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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scDiagnostics_1.7.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scDiagnostics ────────────────────────────────────────────────────
✔ Package installed successfully
── scDiagnostics session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEcOvYR/file12a8bf370efa30/scDiagnostics
→ BiocVersion: 3.24
→ Package: scDiagnostics
→ PackageVersion: 1.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpEcOvYR/file12a8bf370efa30/scDiagnostics
→ installDir: /tmp/RtmpEcOvYR/file12a8bf1843f4c1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDiagnostics ──────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.4.0 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: Regression
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 (16%).
* 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:
    • AnnotationAnomalies.Rmd
    • ...
    • VisualizationTools.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpEcOvYR/file12a8bf370efa30/scDiagnostics/vignettes/AnnotationAnomalies.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpEcOvYR/file12a8bf370efa30/scDiagnostics/vignettes/DatasetMarkerGeneAlignment.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpEcOvYR/file12a8bf370efa30/scDiagnostics/vignettes/scDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpEcOvYR/file12a8bf370efa30/scDiagnostics/vignettes/VisualizationTools.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scDiagnostics...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/calculateGraphIntegration.R (line 487, column 30)
    • ...
    • R/plot.regressPCObject.R (line 731, column 32)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • boxplotPCA.R (line 70, column 36)
    • ...
    • selectCellTypes.R (line 180, column 62)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/calculateGeneShifts.R (line 267, column 14)
    • ...
    • R/plot.calculateGeneShiftsObject.R (line 203, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/calculateGeneShifts.R (line 250, column 54)
    • R/compareMarkers.R (line 154, column 54)
    • R/plot.calculateGeneShiftsObject.R (line 1299, column 14)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/downsampleSCE.R (line 67, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/calculateGeneShifts.R (line 251, column 29)
  • <<- in R/compareMarkers.R (line 155, column 28)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
  • suppressWarnings() in R/calculateGeneShifts.R (line 702, column 24)
  • ...
  • suppressWarnings() in R/projectSIR.R (line 229, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 64
functions greater than 50 lines.
  The longest 5 functions are:
    • plot.calculateGraphIntegrationObject()
    (R/plot.calculateGraphIntegrationObject.R): 950 lines
    • ...
    • plot.detectAnomalyObject() (R/plot.detectAnomalyObject.R): 536 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • calculateGeneShifts.Rd
  • plotCellTypePCA.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; 2183 lines (13%) are > 80 characters long.
  First few lines:
    • R/argumentCheck.R#L4 #' This function validates the input arg ...
    • ...
    • vignettes/VisualizationTools.Rmd#L362 ```{r SessionInfo, echo=FALSE,
    message=F ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1542 lines (9%) are
not.
  First few lines:
    • R/argumentCheck.R#L49 reference_data ...
    • ...
    • vignettes/VisualizationTools.Rmd#L351 pc_subset = 1:3) ...
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 16 NOTES
ℹ See the scDiagnostics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.