##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('BOBaFIT_1.17.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing BOBaFIT ──────────────────────────────────────────────────────────
✔ Package installed successfully
── BOBaFIT session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp3Hc0N2/file5f5c85ad16a1a/BOBaFIT
→ BiocVersion: 3.24
→ Package: BOBaFIT
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/BOBaFIT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp3Hc0N2/file5f5c85ad16a1a/BOBaFIT
→ installDir: /tmp/Rtmp3Hc0N2/file5f5c850a00970
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BOBaFIT ────────────────────────────────────────────────
* 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 2.10 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...
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 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...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/BOBaFIT.Rmd (chunk no. 14, line 154, column 28)
    • vignettes/BOBaFIT.Rmd (chunk no. 15, line 165, column 28)
    • vignettes/BOBaFIT.Rmd (chunk no. 17, line 182, column 37)
* Checking package installation calls in R code...
* Checking for library/require of BOBaFIT...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/computeNormalChromosomes.R (line 88, column 3)
    • ...
    • print() in R/PlotChrCluster.R (line 228, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Popeye.R (line 38, column 4)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • F in R/DRrefit_plot.R (line 41, column 39)
    • F in R/DRrefit_plot.R (line 42, column 38)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • DRrefit() (R/DRrefit.R): 226 lines
    • ...
    • DRrefit_plot() (R/DRrefit_plot.R): 74 lines
* Checking man page documentation...
Warning: replacing previous import 'ggplot2::geom_segment' by 'ggbio::geom_segment' when loading 'BOBaFIT'
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • pipe.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 99 lines (8%) are > 80 characters long.
  First few lines:
    • R/computeNormalChromosomes.R#L3 #' @description This function compute th
    ...
    • ...
    • vignettes/Data-Preparation.Rmd#L96 The last step is the computation of
    the ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain tabs.
  First few lines:
    • vignettes/BOBaFIT.Rmd#L59 tolerance_val = 0.25) ...
    • ...
    • vignettes/Data-Preparation.Rmd#L70 "Segment_Mean","Sample") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 387 lines (33%) are
not.
  First few lines:
    • R/computeNormalChromosomes.R#L29 tol ...
    • ...
    • vignettes/Data-Preparation.Rmd#L58 ...
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 | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the BOBaFIT.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.