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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('systemPipeShiny_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing systemPipeShiny ──────────────────────────────────────────────────
✔ Package installed successfully
── systemPipeShiny session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpWePrHc/file149f4560370e54/systemPipeShiny
→ BiocVersion: 3.24
→ Package: systemPipeShiny
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/systemPipeShiny.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpWePrHc/file149f4560370e54/systemPipeShiny
→ installDir: /tmp/RtmpWePrHc/file149f45a4b62b5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on systemPipeShiny ────────────────────────────────────────
* 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 4.0.0 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:
WorkflowManagement
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...
* Checking for Bioconductor software dependencies...
ℹ NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • systemPipeShiny.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
  Found in files:
    • vignettes/systemPipeShiny.Rmd
* Checking package installation calls in R code...
* Checking for library/require of systemPipeShiny...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • tab_vs_esq.R (line 184, column 56)
    • tab_vs_rnaseq_normal.R (line 577, column 48)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/spsCore.R (line 364, column 54)
    • ...
    • print() in R/tab_wf_wf.R (line 486, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/spsCore.R (line 296, column 22)
    • ...
    • R/tab_wf.R (line 137, column 34)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/tab_wf_setup.R (line 347, column 57)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/tab_admin_info.R (line 6, column 23)
    • ...
    • system() in R/tab_admin_info.R (line 128, column 26)
✖ ERROR: Avoid references to external hosting platforms
  Found in files:
    • tab_core_about.R (line 88, column 25)
    • ...
    • tab_wf.R (line 89, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 10 times)
  • <<- in R/tab_core_top.R (line 434, column 35)
  • ...
  • <<- in R/tab_wf_run.R (line 214, column 27)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/spsClasses.R (line 428, column 17)
  • ...
  • suppressMessages() in R/tab_wf_wf.R (line 486, column 23)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 65
functions greater than 50 lines.
  The longest 5 functions are:
    • wf_wfServer() (R/tab_wf_wf.R): 582 lines
    • ...
    • core_topServer() (R/tab_core_top.R): 337 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/spsAccount.Rd
    • man/spsDb.Rd
    • man/spsEncryption.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • spsEzUI.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 6% of man
pages use at least one of these tags.
  Found in files:
    • spsDb.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • spsDb.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-02interactive_funcs.R
test-03sps_tabs.R test-04imports.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 1522 lines (10%) are > 80 characters long.
  First few lines:
    • R/canvas.R#L6 #' use it under SPS projects. For you ow ...
    • ...
    • vignettes/systemPipeShiny.Rmd#L750 To read the detailed advanced
    features, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 644 lines (4%) are
not.
  First few lines:
    • R/canvas.R#L26 placement = "top") ...
    • ...
    • vignettes/systemPipeShiny.Rmd#L508 change options above and try again.
    ...
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 21 NOTES
ℹ See the systemPipeShiny.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.