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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('pipeComp_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing pipeComp ─────────────────────────────────────────────────────────
✔ Package installed successfully
── pipeComp session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpY5bNMC/fileffdac5b6187b6/pipeComp
→ BiocVersion: 3.24
→ Package: pipeComp
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/pipeComp.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpY5bNMC/fileffdac5b6187b6/pipeComp
→ installDir: /tmp/RtmpY5bNMC/fileffdac38291529
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pipeComp ───────────────────────────────────────────────
* 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 4.1 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
    • pipeComp_dea.Rmd
    • pipeComp_scRNA.Rmd
    • pipeComp.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/pipeComp_dea.Rmd
    • vignettes/pipeComp_scRNA.Rmd
    • vignettes/pipeComp.Rmd
* Checking package installation calls in R code...
* Checking for library/require of pipeComp...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/scrna_plot.R (line 356, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • aggregation.R (line 190, column 52)
    • scrna_plot.R (line 405, column 44)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/aggregation.R (line 193, column 15)
    • ...
    • print() in R/scrna_evaluationFunctions.R (line 120, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/dea_evaluationFunctions.R (line 43, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/runPipeline.R (line 111, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/runPipeline.R (line 211, column 13)
    • R/runPipeline.R (line 249, column 26)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/evalHeatmap.R (line 128, column 3)
  • ...
  • suppressWarnings() in R/scrna_plot.R (line 277, column 8)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • runPipeline() (R/runPipeline.R): 165 lines
    • ...
    • match_evaluate_multiple() (R/scrna_evaluationFunctions.R): 127 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • defaultStepAggregation.Rd
  • scrna_describeDatasets.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; 133 lines (3%) are > 80 characters long.
  First few lines:
    • R/dea_evaluationFunctions.R#L81 d <- aggregate(res[,c("FDR","TPR")], b
    ...
    • ...
    • vignettes/pipeComp.Rmd#L289 For a more complex, 'real-life' example ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1577 lines (36%) are
not.
  First few lines:
    • R/aggregation.R#L20 if ( (!is.null(path) && !is.null(resfi ...
    • ...
    • vignettes/pipeComp.Rmd#L248 2^x ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 16 NOTES
ℹ See the pipeComp.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.