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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ctsGE_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ctsGE ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ctsGE session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpQt8mGX/file7bde61f2a0241/ctsGE
→ BiocVersion: 3.24
→ Package: ctsGE
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ctsGE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpQt8mGX/file7bde61f2a0241/ctsGE
→ installDir: /tmp/RtmpQt8mGX/file7bde651c3a0a3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ctsGE ──────────────────────────────────────────────────
* 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 3.2 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...
* 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (12%).
* 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:
    • ctsGE.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ctsGE.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ctsGE...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ClustIndexes.R (line 69, column 35)
    • ...
    • PlotIndexesClust.R (line 94, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ctsGE.R (line 107, column 9)
    • print() in R/ctsGEShinyApp.R (line 71, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ClustIndexes.R (line 56, column 14)
    • ...
    • R/PreparingTheIndexes.R (line 137, column 26)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ctsGE.R (line 65, column 22)
    • R/ctsGE.R (line 76, column 22)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/ctsGEShinyApp.R (line 110, column 17)
  • set.seed() in R/PlotIndexesClust.R (line 41, column 5)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • ctsGEShinyApp() (R/ctsGEShinyApp.R): 121 lines
    • ...
    • server() (R/ctsGEShinyApp.R): 59 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • ctsGEShinyApp.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • ctsGEShinyApp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ctsGEShinyApp.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 15 lines (1%) are > 80 characters long.
  First few lines:
    • R/ClustIndexes.R#L20 #' percentage of variance explained as ...
    • ...
    • vignettes/ctsGE.Rmd#L289 step altogether and directly view a spec ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 40 lines (4%) are not.
  First few lines:
    • R/ClustIndexes.R#L65 ...
    • ...
    • vignettes/ctsGE.Rmd#L276 ...
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 | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the ctsGE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.