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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RMassBank_3.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RMassBank ────────────────────────────────────────────────────────
✔ Package installed successfully
── RMassBank session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpt7nCQk/file121aa06458dbba/RMassBank
→ BiocVersion: 3.24
→ Package: RMassBank
→ PackageVersion: 3.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RMassBank.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpt7nCQk/file121aa06458dbba/RMassBank
→ installDir: /tmp/Rtmpt7nCQk/file121aa0312f729e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RMassBank ──────────────────────────────────────────────
* 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...
! WARNING: Invalid BiocViews term(s):
  • 'Bioinformatics'
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: 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...
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (15%).
* 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:
    • RMassBank.Rmd
    • RMassBankNonstandard.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RMassBank...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/alternateAnalyze.R (line 244, column 80)
    • ...
    • R/webAccess.R (line 794, column 37)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • alternateAnalyze.R (line 7, column 12)
    • ...
    • validateMassBank.R (line 126, column 49)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/createCompoundlist.R (line 23, column 17)
    • ...
    • cat() in R/webAccess.R (line 25, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/alternateAnalyze.R (line 384, column 22)
    • ...
    • R/tools.R (line 47, column 25)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/alternateAnalyze.R (line 124, column 25)
    • ...
    • R/webAccess.R (line 501, column 19)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/leCsvAccess.R (line 526, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 8 times:
    • F in R/getSplash.R (line 26, column 44)
    • ...
    • T in R/settings_example.R (line 345, column 55)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • buildRecord.R (line 374, column 52)
    • ...
    • RmbWorkspace.R (line 483, column 30)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/createMassBank.R (line 452, column 24)
    • ...
    • system() in R/createMassBank.R (line 992, column 34)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/problematicPeaks.Rd
ℹ Found @ in vignettes/RMassBank.Rmd
ℹ Found @ in vignettes/RMassBankNonstandard.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 40 times)
  • <<- in R/alternateAnalyze.R (line 55, column 11)
  • ...
  • <<- in R/zzz.R (line 34, column 17)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 22 times)
  • suppressWarnings() in R/alternateAnalyze.R (line 64, column 3)
  • ...
  • suppressWarnings() in R/validateMassBank.R (line 212, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 66
functions greater than 50 lines.
  The longest 5 functions are:
    • analyzeMsMs.formula() (R/leMsMs.r): 369 lines
    • ...
    • msmsWorkflow() (R/leMsMs.r): 255 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/archiveResults.Rd
    • ...
    • man/validate.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addMB.Rd
    • ...
    • validate.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 44% of man
pages use at least one of these tags.
  Found in files:
    • addMB.Rd
    • ...
    • validate.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addMB.Rd
    • ...
    • validate.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; 1611 lines (11%) are > 80 characters long.
  First few lines:
    • R/AggregateMethods.R#L5 #' @return Selects the peaks from the ag ...
    • ...
    • vignettes/RMassBankNonstandard.Rmd#L154 # Here we artificially cut
    spectra out t ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6053 lines (40%) contain tabs.
  First few lines:
    • R/AggregateMethods.R#L6 #' (\code{peaksUnmatched}). ...
    • ...
    • vignettes/RMassBankNonstandard.Rmd#L159 s ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2128 lines (14%) are
not.
  First few lines:
    • R/AggregateMethods.R#L74 if(missing(filter)) ...
    • ...
    • vignettes/RMassBank.Rmd#L493 after the MassBank entry prefix. ...
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 | ⚠ 4 WARNINGS | ℹ 23 NOTES
ℹ See the RMassBank.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.