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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('PhosR_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing PhosR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── PhosR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpASeM1k/fileff7206103ded/PhosR
→ BiocVersion: 3.24
→ Package: PhosR
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/PhosR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpASeM1k/fileff7206103ded/PhosR
→ installDir: /tmp/RtmpASeM1k/fileff72069ff4da3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PhosR ──────────────────────────────────────────────────
* 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 4.2.0 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: Pathways
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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (21%).
* 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:
    • PhosR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of PhosR...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plotFunctions.R (line 109, column 13)
    • print() in R/plotFunctions.R (line 126, column 9)
    • print() in R/plotFunctions.R (line 133, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/data.R (line 268, column 9)
    • ...
    • R/toolBox.R (line 515, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Impute.R (line 292, column 17)
    • ...
    • R/Signalomes.R (line 403, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/getSPS.R (line 109, column 21)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • ptImpute() (R/Impute.R): 91 lines
    • ...
    • plotKinaseNetwork() (R/plotFunctions.R): 67 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/PhosphoExperiment-methods.Rd
    • man/PhosphoExperiment-operate.Rd
    • man/PhosphoExperiment.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • kinaseSubstrateHeatmap.Rd
  • ...
  • Signalomes.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • kinaseSubstrateHeatmap.Rd
    • ...
    • Signalomes.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; 118 lines (2%) are > 80 characters long.
  First few lines:
    • R/filter.R#L25 #' 'percent' quantification in one or mo ...
    • ...
    • vignettes/PhosR.Rmd#L904 plotKinaseNetwork(KSR = L6.matrices, pre ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 99 lines (2%) are not.
  First few lines:
    • R/data.R#L270 package = pkgname, envir=parent ...
    • ...
    • vignettes/PhosR.Rmd#L828 ";", sep = "") ...
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 PhosR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.