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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('made4_1.87.0.tar.gz','quit-with-status'=TRUE)"
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── Installing made4 ────────────────────────────────────────────────────────────
✔ Package installed successfully
── made4 session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpduRoSb/filecc4b637718b82/made4
→ BiocVersion: 3.24
→ Package: made4
→ PackageVersion: 1.87.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/made4.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpduRoSb/filecc4b637718b82/made4
→ installDir: /tmp/RtmpduRoSb/filecc4b65c4666ba
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on made4 ──────────────────────────────────────────────────
* 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...
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpduRoSb/filecc4b637718b82/made4/man/asDataFrame.Rd'
* 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...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • introduction.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/introduction.Rmd
* Checking package installation calls in R code...
* Checking for library/require of made4...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/asDataFrame.R (line 12, column 20)
    • ...
    • R/prettyDend.R (line 35, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • asDataFrame.R (line 23, column 22)
    • ...
    • topgenes.R (line 66, column 63)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/comparelists.R (line 42, column 9)
    • ...
    • print() in R/prettyDend.R (line 48, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/asDataFrame.R (line 5, column 11)
    • ...
    • R/topgenes.R (line 41, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/asDataFrame.R (line 33, column 16)
    • ...
    • R/suppl.R (line 115, column 37)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • s.var.R (line 24, column 25)
* 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 17
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.1() (R/suppl.R): 251 lines
    • ...
    • _anonymous_.2() (R/bet.coinertia.R): 93 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/between.graph.Rd
    • ...
    • man/prettyDend.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • asDataFrame.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:
    • html3D.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • html3D.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...
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; 715 lines (15%) are > 80 characters long.
  First few lines:
    • R/asDataFrame.R#L17 stop("affy package is requir ...
    • ...
    • vignettes/introduction.Rmd#L409 | comparelists | Return the intersect, d
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 259 lines (5%) contain tabs.
  First few lines:
    • R/bet.coinertia.R#L50 U <- normalise.w(U, dudiX$l ...
    • ...
    • vignettes/introduction.Rmd#L390 | s.match.col | Use plotarrays instead.
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1210 lines (25%) are
not.
  First few lines:
    • R/asDataFrame.R#L8 if (!is.numeric(indata)) ...
    • ...
    • vignettes/introduction.Rmd#L291 **cia** calls **coinertia** in the *ade
    ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 20 NOTES
ℹ See the made4.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.