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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('gmapR_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing gmapR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── gmapR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpMC5Zvl/filea78507fc59ac7/gmapR
→ BiocVersion: 3.24
→ Package: gmapR
→ PackageVersion: 1.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/gmapR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpMC5Zvl/filea78507fc59ac7/gmapR
→ installDir: /tmp/RtmpMC5Zvl/filea78504b49f0c1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gmapR ──────────────────────────────────────────────────
* 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 2.15.0 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/RtmpMC5Zvl/filea78507fc59ac7/gmapR/man/makeGmapGenomePackage.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, GenomeAssembly, VariantAnnotation
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 (88%).
* 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:
    • gmapR.Rnw
* Checking package installation calls in R code...
* Checking for library/require of gmapR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/BamTallyParam-class.R (line 173, column 3)
    • ...
    • R/system.R (line 93, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/BamTallyParam-class.R (line 59, column 14)
    • ...
    • R/iit_store-command.R (line 47, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/GmapGenomeDirectory-class.R (line 42, column 10)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/system.R (line 121, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/GmapGenome-class.R (line 35, column 3)
* 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:
    • variantSummary() (R/bam_tally-command.R): 88 lines
    • ...
    • makeGmapGenomePackage() (R/makeGmapGenomePackage.R): 60 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/gmap_build-methods.Rd
  • man/GmapGenomeDirectory-class.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/BamTallyParam-class.Rd
    • ...
    • man/makeGmapGenomePackage.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • bam_tally-methods.Rd
    • ...
    • makeGmapGenomePackage.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 27% of man
pages use at least one of these tags.
  Found in files:
    • cmetindex.Rd
    • ...
    • makeGmapGenomePackage.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cmetindex.Rd
    • ...
    • makeGmapGenomePackage.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • gmapR/NEWS
    • gmap/NEWS
    • gstruct/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; 17 lines (0%) are > 80 characters long.
  First few lines:
    • R/BamTallyParam-class.R#L75 stop("No map matching the patter ...
    • ...
    • vignettes/gmapR.Rnw#L188 packageVersio ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • man/GmapSnpDirectory-class.Rd#L26 } ...
    • man/GmapSnps-class.Rd#L37 that is the parent of the directory con ...
    • man/GmapSnps-class.Rd#L38 this \code{GmapSnps} object.} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1454 lines (35%) are
not.
  First few lines:
    • R/asSystemCall.R#L5 expr <- substitute(x) ...
    • ...
    • vignettes/gmapR.Rnw#L373 INSTALL GmapGenome.Hsapiens.UCSC.hg19} ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the gmapR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.