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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DTA_2.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DTA ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── DTA session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDSRYWJ/file859b34b37c98b/DTA
→ BiocVersion: 3.24
→ Package: DTA
→ PackageVersion: 2.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DTA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpDSRYWJ/file859b34b37c98b/DTA
→ installDir: /tmp/RtmpDSRYWJ/file859b368313193
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DTA ────────────────────────────────────────────────────
* 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 2.10 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:
Transcriptomics, KEGG, RNASeq
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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • DTA.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • DTA.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DTA.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DTA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/DTA.dynamic.generate.R (line 36, column 19)
    • ...
    • R/DTA.dynamic.generate.R (line 78, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • DTA.dynamic.estimate.r (line 243, column 51)
    • ...
    • wtls.R (line 149, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/DTA.dynamic.estimate.r (line 80, column 27)
    • ...
    • print() in R/wtls.R (line 135, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DTA.dynamic.estimate.r (line 6, column 22)
    • ...
    • R/wtls.R (line 161, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/DTA.dynamic.estimate.r (line 86, column 105)
    • ...
    • R/wtls.R (line 64, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 70 times:
    • T in R/DTA.estimate.r (line 136, column 25)
    • ...
    • T in R/wtls.R (line 133, column 45)
* 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 8
functions greater than 50 lines.
  The longest 5 functions are:
    • DTA.singleestimate() (R/DTA.estimate.r): 1493 lines
    • ...
    • DTA.generate() (R/DTA.generate.r): 133 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/DTA.map.it.Rd
    • man/DTA.normalize.Rd
    • man/DTA.plot.it.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • DTA.map.it.Rd
    • DTA.normalize.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; 1026 lines (22%) are > 80 characters long.
  First few lines:
    • R/DTA.dynamic.estimate.r#L3 ### estimate uses an experiment, given b ...
    • ...
    • vignettes/DTA.Rnw#L430 We thank Patrick Cramer, Kerstin Maier, ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2753 lines (59%) contain tabs.
  First few lines:
    • R/DTA.dynamic.estimate.r#L7 phenomat = NULL, # phenotype matri ...
    • ...
    • vignettes/DTA.Rnw#L71 \item The histogram of the (log-)expres ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 201 lines (4%) are
not.
  First few lines:
    • R/wtls.R#L111 if(!is.matrix(A)){A = as.matrix(A)} ...
    • ...
    • vignettes/DTA.Rnw#L377 \centering ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the DTA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.