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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CoGAPS_3.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CoGAPS ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CoGAPS session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPrgsYm/file77c2431bb715/CoGAPS
→ BiocVersion: 3.24
→ Package: CoGAPS
→ PackageVersion: 3.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CoGAPS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPrgsYm/file77c2431bb715/CoGAPS
→ installDir: /tmp/RtmpPrgsYm/file77c24d8d4558
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CoGAPS ─────────────────────────────────────────────────
* 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 3.5.0 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...
✖ 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 (32%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CoGAPS.Rmd
* Checking package installation calls in R code...
* Checking for library/require of CoGAPS...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/class-CogapsParams.R (line 186, column 26)
    • ...
    • R/SubsetData.R (line 114, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • class-CogapsResult.R (line 44, column 38)
    • ...
    • SubsetData.R (line 67, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/HelperFunctions.R (line 54, column 9)
    • ...
    • print() in R/methods-CogapsResult.R (line 615, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CoGAPS.R (line 112, column 29)
    • ...
    • R/methods-CogapsResult.R (line 679, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/CoGAPS.R (line 178, column 13)
    • R/CoGAPS.R (line 218, column 13)
    • R/HelperFunctions.R (line 180, column 14)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/DistributedCogaps.R (line 51, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/CoGAPS.Rmd
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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • distributedCogaps() (R/DistributedCogaps.R): 72 lines
    • ...
    • _anonymous_.95() (R/methods-CogapsParams.R): 63 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/GIST.data_frame.Rd
    • ...
    • man/GIST.uncertainty.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calcCoGAPSStat-methods.Rd
    • ...
    • toCSV-methods.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:
    • GWCoGAPS.Rd
    • scCoGAPS.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • GWCoGAPS.Rd
    • scCoGAPS.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; 129 lines (4%) are > 80 characters long.
  First few lines:
    • R/class-CogapsParams.R#L40 #' @slot checkpointInterval how many ite ...
    • ...
    • vignettes/CoGAPS.Rmd#L434 The function will print out the MANOVA r ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • R/data.R#L12 #' @format 'data.frame': 25 obs. of 20 ...
    • vignettes/CoGAPS.Rmd#L232 seed=42, # for consisten ...
    • vignettes/CoGAPS.Rmd#L233 nPatterns=8, # each thre ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 144 lines (4%) are
not.
  First few lines:
    • R/class-CogapsResult.R#L82 # "negative values in feature ...
    • ...
    • vignettes/CoGAPS.Rmd#L420 patterngeneset = hallmarks_ora, whichp ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the CoGAPS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.