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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SmartPhos_1.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SmartPhos ────────────────────────────────────────────────────────
✔ Package installed successfully
── SmartPhos session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpK2nMox/file133dd430cc878/SmartPhos
→ BiocVersion: 3.24
→ Package: SmartPhos
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SmartPhos.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpK2nMox/file133dd430cc878/SmartPhos
→ installDir: /tmp/RtmpK2nMox/file133dd479d2d872
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SmartPhos ──────────────────────────────────────────────
* 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 4.4.0 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...
* 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 (22%).
* 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:
    • SmartPhos_Shiny.Rmd
    • SmartPhos.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SmartPhos...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/enrichment.R (line 788, column 23)
    • ...
    • R/time_series_clustering.R (line 312, column 19)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • enrichment.R (line 598, column 37)
    • ...
    • enrichment.R (line 712, column 46)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/helper.R (line 916, column 5)
    • print() in R/preprocess_proteome_phospho.R (line 207, column 7)
    • print() in R/preprocess_proteome_phospho.R (line 419, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/enrichment.R (line 668, column 21)
    • R/enrichment.R (line 786, column 16)
    • R/time_series_clustering.R (line 171, column 49)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/helper.R (line 54, column 10)
    • ...
    • R/helper.R (line 768, column 12)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/enrichment.R (line 602, column 22)
  • ...
  • suppressWarnings() in R/enrichment.R (line 637, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
  The longest 5 functions are:
    • runGSEAforPhospho() (R/enrichment.R): 347 lines
    • ...
    • preprocessProteome() (R/preprocess_proteome_phospho.R): 144 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • checkRatioMat.Rd
  • ...
  • runSmartPhos.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 multiples of 4 spaces for line indents; 1591 lines (24%) are
not.
  First few lines:
    • R/basic_visualizations.R#L39 perNA <- NULL ...
    • ...
    • vignettes/SmartPhos.Rmd#L325 ifFDR = FALSE) ...
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 | ⚠ 0 WARNINGS | ℹ 13 NOTES
ℹ See the SmartPhos.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.