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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ropls_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ropls ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ropls session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmppY5MbU/file123c374d5dcbcb/ropls
→ BiocVersion: 3.24
→ Package: ropls
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ropls.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmppY5MbU/file123c374d5dcbcb/ropls
→ installDir: /tmp/RtmppY5MbU/file123c375dcf7854
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ropls ──────────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (36%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of ropls...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/helpers.R (line 239, column 29)
    • ...
    • R/plot-methods.R (line 1809, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • helpers.R (line 557, column 24)
    • ...
    • plot-methods.R (line 1873, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/opls-functions.R (line 607, column 13)
    • ...
    • print() in R/opls-methods.R (line 1726, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/helpers.R (line 1477, column 19)
    • R/helpers.R (line 1482, column 39)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/helpers.R (line 1593, column 15)
    • R/helpers.R (line 1612, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/opls.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/helpers.R (line 860, column 24)
  • suppressWarnings() in R/helpers.R (line 1167, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • .coreF() (R/opls-functions.R): 1389 lines
    • ...
    • ploPclF() (R/plot-methods.R): 371 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot.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; 559 lines (6%) are > 80 characters long.
  First few lines:
    • R/allClasses.R#L28 #' An S4 class to store PCA and (O)PLS(- ...
    • ...
    • vignettes/ropls-vignette.Rmd#L1049 | **`mds2mae`** | Conve ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4008 lines (43%) are
not.
  First few lines:
    • R/allClasses.R#L22 representation = representation ...
    • ...
    • vignettes/ropls-vignette.Rmd#L1027 GRa ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the ropls.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.