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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('rGREAT_2.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing rGREAT ───────────────────────────────────────────────────────────
✔ Package installed successfully
── rGREAT session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEd2VSP/file11acce2f70eba2/rGREAT
→ BiocVersion: 3.24
→ Package: rGREAT
→ PackageVersion: 2.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/rGREAT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpEd2VSP/file11acce2f70eba2/rGREAT
→ installDir: /tmp/RtmpEd2VSP/file11acce354d1ae4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rGREAT ─────────────────────────────────────────────────
* 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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (22%).
* 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...
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/utils.R (line 25, column 41)
    • ...
    • install() in R/utils.R (line 53, column 70)
* Checking for library/require of rGREAT...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/extend.R (line 130, column 23)
    • ...
    • R/utils.R (line 251, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • extend.R (line 611, column 74)
    • ...
    • utils.R (line 210, column 40)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/00_global.R (line 1, column 17)
    • ...
    • R/zzz.R (line 5, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/great_client.R (line 404, column 14)
    • R/great_client.R (line 416, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/great_client.R (line 373, column 25)
    • ...
    • R/great_client.R (line 853, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 16 times)
  • suppressWarnings() in R/extend.R (line 565, column 25)
  • ...
  • suppressWarnings() in R/utils.R (line 261, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
  The longest 5 functions are:
    • great() (R/great_local.R): 531 lines
    • ...
    • get_defaultly_suppported_gene_sets() (R/great_local.R): 138 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/getEnrichmentTable-dispatch.Rd
    • ...
    • man/shinyReport-dispatch.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; 628 lines (9%) are > 80 characters long.
  First few lines:
    • R/00_global.R#L43 great_opt = function(..., RESET = FALSE, ...
    • ...
    • man/submitGreatJob.rd#L110 job = submitGreatJob(gr, adv_upstrea ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2327 lines (35%) contain tabs.
  First few lines:
    • R/00_global.R#L5 "4.0.4" = "http://great.stanfo ...
    • ...
    • R/volcano.R#L157 text(size$rect$left, size$rect$top - si ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 270 lines (4%) are
not.
  First few lines:
    • R/great_client.R#L199 ranges = IRanges(st ...
    • ...
    • man/submitGreatJob.rd#L91 \item \code{\link{shinyReport,GreatObj ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the rGREAT.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.