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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TCseq_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TCseq ────────────────────────────────────────────────────────────
✔ Package installed successfully
── TCseq session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpQ6qW0n/file14ac86591a39c1/TCseq
→ BiocVersion: 3.24
→ Package: TCseq
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TCseq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpQ6qW0n/file14ac86591a39c1/TCseq
→ installDir: /tmp/RtmpQ6qW0n/file14ac866b8a4e6d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TCseq ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.4 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...
* 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 (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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • TCseq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • TCseq.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/TCseq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of TCseq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/timecourseTable.R (line 112, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plots.R (line 108, column 33)
    • plots.R (line 215, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plots.R (line 209, column 5)
    • print() in R/plots.R (line 218, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DBanalysis.R (line 116, column 11)
    • ...
    • R/plots.R (line 203, column 12)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Classes.R (line 246, column 30)
    • ...
    • plots.R (line 77, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/DBresults.R (line 187, column 12)
  • suppressWarnings() in R/DBresults.R (line 234, column 12)
  • suppressWarnings() in R/plots.R (line 197, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • timeclustplot() (R/plots.R): 140 lines
    • ...
    • peakreference() (R/peakreference.R): 59 lines
* Checking man page documentation...
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘TCseq’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • clust.accessors.Rd
  • countReads.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 79 lines (4%) are > 80 characters long.
  First few lines:
    • R/Classes.R#L70 stop("Number of columns in 'counts ...
    • ...
    • vignettes/TCseq.Rnw#L160 \bibitem{lokesh} L. Kumar and M. Futschi ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 486 lines (23%) are
not.
  First few lines:
    • R/Classes.R#L32 dis ...
    • ...
    • vignettes/TCseq.Rnw#L67 counts = countsTable) ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the TCseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.