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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GeneRegionScan_1.69.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GeneRegionScan ───────────────────────────────────────────────────
✔ Package installed successfully
── GeneRegionScan session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2XHuIV/filea39b47de56811/GeneRegionScan
→ BiocVersion: 3.24
→ Package: GeneRegionScan
→ PackageVersion: 1.69.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GeneRegionScan.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp2XHuIV/filea39b47de56811/GeneRegionScan
→ installDir: /tmp/Rtmp2XHuIV/filea39b44856660d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GeneRegionScan ─────────────────────────────────────────
* 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/Rtmp2XHuIV/filea39b47de56811/GeneRegionScan/man/exampleProbeLevelSet.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2XHuIV/filea39b47de56811/GeneRegionScan/man/genomic.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2XHuIV/filea39b47de56811/GeneRegionScan/man/mrna.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2XHuIV/filea39b47de56811/GeneRegionScan/man/ProbeLevelSet-class.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: ExonArray,
Sequencing, Alignment, SequenceMatching
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 (75%).
* 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:
    • GeneRegionScan.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GeneRegionScan...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/creationFunctions.R (line 123, column 13)
    • ...
    • require() in R/creationFunctions.R (line 877, column 25)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • analysisFunctions.R (line 22, column 34)
    • ...
    • creationFunctions.R (line 1684, column 18)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/analysisFunctions.R (line 606, column 31)
    • R/analysisFunctions.R (line 864, column 39)
    • R/analysisFunctions.R (line 920, column 35)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/analysisFunctions.R (line 16, column 62)
    • ...
    • R/creationFunctions.R (line 1582, column 51)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/analysisFunctions.R (line 541, column 39)
    • ...
    • R/creationFunctions.R (line 1627, column 30)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • analysisFunctions.R (line 233, column 58)
    • ...
    • creationFunctions.R (line 850, column 49)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/creationFunctions.R (line 422, column 47)
    • ...
    • system() in R/creationFunctions.R (line 1624, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • getLocalProbeIntensities() (R/creationFunctions.R): 348 lines
    • ...
    • getServerProbeIntensities() (R/creationFunctions.R): 186 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addSnpPdata.rd
    • ...
    • getServerProbeIntensities.rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 37% of man
pages use at least one of these tags.
  Found in files:
    • addSnpPdata.rd
    • ...
    • getServerProbeIntensities.rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addSnpPdata.rd
    • ...
    • getServerProbeIntensities.rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 889 lines (22%) are > 80 characters long.
  First few lines:
    • R/analysisFunctions.R#L2 setGeneric("doProbeLinear", function(obj ...
    • ...
    • vignettes/GeneRegionScan.Rnw#L127 geneRegionScan(exampleProbeLevelSet,
    gen ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2705 lines (68%) contain tabs.
  First few lines:
    • R/analysisFunctions.R#L4 function(object,label,testType="linear ...
    • ...
    • man/translateSampleNames.rd#L52 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 190 lines (5%) are
not.
  First few lines:
    • man/addSnpPdata.rd#L15 \item{object}{A ProbeLevelSet object o ...
    • ...
    • man/translateSampleNames.rd#L18 \item{to}{Character string with the tr
    ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the GeneRegionScan.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.