##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('dcGSA_1.41.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing dcGSA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── dcGSA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpU2qB1F/file7e2c42557778d/dcGSA
→ BiocVersion: 3.24
→ Package: dcGSA
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/dcGSA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpU2qB1F/file7e2c42557778d/dcGSA
→ installDir: /tmp/RtmpU2qB1F/file7e2c475c36dee
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dcGSA ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.3 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 (50%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • dcGSA.Rmd
✖ ERROR: No 'VignetteEngine' specified in vignette.
  Add 'VignetteEngine' to the following files:
    • vignettes/dcGSA.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • dcGSA.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • dcGSA.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/dcGSA.Rmd
* Checking package installation calls in R code...
* Checking for library/require of dcGSA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dcGSA.R (line 58, column 11)
    • ...
    • R/readGMT.R (line 12, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dcGSA.R (line 98, column 50)
    • LDcov.R (line 38, column 11)
    • readGMT.R (line 13, column 45)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/dcGSA.R (line 72, column 36)
    • R/dcGSA.R (line 129, column 13)
    • R/LDcov.R (line 36, column 4)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/dcGSA.R (line 66, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • dcGSA() (R/dcGSA.R): 92 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/dcGSAtest.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 25% of man
pages use at least one of these tags.
  Found in files:
    • LDcov.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • LDcov.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; 16 lines (5%) are > 80 characters long.
  First few lines:
    • R/dcGSAtest.R#L6 #' ID, data (phenotypes of interest), ge ...
    • ...
    • vignettes/dcGSA.Rmd#L78 The 'OverlapSize' in the result indicate ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 57 lines (19%) are
not.
  First few lines:
    • R/dcGSA.R#L47 parallel=FALSE,BPparam ...
    • ...
    • R/readGMT.R#L14 return(geneset) ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the dcGSA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.