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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('annotate_1.90.0.tar.gz','quit-with-status'=TRUE)"
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── Installing annotate ─────────────────────────────────────────────────────────
✔ Package installed successfully
── annotate session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAAzBst/file71b411f1bf61b/annotate
→ BiocVersion: 3.23
→ Package: annotate
→ PackageVersion: 1.90.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/annotate.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpAAzBst/file71b411f1bf61b/annotate
→ installDir: /tmp/RtmpAAzBst/file71b4190b82d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on annotate ───────────────────────────────────────────────
* 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...
ℹ NOTE: Update R version dependency from 2.10 to 4.6.0
* 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/RtmpAAzBst/file71b411f1bf61b/annotate/man/getTDRows.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Microarray
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 (27%).
* 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:
    • annotate.Rnw
    • ...
    • useProbeInfo.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • annotate.Rnw
    • ...
    • useProbeInfo.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/chromLOC.Rmd
    • vignettes/GOusage.Rnw
* Checking package installation calls in R code...
* Checking for library/require of annotate...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/AnnMaps.R (line 48, column 32)
    • ...
    • require() in R/serializeEnv.R (line 36, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ACCNUMStats.R (line 4, column 25)
    • ...
    • R/readGEOAnn.R (line 48, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • chromLocation.R (line 95, column 19)
    • ...
    • pubMedAbst.R (line 196, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/chromLocation.R (line 375, column 17)
    • ...
    • print() in R/serializeEnv.R (line 62, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Amat.R (line 4, column 8)
    • ...
    • R/query.R (line 588, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/compatipleVersions.R (line 13, column 18)
    • ...
    • R/readGEOAnn.R (line 75, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 22 times)
  • <<- in R/getPMInfo.R (line 14, column 12)
  • ...
  • <<- in R/getPMInfo.R (line 112, column 15)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/AnnMaps.R (line 48, column 15)
  • suppressWarnings() in R/AnnMaps.R (line 55, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • chrCats() (R/chromLocation.R): 395 lines
    • ...
    • add() (R/getPMInfo.R): 76 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ACCNUMStats.Rd
    • ...
    • man/setRepository.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getTDRows.Rd
  • ...
  • updateSymbolsToValidKeys.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:
    • isValidkey.Rd
    • LL2homology.Rd
    • updateSymbolsToValidKeys.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • isValidkey.Rd
    • LL2homology.Rd
    • updateSymbolsToValidKeys.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; 114 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L1 ## S4 methods so we can use non-package ...
    • ...
    • vignettes/useProbeInfo.Rnw#L151 this general idea is something that an e
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • R/pmid2MIAME.R#L19 caa = xmlChildren(cart[["Abstract"]]) ...
    • R/query.R#L207 retVal <- paste(retVal, collapse=",") ...
    • man/serializeEnv.Rd#L41 </entry> ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2263 lines (29%) are
not.
  First few lines:
    • R/ACCNUMStats.R#L16 accs[1]) > 0){ ...
    • ...
    • vignettes/query.Rnw#L259 \caption{pmAbst2HTML with fram ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 22 NOTES
ℹ See the annotate.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.