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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('esetVis_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing esetVis ──────────────────────────────────────────────────────────
✔ Package installed successfully
── esetVis session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpg0wkAB/file979742729ae18/esetVis
→ BiocVersion: 3.24
→ Package: esetVis
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/esetVis.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpg0wkAB/file979742729ae18/esetVis
→ installDir: /tmp/Rtmpg0wkAB/file979741214fe60
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on esetVis ────────────────────────────────────────────────
* 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...
* 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 (18%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/esetVis-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of esetVis...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getGeneSetsForPlot.R (line 65, column 35)
    • ...
    • R/plotTopElements.R (line 184, column 61)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • esetLda.R (line 51, column 17)
    • ...
    • plotTopElements.R (line 127, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/esetLda.R (line 108, column 22)
    • ...
    • R/plotTopElements.R (line 148, column 25)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/esetTsne.R (line 110, column 9)
! WARNING: .Deprecated / .Defunct usage (found 4 times)
  • .Deprecated() in R/esetLda.R (line 96, column 17)
  • ...
  • .Deprecated() in R/esetTsne.R (line 95, column 17)
* 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:
    • ggvisPlotEset() (R/plotEset-ggvis.R): 247 lines
    • ...
    • esetSpectralMap() (R/esetSpectralMap.R): 152 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • esetPlot-class.Rd
    • ...
    • plotlyEsetPlot-class.Rd
* Checking package NEWS...
* 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; 225 lines (7%) are > 80 characters long.
  First few lines:
    • R/esetLda.R#L1 #' @title plot a biplot of a linear disc ...
    • ...
    • vignettes/esetVis-vignette.Rmd#L438 title = "Acute lymphoblastic leukemia
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1923 lines (57%) contain tabs.
  First few lines:
    • R/esetLda.R#L20 #' \item{dataPlotSamples: }{coordinate ...
    • ...
    • vignettes/esetVis-vignette.Rmd#L701 rm(ALLBCell);tmp <- gc(verbose =
    FALSE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 18 lines (1%) are not.
  First few lines:
    • vignettes/esetVis-vignette.Rmd#L194
    [hexbin](https://cran.r-project.org/we ...
    • ...
    • vignettes/esetVis-vignette.Rmd#L539 `Rtsne` function ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 12 NOTES
ℹ See the esetVis.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.