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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ACME_2.69.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ACME ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── ACME session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbCbdcs/file467fd6ddd6cc3/ACME
→ BiocVersion: 3.24
→ Package: ACME
→ PackageVersion: 2.69.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ACME.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpbCbdcs/file467fd6ddd6cc3/ACME
→ installDir: /tmp/RtmpbCbdcs/file467fd16c38b30
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ACME ───────────────────────────────────────────────────
* 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 2.10 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: WholeGenome
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • ACME.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ACME.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ACME.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ACME...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Classes.R (line 131, column 16)
    • ...
    • write.sgr.R (line 2, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Classes.R (line 195, column 3)
    • ...
    • cat() in R/write.sgr.R (line 13, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/write.bedGraph.R (line 9, column 11)
    • R/write.bedGraph.R (line 24, column 9)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 8 times:
    • T in R/Classes.R (line 167, column 13)
    • ...
    • F in R/read.resultsGFF.R (line 13, column 35)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • write.bedGraph.R (line 4, column 18)
    • write.sgr.R (line 3, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/write.bedGraph.Rd
    • man/write.sgr.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...
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; 28 lines (2%) are > 80 characters long.
  First few lines:
    • R/Classes.R#L12 msg <- "Column names of fea ...
    • ...
    • vignettes/ACME.Rnw#L75 The Affymetrix Integrated Genome Browser ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (1%) contain tabs.
  First few lines:
    • man/ACMECalcSet-class.Rd#L22 \describe{ ...
    • ...
    • man/aGFFCalc-class.Rd#L44 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 468 lines (39%) are
not.
  First few lines:
    • R/Classes.R#L6 contains="ExpressionSet", ...
    • ...
    • man/write.sgr.Rd#L21 \item{directory}{Give a directory for ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the ACME.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.