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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methylclock_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing methylclock ──────────────────────────────────────────────────────
✔ Package installed successfully
── methylclock session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpSFnkYO/filed5f621491e552/methylclock
→ BiocVersion: 3.24
→ Package: methylclock
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methylclock.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpSFnkYO/filed5f621491e552/methylclock
→ installDir: /tmp/RtmpSFnkYO/filed5f626bd22df8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methylclock ────────────────────────────────────────────
* 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 4.1.0 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...
* 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 (26%).
* 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/methylclock.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/DNAmGA.R (line 232, column 21)
* Checking for library/require of methylclock...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/checkClocks.R (line 73, column 9)
    • ...
    • print() in R/internals.R (line 146, column 27)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/DNAmAge.R (line 141, column 25)
    • R/DNAmAge.R (line 225, column 22)
    • R/meffilEstimateCellCountsFromBetas.R (line 77, column 25)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • DNAmAge() (R/DNAmAge.R): 310 lines
    • ...
    • checkClocksGA() (R/checkClocksGA.R): 60 lines
* Checking man page documentation...
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ExperimentHubData’
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
Registered S3 methods overwritten by 'ggpp':
  method                  from   
  heightDetails.titleGrob ggplot2
  widthDetails.titleGrob  ggplot2
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plotCorClocks.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • plotCorClocks.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; 11 lines (0%) are > 80 characters long.
  First few lines:
    • R/DNAmAge.R#L96 stop("Data seems to do not be be ...
    • ...
    • vignettes/methylclock.Rmd#L690 (https://static-content.springer.com/esm
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 52 lines (2%) are not.
  First few lines:
    • R/checkClocks.R#L40 ...
    • ...
    • vignettes/methylclock.Rmd#L590 family="binomial" ...
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 12 NOTES
ℹ See the methylclock.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.