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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChIPpeakAnno_3.47.1.tar.gz','quit-with-status'=TRUE)"
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── Installing ChIPpeakAnno ─────────────────────────────────────────────────────
✔ Package installed successfully
── ChIPpeakAnno session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpogsPbp/file659b012c5b619/ChIPpeakAnno
→ BiocVersion: 3.24
→ Package: ChIPpeakAnno
→ PackageVersion: 3.47.1
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChIPpeakAnno.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpogsPbp/file659b012c5b619/ChIPpeakAnno
→ installDir: /tmp/RtmpogsPbp/file659b055a263a7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChIPpeakAnno ───────────────────────────────────────────
* 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 3.5 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: Transcription,
MotifAnnotation, GO
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 (58%).
* 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:
    • ChIPpeakAnno.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/addGeneIDs.R (line 179, column 26)
* Checking for library/require of ChIPpeakAnno...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/addGeneIDs.R (line 183, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/addGeneIDs.R (line 278, column 22)
    • ...
    • R/xget.R (line 28, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • addGeneIDs.R (line 337, column 24)
    • ...
    • write2FASTA.R (line 44, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/genomicElementDistribution.R (line 438, column 7)
    • cat() in R/summarizePatternInPeaks.R (line 601, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/addAncestors.R (line 26, column 14)
    • ...
    • R/translatePattern.R (line 34, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/addGeneIDs.R (line 214, column 31)
    • ...
    • R/toGRanges.R (line 32, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/addGeneIDs.R (line 312, column 20)
    • ...
    • R/getAllPeakSequence.R (line 150, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • addMetadata.R (line 36, column 24)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/peakPermTest.R (line 77, column 5)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/findOverlappingPeaks.R (line 97, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/countPatternInSeqs.R (line 49, column 19)
  • <<- in R/toGRanges.R (line 35, column 24)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 23 times)
  • suppressWarnings() in R/binOverGene.R (line 108, column 5)
  • ...
  • suppressWarnings() in R/randPeaks.R (line 35, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 51
functions greater than 50 lines.
  The longest 5 functions are:
    • annotatePeakInBatch() (R/annotatePeakInBatch.R): 618 lines
    • ...
    • genomicElementDistribution() (R/genomicElementDistribution.R): 376 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/annoGR.Rd
    • ...
    • man/TxDb2GR.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • cumulativePercentage.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • cumulativePercentage.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cumulativePercentage.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; 397 lines (2%) are > 80 characters long.
  First few lines:
    • R/addGeneIDs.R#L131 stop("Currently only the fol ...
    • ...
    • vignettes/ChIPpeakAnno.Rmd#L1732 Here is the output of `sessionInfo()` on
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 26 lines (0%) contain tabs.
  First few lines:
    • R/addAncestors.R#L57 Ancestors = do.call(rbind, lappl ...
    • ...
    • vignettes/ChIPpeakAnno.Rmd#L107 AnnotationData = ensembl.hs86 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3899 lines (25%) are
not.
  First few lines:
    • R/addAncestors.R#L25 requireNamespace("GO.d ...
    • ...
    • vignettes/ChIPpeakAnno.Rmd#L1715 value.name = "merged_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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 22 NOTES
ℹ See the ChIPpeakAnno.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.