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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ideal_2.7.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ideal ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ideal session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJgEDUq/fileb385fee1ed47/ideal
→ BiocVersion: 3.24
→ Package: ideal
→ PackageVersion: 2.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ideal.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpJgEDUq/fileb385fee1ed47/ideal
→ installDir: /tmp/RtmpJgEDUq/fileb385f659d92da
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ideal ──────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
Transcriptomics, Pathways, SystemsBiology, GO
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (31%).
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • ideal-usersguide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ideal...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/ideal.R (line 1856, column 9)
    • ...
    • require() in R/ideal.R (line 3570, column 11)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/genesignatures.R (line 27, column 22)
    • ...
    • R/ideal.R (line 2288, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/ideal.R (line 2084, column 7)
    • ...
    • print() in R/ideal.R (line 4033, column 7)
! WARNING: .Deprecated / .Defunct usage (found 7 times)
  • .Deprecated() in R/ggplotCounts.R (line 41, column 3)
  • ...
  • .Deprecated() in R/table-enhancers.R (line 18, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/ideal.R (line 76, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • ideal() (R/ideal.R): 5133 lines
    • ...
    • shake_topGOtableResult() (R/helpers.R): 70 lines
* Checking man page documentation...

ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • read_gmt.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 38% of man
pages use at least one of these tags.
  Found in files:
    • goseqTable.Rd
    • ...
    • wrapup_for_iSEE.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • goseqTable.Rd
    • ...
    • wrapup_for_iSEE.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; 785 lines (11%) are > 80 characters long.
  First few lines:
    • R/deprecated.R#L26 #' - The internally defined functions `c ...
    • ...
    • vignettes/ideal-usersguide.Rmd#L841 Improvements, suggestions, bugs,
    issues ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2808 lines (39%) are
not.
  First few lines:
    • R/genesignatures.R#L21 # TODO: some checks on the gmt file fo ...
    • ...
    • vignettes/ideal-usersguide.Rmd#L767 as_short_link = FALSE ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the ideal.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.