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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('siggenes_1.87.0.tar.gz','quit-with-status'=TRUE)"
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── Installing siggenes ─────────────────────────────────────────────────────────
✔ Package installed successfully
── siggenes session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpotEg8m/file3ec25654fa9668/siggenes
→ BiocVersion: 3.24
→ Package: siggenes
→ PackageVersion: 1.87.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/siggenes.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpotEg8m/file3ec25654fa9668/siggenes
→ installDir: /tmp/RtmpotEg8m/file3ec2563a0e77ed
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on siggenes ───────────────────────────────────────────────
* 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: KEGG,
Regression
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...
✖ 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 (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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • siggenes.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • siggenes.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/siggenes.Rnw
* Checking package installation calls in R code...
* Checking for library/require of siggenes...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/EBAM-class.R (line 1, column 1)
    • ...
    • require() in R/sumSAM-class.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/formatSAM.R (line 11, column 30)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • add.target2href.R (line 3, column 18)
    • ...
    • z.find.R (line 30, column 33)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/args.ebam.R (line 8, column 17)
    • ...
    • print() in R/sumSAM-class.R (line 65, column 41)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/adjust.for.mt.R (line 12, column 30)
    • R/adjust.for.mt.R (line 52, column 30)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • chisq.ebam.R (line 79, column 23)
! WARNING: Remove set.seed usage (found 6 times)
  • set.seed() in R/find.a0.R (line 21, column 17)
  • ...
  • set.seed() in R/z.ebam.R (line 5, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/siggenes.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
  The longest 5 functions are:
    • siggenes2html() (R/siggenes2html.R): 201 lines
    • ...
    • wilc.ebam() (R/wilc.ebam.R): 94 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/link.genes.Rd
    • ...
    • man/siggenes2html.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • chisq.ebam.Rd
    • ...
    • z.ebam.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 48% of man
pages use at least one of these tags.
  Found in files:
    • chisq.ebam.Rd
    • ...
    • trend.stat.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • chisq.ebam.Rd
    • ...
    • trend.stat.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; 1135 lines (13%) are > 80 characters long.
  First few lines:
    • R/adjust.for.mt.R#L12 stop(paste("Negative values are only ...
    • ...
    • vignettes/siggenes.Rnw#L991 \item[Schwender, H.,] Krause, A., and Ic ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3738 lines (42%) contain tabs.
  First few lines:
    • R/add.target2href.R#L2 tmp<-strsplit(tr,split) ...
    • ...
    • siggenes/NAMESPACE#L30 fuzzy.stat, fuzzy.ebam) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2113 lines (24%) are
not.
  First few lines:
    • R/adjust.for.mt.R#L88 ...
    • ...
    • vignettes/siggenes.Rnw#L878 ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the siggenes.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.