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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('phosphonormalizer_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing phosphonormalizer ────────────────────────────────────────────────
✔ Package installed successfully
── phosphonormalizer session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmphtUzWh/fileff43d72611032/phosphonormalizer
→ BiocVersion: 3.24
→ Package: phosphonormalizer
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/phosphonormalizer.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmphtUzWh/fileff43d72611032/phosphonormalizer
→ installDir: /tmp/RtmphtUzWh/fileff43d16a32acc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on phosphonormalizer ──────────────────────────────────────
* 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 4.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmphtUzWh/fileff43d72611032/phosphonormalizer/vignettes/phosphonormalizer.Rnw'
* 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...
! WARNING: 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • phosphonormalizer.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • phosphonormalizer.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/phosphonormalizer.Rnw
    • vignettes/vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of phosphonormalizer...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/normalizePhospho.R (line 63, column 7)
    • R/normalizePhospho.R (line 63, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/normalizePhospho.R (line 164, column 11)
    • R/normalizePhospho.R (line 165, column 11)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • normalizePhospho() (R/normalizePhospho.R): 160 lines
* Checking man page documentation...
* 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; 73 lines (14%) are > 80 characters long.
  First few lines:
    • R/normalizePhospho.R#L8 normalizePhospho <- function(enriched, n ...
    • ...
    • vignettes/vignette.Rmd#L67 norm <- normalizePhospho(enriched = enr ...
ℹ NOTE: Consider 4 spaces instead of tabs; 28 lines (5%) contain tabs.
  First few lines:
    • R/normalizePhospho.R#L150 if(!is.null(plot.fc)) { ...
    • ...
    • vignettes/vignette.Rmd#L69 plot.fc = plot.param) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 111 lines (22%) are
not.
  First few lines:
    • R/normalizePhospho.R#L10 #Check if all the necessary arguments ...
    • ...
    • vignettes/vignette.Rmd#L33 head(non.enriched.rd) ...
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 | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the phosphonormalizer.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.