##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('rifiComparative_1.13.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing rifiComparative ──────────────────────────────────────────────────
✔ Package installed successfully
── rifiComparative session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpi3Cdrp/file11f43e14ff48ff/rifiComparative
→ BiocVersion: 3.24
→ Package: rifiComparative
→ PackageVersion: 1.13.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/rifiComparative.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpi3Cdrp/file11f43e14ff48ff/rifiComparative
→ installDir: /tmp/Rtmpi3Cdrp/file11f43e6ec7b09c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rifiComparative ────────────────────────────────────────
* 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 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...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (15%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
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:
    • rifiComparative.Rmd
* Checking package installation calls in R code...
* Checking for library/require of rifiComparative...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plot_histogram.r (line 15, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • loading_fun.r (line 63, column 30)
    • ...
    • plot_histogram.r (line 18, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/empty_data_positive.r (line 10, column 5)
    • ...
    • print() in R/rifi_visualization_comparison.r (line 167, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/empty_data_negative.r (line 9, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/rifi_visualization_comparison.r (line 164, column
  9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • annotation_plot() (R/annotation_plot_comp.r): 680 lines
    • ...
    • fragment_inty() (R/fragment_inty.r): 138 lines
* Checking man page documentation...
* 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; 105 lines (2%) are > 80 characters long.
  First few lines:
    • R/adjusting_HLToInt.r#L275 # multiplica ...
    • ...
    • vignettes/rifiComparative.Rmd#L510 system.file("extdata", "gff_synechocy
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1007 lines (19%) are
not.
  First few lines:
    • R/adjusting_HLToInt.r#L75 Strand = c("+", "-"), ...
    • ...
    • vignettes/rifiComparative.Rmd#L511 )) ...
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 15 NOTES
ℹ See the rifiComparative.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.