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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('xcms_4.10.0.tar.gz','quit-with-status'=TRUE)"
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── Installing xcms ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── xcms session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuC7Hye/file9a98a123f8bc0/xcms
→ BiocVersion: 3.23
→ Package: xcms
→ PackageVersion: 4.10.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/xcms.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpuC7Hye/file9a98a123f8bc0/xcms
→ installDir: /tmp/RtmpuC7Hye/file9a98a749a66fe
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on xcms ───────────────────────────────────────────────────
* 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 that Package field matches directory/tarball name...
* 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 (75%).
* 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:
    • LC-MS-feature-grouping.Rmd
    • ...
    • xcms.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/xcms.Rmd (chunk no. 32, line 573, column 1)
    • vignettes/xcms.Rmd (chunk no. 32, line 577, column 10)
    • vignettes/xcms.Rmd (chunk no. 32, line 579, column 5)
* Checking package installation calls in R code...
* Checking for library/require of xcms...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/Deprecated.R (line 18, column 58)
    • ...
    • library() in R/writemztab.R (line 186, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cwTools.R (line 285, column 27)
    • ...
    • R/methods-xcmsSet.R (line 1265, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • c.R (line 351, column 18)
    • ...
    • XcmsExperimentHdf5-functions.R (line 675, column 32)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • cwTools.R (line 744, column 22)
    • cwTools.R (line 744, column 40)
    • cwTools.R (line 751, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Deprecated.R (line 32, column 21)
    • ...
    • cat() in R/mzClust.R (line 181, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cwTools.R (line 345, column 11)
    • ...
    • R/XcmsExperimentHdf5.R (line 789, column 22)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/functions-OnDiskMSnExp.R (line 675, column 14)
    • ...
    • R/methods-xcmsSet.R (line 1822, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/do_findChromPeaks-functions.R (line 1415, column 14)
    • ...
    • R/methods-xcmsSet.R (line 259, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • T in R/databases.R (line 21, column 55)
    • ...
    • T in R/writemzdata.R (line 85, column 81)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • cwTools.R (line 434, column 20)
    • ...
    • plotQC.R (line 78, column 29)
! WARNING: .Deprecated / .Defunct usage (found 17 times)
  • .Deprecated() in R/c.R (line 49, column 5)
  • ...
  • .Deprecated() in R/methods-XCMSnExp.R (line 2916, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/fillChromPeaks.Rd
ℹ Found @ in man/sub-xcmsRaw-logicalOrNumeric-missing-missing-method.Rd
ℹ Found @ in vignettes/xcms-lcms-ms.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 7 times)
  • <<- in R/do_findChromPeaks-functions.R (line 327, column 20)
  • ...
  • <<- in R/methods-xcmsRaw.R (line 1121, column 18)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29 times)
  • suppressWarnings() in R/do_adjustRtime-functions.R (line 219, column 23)
  • ...
  • suppressMessages() in R/XcmsExperiment-plotting.R (line 280, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 145
functions greater than 50 lines.
  The longest 5 functions are:
    • .centWave_orig() (R/do_findChromPeaks-functions.R): 554 lines
    • ...
    • _anonymous_.64() (R/Deprecated.R): 236 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/chromPeakChromatograms.Rd
    • ...
    • man/xcmsSource-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • absent-methods.Rd
    • ...
    • xcmsSource-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • AutoLockMass-methods.Rd
    • ...
    • xcmsRaw.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • AutoLockMass-methods.Rd
    • ...
    • xcmsRaw.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; 897 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L11 setGeneric("addParams<-", function(objec ...
    • ...
    • vignettes/xcms.Rmd#L1551 - [MetaboAnnotationTutorials](https://jo ...
ℹ NOTE: Consider 4 spaces instead of tabs; 30 lines (0%) contain tabs.
  First few lines:
    • R/cwTools.R#L155 ## and find the maximum position at ...
    • ...
    • xcms/NAMESPACE#L404 "groupSimilarityMatrix") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 7049 lines (15%) are
not.
  First few lines:
    • R/AllGenerics.R#L278 standardGeneric("adjustRtimeP ...
    • ...
    • vignettes/xcms.Rmd#L1556 and its functionality. ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the xcms.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.