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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('MsCoreUtils_1.24.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MsCoreUtils ──────────────────────────────────────────────────────
✔ Package installed successfully
── MsCoreUtils session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjAqFfV/file83fb1157e81ec/MsCoreUtils
→ BiocVersion: 3.23
→ Package: MsCoreUtils
→ PackageVersion: 1.24.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MsCoreUtils.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpjAqFfV/file83fb1157e81ec/MsCoreUtils
→ installDir: /tmp/RtmpjAqFfV/file83fb16d1fe035
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MsCoreUtils ────────────────────────────────────────────
* 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 3.6.0 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...
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* 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:
    • MsCoreUtils.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MsCoreUtils...
* Checking coding practice...
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • valleys.R (line 63, column 29)
    • valleys.R (line 63, column 42)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/imputation.R (line 467, column 29)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/retry.R (line 65, column 29)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 5 times:
    • F in R/smooth.R (line 140, column 5)
    • ...
    • F in R/smooth.R (line 148, column 5)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Deprecated() in R/distance.R (line 141, column 5)
  • .Defunct() in R/imputation.R (line 356, column 5)
* 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:
    • impute_matrix() (R/imputation.R): 66 lines
    • ...
    • closest() (R/matching.R): 52 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/coerce.Rd
    • man/refineCentroids.Rd
    • man/retry.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • retry.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • retry.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • retry.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; 20 lines (0%) are > 80 characters long.
  First few lines:
    • R/aggregate_by_matrix.R#L63 stop("The colum names of 'MAT' h ...
    • ...
    • vignettes/MsCoreUtils.Rmd#L87 guide](https://rformassspectrometry.gith
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 93 lines (2%) are not.
  First few lines:
    • R/aggregate_by_matrix.R#L56 "'HDF5Matrix'.") ...
    • ...
    • vignettes/MsCoreUtils.Rmd#L72 function for `QFeatures` objects. ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 13 NOTES
ℹ See the MsCoreUtils.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.