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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('iSEE_2.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing iSEE ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── iSEE session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzKxm9y/filec532d671a8f28/iSEE
→ BiocVersion: 3.24
→ Package: iSEE
→ PackageVersion: 2.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/iSEE.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpzKxm9y/filec532d671a8f28/iSEE
→ installDir: /tmp/RtmpzKxm9y/filec532d446a195e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on iSEE ───────────────────────────────────────────────────
* 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: Sequencing,
Coverage, DataImport
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (19%).
* 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:
    • basic.Rmd
    • ...
    • voice.Rmd
* Checking package installation calls in R code...
* Checking for library/require of iSEE...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/utils_tooltip.R (line 25, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/constants.R (line 151, column 28)
    • ...
    • R/iSEE-options.R (line 134, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ExperimentColorMap.R (line 845, column 18)
! WARNING: .Deprecated / .Defunct usage (found 34 times)
  • .Deprecated() in R/family_ColumnDotPlot.R (line 138, column 9)
  • ...
  • .Deprecated() in R/panel_ComplexHeatmapPlot.R (line 355, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/iSEE-options.R (line 29, column 36)
  • <<- in R/iSEE-options.R (line 33, column 49)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 60
functions greater than 50 lines.
  The longest 5 functions are:
    • .create_visual_box_for_complexheatmap() (R/interface_visual.R): 325 lines
    • ...
    • _anonymous_.944() (R/family_DotPlot.R): 151 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ColumnDataPlot-class.Rd
    • ...
    • man/visual-parameters-generics.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addCustomLabelsCommands.Rd
    • ...
    • visual-parameters-generics.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; 3593 lines (15%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L28 #' An overview of the generics for defin ...
    • ...
    • vignettes/voice.Rmd#L121 - "**Send selection to <Reduced dimensio ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/jitterPoints.R#L64 current <- data.frame(X=X[grp], Y=Y[gr ...
    • ...
    • R/jitterPoints.R#L76 } else if (nlevels(Y)!=1L && nlevels(X ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 114 lines (0%) are
not.
  First few lines:
    • R/createLandingPage.R#L107 seUI(.initializeSE), ...
    • ...
    • vignettes/custom.Rmd#L86 This may be `NULL` if no transmitting ...
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 | ⚠ 2 WARNINGS | ℹ 12 NOTES
ℹ See the iSEE.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.