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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TFEA.ChIP_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TFEA.ChIP ────────────────────────────────────────────────────────
✔ Package installed successfully
── TFEA.ChIP session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpK3346j/file14bdcd7643fb75/TFEA.ChIP
→ BiocVersion: 3.24
→ Package: TFEA.ChIP
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TFEA.ChIP.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpK3346j/file14bdcd7643fb75/TFEA.ChIP
→ installDir: /tmp/RtmpK3346j/file14bdcd4ab95926
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TFEA.ChIP ──────────────────────────────────────────────
* 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 4.2.0 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • BiocStyle
* Checking package installation calls in R code...
* Checking for library/require of TFEA.ChIP...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/All-functions.R (line 304, column 20)
    • ...
    • R/All-functions.R (line 1244, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • All-functions.R (line 89, column 32)
    • ...
    • All-functions.R (line 1685, column 39)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/All-functions.R (line 302, column 7)
    • ...
    • cat() in R/All-functions.R (line 1998, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/All-functions.R (line 91, column 23)
    • R/All-functions.R (line 184, column 23)
    • R/All-functions.R (line 383, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/All-functions.R (line 65, column 12)
    • ...
    • R/All-functions.R (line 1982, column 36)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/All-functions.R (line 1786, column 17)
  • <<- in R/All-functions.R (line 1791, column 26)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/All-functions.R (line 270, column 24)
  • ...
  • suppressMessages() in R/All-functions.R (line 709, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • txt2GR() (R/All-functions.R): 207 lines
    • ...
    • plot_RES() (R/All-functions.R): 121 lines
* Checking man page documentation...


ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • filter_expressed_TFs.Rd
  • ...
  • plot_ES.Rd
* Checking package NEWS...
* 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; 139 lines (5%) are > 80 characters long.
  First few lines:
    • R/All-functions.R#L510 if (!(all(c("Genes", "pvalue", "log2 ...
    • ...
    • vignettes/TFEA.ChIP.Rmd#L375 At the beginning of a session, use the f ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain tabs.
  First few lines:
    • R/All-functions.R#L746 mouse.ensembl.ID = all.IDs$ense ...
    • ...
    • R/All-functions.R#L749 stringsAsFactors = ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1331 lines (50%) are
not.
  First few lines:
    • R/All-functions.R#L22 ...
    • ...
    • vignettes/TFEA.ChIP.Rmd#L353 - ChIP Targets: list of vectors, one p ...
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 | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the TFEA.ChIP.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.