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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('mgsa_1.61.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mgsa ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── mgsa session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpcBaDwB/filed78d75f769fec/mgsa
→ BiocVersion: 3.24
→ Package: mgsa
→ PackageVersion: 1.61.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/mgsa.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpcBaDwB/filed78d75f769fec/mgsa
→ installDir: /tmp/RtmpcBaDwB/filed78d710785993
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mgsa ───────────────────────────────────────────────────
* 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 2.14.0 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • mgsa.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • mgsa.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/mgsa.Rnw
* Checking package installation calls in R code...
* Checking for library/require of mgsa...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/MgsaGoSets-class.R (line 44, column 9)
    • ...
    • require() in R/MgsaResults-class.R (line 339, column 25)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dottedTable.R (line 3, column 14)
    • ...
    • R/MgsaSets-class.R (line 292, column 44)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dottedTable.R (line 10, column 40)
    • ...
    • MgsaSets-class.R (line 102, column 72)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/dottedTable.R (line 3, column 12)
    • ...
    • R/MgsaResults-class.R (line 342, column 28)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/mgsa-methods.R (line 149, column 30)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/MgsaResults-class.R (line 379, column 50)
* 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:
    • def() (R/MgsaSets-class.R): 72 lines
    • ...
    • readGAF() (R/MgsaGoSets-class.R): 58 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/example-go.Rd
    • man/example-o.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/createMgsaGoSets.Rd
    • man/plot-MgsaResults-method.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • alphaMcmcPost-methods.Rd
    • ...
    • subMgsaSets-methods.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 245 lines (11%) are > 80 characters long.
  First few lines:
    • R/mgsa-methods.R#L10 mgsa.trampoline <- function(o, sets, n, ...
    • ...
    • vignettes/mgsa.Rnw#L124 In case \texttt{mgsa} must be run on sev ...
ℹ NOTE: Consider 4 spaces instead of tabs; 563 lines (25%) contain tabs.
  First few lines:
    • R/dottedTable.R#L3 nc = sapply(x, nchar) ...
    • ...
    • vignettes/mgsa.Rnw#L112 ) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 19 lines (1%) are not.
  First few lines:
    • R/mgsa-methods.R#L58 ...
    • ...
    • vignettes/mgsa.Rnw#L95 ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 6 WARNINGS | ℹ 14 NOTES
ℹ See the mgsa.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.