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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Mulcom_1.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Mulcom ───────────────────────────────────────────────────────────
✔ Package installed successfully
── Mulcom session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPXy1Qz/filef27f61c9e16cc/Mulcom
→ BiocVersion: 3.24
→ Package: Mulcom
→ PackageVersion: 1.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Mulcom.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPXy1Qz/filef27f61c9e16cc/Mulcom
→ installDir: /tmp/RtmpPXy1Qz/filef27f64269aea2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Mulcom ─────────────────────────────────────────────────
* 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 2.10 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* 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 (17%).
* 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...
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • Mulcom.Rmd
✖ ERROR: No 'VignetteEngine' specified in vignette.
  Add 'VignetteEngine' to the following files:
    • vignettes/Mulcom.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • Mulcom.Rmd
* Checking package installation calls in R code...
* Checking for library/require of Mulcom...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • harmonicMean.R (line 4, column 12)
    • ...
    • samOptPars.R (line 15, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/mulOptPars.R (line 8, column 10)
    • print() in R/mulParOpt.R (line 7, column 16)
    • print() in R/samOptPars.R (line 6, column 40)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/mulCAND.R (line 18, column 17)
    • ...
    • R/mulParOpt.R (line 10, column 27)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/mulCalc.R (line 12, column 12)
    • ...
    • R/mulScores.R (line 75, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/mulParOpt.R (line 18, column 26)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • mulCalc.R (line 3, column 23)
    • ...
    • mulScores.R (line 39, column 25)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/mulIndex.R (line 2, column 4)
  • set.seed() in R/mulPerm.R (line 9, column 11)
* 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 2
functions greater than 50 lines.
  The longest 5 functions are:
    • mulScores() (R/mulScores.R): 79 lines
    • mulPerm() (R/mulPerm.R): 61 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Affy.Rd
    • ...
    • man/samIlmnSymbols.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 93 lines (7%) are > 80 characters long.
  First few lines:
    • R/harmonicMean.R#L5 harmonic_mean[i] <- (2/((1/length(i ...
    • ...
    • vignettes/Mulcom.Rmd#L6 with several "test" groups, like in the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 460 lines (34%) are
not.
  First few lines:
    • R/harmonicMean.R#L3 harmonic_mean <- rep(NA, length(levels ...
    • ...
    • vignettes/Mulcom.Rmd#L23 rmarkdown::html_document: ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 6 WARNINGS | ℹ 12 NOTES
ℹ See the Mulcom.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.