plotting_functions.R (line 111, column 52)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • annotate.genes.R (line 5, column 29)
    • check.eg.ids.R (line 17, column 29)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/AllClasses.R (line 65, column 26)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/annotate.genes.R (line 18, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • makeOldHTMLReport() (R/AllOldClasses.R): 123 lines
    • ...
    • startHTMLReport() (R/openPage.R): 94 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/Link.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/mockRnaSeqData.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/addReportColumns-methods.Rd
    • ...
    • man/toReportDF-methods.Rd


✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addReportColumns-methods.Rd
    • ...
    • toReportDF-methods.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: Add content to the empty file R/refClasses.R
ℹ NOTE: Consider shorter lines; 371 lines (6%) are > 80 characters long.
  First few lines:
    • R/addReportColumns-methods.R#L11 selectedIDs = geneIds(obje ...
    • ...
    • vignettes/shiny.Rnw#L113 presentation toolkit for high throughput ...
ℹ NOTE: Consider 4 spaces instead of tabs; 261 lines (4%) contain tabs.
  First few lines:
    • R/addReportColumns-methods.R#L24 check.ids(selectedIDs, annotation.db, k
    ...
    • ...
    • vignettes/rnaseqAnalysis.Rnw#L198 reportDirectory = "./reports") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 653 lines (10%) are
not.
  First few lines:
    • R/addReportColumns-methods.R#L2 signature = signature( ...
    • ...
    • vignettes/shiny.Rnw#L103 }) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 7 WARNINGS | ℹ 19 NOTES
ℹ See the ReportingTools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.