##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('clusterExperiment_2.33.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing clusterExperiment ────────────────────────────────────────────────
✔ Package installed successfully
── clusterExperiment session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpdCzsEe/file75ebd4b37fd95/clusterExperiment
→ BiocVersion: 3.24
→ Package: clusterExperiment
→ PackageVersion: 2.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/clusterExperiment.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpdCzsEe/file75ebd4b37fd95/clusterExperiment
→ installDir: /tmp/RtmpdCzsEe/file75ebd35cc2fc4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on clusterExperiment ──────────────────────────────────────
* 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 3.6.0 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:
ImmunoOncology, 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...
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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (38%).
* 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:
    • clusterExperimentTutorial.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/largeDataSets.Rmd
* Checking package installation calls in R code...
* Checking for library/require of clusterExperiment...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllChecks.R (line 176, column 22)
    • ...
    • R/workflowClusters.R (line 75, column 101)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllChecks.R (line 244, column 42)
    • ...
    • subset.R (line 213, column 53)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllHelper.R (line 383, column 25)
    • ...
    • cat() in R/seqCluster.R (line 383, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllHelper.R (line 88, column 22)
    • ...
    • R/workflowClusters.R (line 87, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllChecks.R (line 25, column 14)
    • ...
    • R/workflowClusters.R (line 125, column 111)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AllChecks.R (line 25, column 20)
    • ...
    • R/workflowClusters.R (line 166, column 56)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • rsec.R (line 212, column 67)
! WARNING: Remove set.seed usage (found 5 times)
  • set.seed() in R/AllChecks.R (line 391, column 9)
  • ...
  • set.seed() in R/plottingHelpers.R (line 232, column 9)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Deprecated() in R/deprecateFunctions.R (line 23, column 17)
  • .Deprecated() in R/deprecateFunctions.R (line 31, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 4 times)
  • <<- in R/mergeClusters.R (line 357, column 55)
  • ...
  • <<- in R/updateObject.R (line 206, column 70)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
  • suppressWarnings() in R/builtInClusterFunctions.R (line 165, column 5)
  • ...
  • suppressWarnings() in R/plotHeatmap.R (line 890, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 44
functions greater than 50 lines.
  The longest 5 functions are:
    • .checkArgs() (R/internalClusterFunctions.R): 520 lines
    • ...
    • seqCluster() (R/seqCluster.R): 249 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/clusterExperiment-deprecated.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • assignUnassigned.Rd
    • ...
    • workflowClusters.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 39% of man
pages use at least one of these tags.
  Found in files:
    • assignUnassigned.Rd
    • ...
    • workflowClusters.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • assignUnassigned.Rd
    • ...
    • workflowClusters.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; 2243 lines (11%) are > 80 characters long.
  First few lines:
    • R/addClusterings.R#L38 definition = function(x, y, clusterTyp ...
    • ...
    • vignettes/largeDataSets.Rmd#L70 * *known problem interacting with `mbkme
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2523 lines (13%) contain tabs.
  First few lines:
    • R/AllChecks.R#L62 if(!all(testConsecIntegers)) ret ...
    • ...
    • vignettes/clusterExperimentTutorial.Rmd#L622
    clusterFunction="hierarchical01", seque ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2913 lines (15%) are
not.
  First few lines:
    • R/addClusterings.R#L36 f = "addClusterings", ...
    • ...
    • vignettes/clusterExperimentTutorial.Rmd#L2034 ncores=1, random.seed=1762
    ...
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 | ⚠ 4 WARNINGS | ℹ 22 NOTES
ℹ See the clusterExperiment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.