##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MetaboAnnotation_1.17.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing MetaboAnnotation ─────────────────────────────────────────────────
✔ Package installed successfully
── MetaboAnnotation session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpHbVLUD/filed34fc16ff4ad5/MetaboAnnotation
→ BiocVersion: 3.24
→ Package: MetaboAnnotation
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MetaboAnnotation.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpHbVLUD/filed34fc16ff4ad5/MetaboAnnotation
→ installDir: /tmp/RtmpHbVLUD/filed34fc4c6de752
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaboAnnotation ───────────────────────────────────────
* 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 4.0.0 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 (85%).
* 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:
    • MetaboAnnotation.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MetaboAnnotation...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Matched.R (line 1091, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • matchSpectra.R (line 410, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/Matched.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • validateMatchedSpectra() (R/validateMatchedSpectra.R): 123 lines
    • ...
    • .addMatches() (R/Matched.R): 52 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/CompAnnotationSource.Rd
    • man/CompDbSource.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • matchSpectra.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; 10 lines (0%) are > 80 characters long.
  First few lines:
    • R/group_standards.R#L46 #' "Uric ...
    • ...
    • vignettes/MetaboAnnotation.Rmd#L12 %\VignetteDepends{Spectra,BiocStyle,Ms
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 888 lines (15%) are
not.
  First few lines:
    • R/AllClassUnions.R#L5 " ...
    • ...
    • vignettes/MetaboAnnotation.Rmd#L1026 file = "standard_mixes.txt", ...
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 11 NOTES
ℹ See the MetaboAnnotation.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.