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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('rtracklayer_1.72.0.tar.gz','quit-with-status'=TRUE)"
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── Installing rtracklayer ──────────────────────────────────────────────────────
✔ Package installed successfully
── rtracklayer session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsdLB67/file911b41426fb08/rtracklayer
→ BiocVersion: 3.23
→ Package: rtracklayer
→ PackageVersion: 1.72.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rtracklayer.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpsdLB67/file911b41426fb08/rtracklayer
→ installDir: /tmp/RtmpsdLB67/file911b4e078a8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rtracklayer ────────────────────────────────────────────
* 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 3.5 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage, GenomeBrowsers
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 (62%).
* 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:
    • rtracklayer.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 27 out of 44 code chunks = 61% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • rtracklayer.Rnw
* Checking package installation calls in R code...
* Checking for library/require of rtracklayer...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bam.R (line 71, column 31)
    • ...
    • R/wig.R (line 173, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bed.R (line 376, column 31)
    • trackhub.R (line 413, column 31)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/trackhub.R (line 385, column 5)
    • ...
    • cat() in R/ucsc.R (line 1262, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/trackhub.R (line 384, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ucsc.R (line 307, column 15)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/web.R (line 3, column 10)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • bed.R (line 60, column 30)
    • ...
    • wig.R (line 33, column 30)
! WARNING: .Deprecated / .Defunct usage (found 7 times)
  • .Defunct() in R/ucsc.R (line 183, column 5)
  • ...
  • .Defunct() in R/ucsc.R (line 344, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/bigWig.R (line 125, column 26)
  • <<- in R/chain.R (line 117, column 52)
  • <<- in R/wig.R (line 111, column 22)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/ranges.R (line 81, column 8)
  • suppressWarnings() in R/readGFF.R (line 60, column 16)
  • suppressWarnings() in R/web.R (line 9, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.243() (R/bed.R): 138 lines
    • ...
    • _anonymous_.61() (R/bigBed.R): 112 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/activeView-methods.Rd
    • ...
    • man/wigToBigWig.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • activeView-methods.Rd
    • ...
    • wigToBigWig.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 35% of man
pages use at least one of these tags.
  Found in files:
    • asBED.Rd
    • ...
    • WIGFile-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • asBED.Rd
    • ...
    • WIGFile-class.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; 136 lines (1%) are > 80 characters long.
  First few lines:
    • R/bed.R#L395 setGeneric("import.narrowPeak", function ...
    • ...
    • vignettes/rtracklayer.Rnw#L692 describes DNaseI hypersensitivity for K5
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • man/BigWigFile.Rd#L145 as = c("GRangesList", "RleList", "matri ...
    • man/BigWigFile.Rd#L161 interpolated to yield the matrix result ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4029 lines (32%) are
not.
  First few lines:
    • R/bam.R#L6 function(con, format, text, pa ...
    • ...
    • vignettes/rtracklayer.Rnw#L738 sessionInfo() ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 20 NOTES
ℹ See the rtracklayer.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.