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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RTNsurvival_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RTNsurvival ──────────────────────────────────────────────────────
✔ Package installed successfully
── RTNsurvival session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCAUn7k/file126d076203d3e2/RTNsurvival
→ BiocVersion: 3.24
→ Package: RTNsurvival
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RTNsurvival.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCAUn7k/file126d076203d3e2/RTNsurvival
→ installDir: /tmp/RtmpCAUn7k/file126d074d256410
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RTNsurvival ────────────────────────────────────────────
* 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...
ℹ NOTE: Update R version dependency from 4.4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Network, Clustering, GeneExpression, GeneticVariability
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...
! 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • RTNsurvival.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RTNsurvival...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllChecks.R (line 75, column 13)
    • ...
    • R/tnsSRE.R (line 183, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllChecks.R (line 409, column 24)
    • ...
    • tnsSRE.R (line 184, column 67)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllMethods.R (line 342, column 13)
    • ...
    • cat() in R/AllSupplements.R (line 445, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllSupplements.R (line 218, column 9)
    • ...
    • R/AllSupplementsDuals.R (line 122, column 15)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AllMethods.R (line 1702, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 9 times:
    • T in R/AllChecks.R (line 496, column 69)
    • ...
    • T in R/tnsPlotCovariates.R (line 160, column 89)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllChecks.R (line 374, column 22)
    • ...
    • AllMethods.R (line 1548, column 27)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/tnsPlotCovariates.R (line 298, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
  The longest 5 functions are:
    • .tns.checks() (R/AllChecks.R): 469 lines
    • ...
    • _anonymous_.431() (R/AllMethods.R): 165 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • tnsStratification.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • tnsGSEA2-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • tnsGSEA2-methods.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; 193 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllChecks.R#L70 stop("'excludeAttribs' must be e ...
    • ...
    • vignettes/RTNsurvival.Rmd#L136 <b>Figure 4</b> - Regulon activity of in
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1031 lines (22%) are
not.
  First few lines:
    • R/AllChecks.R#L4 if (type == "survivalData"){ ...
    • ...
    • vignettes/RTNsurvival.Rmd#L131 annotation_legend = 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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the RTNsurvival.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.