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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('esATAC_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing esATAC ───────────────────────────────────────────────────────────
✔ Package installed successfully
── esATAC session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiIQkuo/file977ac313b7a2/esATAC
→ BiocVersion: 3.24
→ Package: esATAC
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/esATAC.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpiIQkuo/file977ac313b7a2/esATAC
→ installDir: /tmp/RtmpiIQkuo/file977ac688e5115
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on esATAC ─────────────────────────────────────────────────
* 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 4.0.0 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:
MotifAnnotation, WorkflowStep, GO, DataImport
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (48%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/esATAC-Introduction.Rmd
* Checking package installation calls in R code...
* Checking for library/require of esATAC...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/RPeakAnno.R (line 80, column 11)
    • library() in R/TSSQC.R (line 77, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/utilities.R (line 195, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CutSiteCountR.R (line 119, column 26)
    • ...
    • utilities.R (line 351, column 41)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/Methods.R (line 229, column 5)
    • print() in R/Methods.R (line 230, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CppInterface.R (line 12, column 20)
    • ...
    • R/utilities.R (line 491, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ConfigVal.R (line 99, column 13)
    • ...
    • R/SamToBed.R (line 66, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/RMotifScanPair.R (line 131, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/PeakCallingMACS2.R (line 200, column 57)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • FastQC.R (line 18, column 56)
    • ...
    • FastQC.R (line 33, column 63)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/PeakCallingMACS2.R (line 78, column 19)
    • system() in R/PeakCallingMACS2.R (line 200, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • atacPipe2() (R/Methods.R): 201 lines
    • ...
    • .qa_ShortRead() (R/utilities.R): 65 lines
* Checking man page documentation...

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • atacPipe2.Rd
    • ...
    • SingleRepReport.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 32% of man
pages use at least one of these tags.
  Found in files:
    • atacPipe2.Rd
    • ...
    • RPeakComp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • atacPipe2.Rd
    • ...
    • RPeakComp.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; 904 lines (10%) are > 80 characters long.
  First few lines:
    • R/ATACProc.R#L63 #' no more method is extended or overrid ...
    • ...
    • vignettes/esATAC-Introduction.Rmd#L84 [3] Boyle, A. P., Guinney, J.,
    Crawford, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 788 lines (9%) are
not.
  First few lines:
    • R/ATACProc.R#L66 contains = "Step" ...
    • ...
    • R/utilities.R#L466 byrow = T ...
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 | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the esATAC.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.