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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChIPseeker_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ChIPseeker ───────────────────────────────────────────────────────
✔ Package installed successfully
── ChIPseeker session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpwu3W6M/file65b627e0f5c36/ChIPseeker
→ BiocVersion: 3.24
→ Package: ChIPseeker
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChIPseeker.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpwu3W6M/file65b627e0f5c36/ChIPseeker
→ installDir: /tmp/Rtmpwu3W6M/file65b62616cf2a1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChIPseeker ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
✖ ERROR: Package dependencies must be on CRAN or Bioconductor. Remove
'Remotes:' from DESCRIPTION
* 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 4.1.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (31%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ChIPseeker.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ChIPseeker...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/addGeneAnno.R (line 14, column 5)
    • ...
    • require() in R/vennplot.R (line 51, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/covplot.R (line 118, column 9)
    • ...
    • R/utilities.R (line 491, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • annotatePeak.R (line 176, column 38)
    • ...
    • vennplot.R (line 59, column 39)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/annotatePeak.R (line 117, column 9)
    • ...
    • cat() in R/utilities.R (line 382, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotatePeak.R (line 314, column 40)
    • ...
    • R/vennplot.R (line 60, column 28)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/csAnno.R (line 138, column 57)
    • F in R/csAnno.R (line 138, column 67)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/GEO.R (line 124, column 13)
    • system() in R/GEO.R (line 129, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
  • suppressWarnings() in R/addGeneAnno.R (line 29, column 9)
  • ...
  • suppressMessages() in R/utilities.R (line 416, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 37
functions greater than 50 lines.
  The longest 5 functions are:
    • getTagMatrix.binning.internal() (R/tagMatrix.R): 415 lines
    • ...
    • peak_Profile_Heatmap() (R/plotTagMatrix.R): 184 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/info.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/check_upstream_and_downstream.Rd
    • ...
    • man/plotMultiProf.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • annotatePeak.Rd
    • ...
    • vennplot.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 6% of man
pages use at least one of these tags.
  Found in files:
    • annotatePeak.Rd
    • ...
    • seq2gene.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annotatePeak.Rd
    • ...
    • seq2gene.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • ChIPseeker/NEWS
    • ChIPseeker/NEWS.md
* 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; 471 lines (6%) are > 80 characters long.
  First few lines:
    • R/addGeneAnno.R#L22 message("geneID type is not supp ...
    • ...
    • vignettes/ChIPseeker.Rmd#L611 Here is the output of `sessionInfo()` on
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
  First few lines:
    • R/getGenomicAnnotation.R#L179 start(peaks) - end(peF), ...
    • ...
    • R/vennplot.R#L65 ggVennDiagram::ggVennDiagram(Sets, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2324 lines (28%) are
not.
  First few lines:
    • R/AllGenerics.R#L9 function(x, r = 0.2, cex = 1.2, ...) ...
    • ...
    • vignettes/ChIPseeker.Rmd#L535 verbose = FALSE) ...
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 | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the ChIPseeker.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.