##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('crisprScore_1.17.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing crisprScore ──────────────────────────────────────────────────────
✔ Package installed successfully
── crisprScore session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRgLSFD/file7b0033e701514/crisprScore
→ BiocVersion: 3.24
→ Package: crisprScore
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/crisprScore.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpRgLSFD/file7b0033e701514/crisprScore
→ installDir: /tmp/RtmpRgLSFD/file7b003c3b4724
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on crisprScore ────────────────────────────────────────────
* 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 4.1 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 (40%).
* 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: Evaluate more vignette chunks.
ℹ 11 out of 22 code chunks = 50% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • crisprScore.Rmd
* Checking package installation calls in R code...
* Checking for library/require of crisprScore...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getCasRxRFScores.R (line 231, column 14)
    • ...
    • R/getCasRxRFScores.R (line 817, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • getCasRxRFScores.R (line 321, column 16)
    • ...
    • getCasRxRFScores.R (line 653, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/getCasRxRFScores.R (line 87, column 9)
    • ...
    • cat() in R/getCasRxRFScores.R (line 374, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getCasRxRFScores.R (line 319, column 18)
    • ...
    • R/getCasRxRFScores.R (line 836, column 9)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • T in R/getCasRxRFScores.R (line 322, column 26)
    • ...
    • F in R/getCasRxRFScores.R (line 468, column 59)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/getCasRxRFScores.R (line 405, column 15)
    • system() in R/getCasRxRFScores.R (line 479, column 13)
    • system() in R/getCasRxRFScores.R (line 512, column 13)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/getCasRxRFScores.R (line 811, column 5)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Avoid 'Sys.setenv' (found 1 times)
  • Sys.setenv() in R/getCasRxRFScores.R (line 450, column 3)
* 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:
    • getCFDScores() (R/getCFDScores.R): 72 lines
    • ...
    • .addNTpointdensities() (R/getCasRxRFScores.R): 53 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; 56 lines (2%) are > 80 characters long.
  First few lines:
    • R/getCasRxRFScores.R#L26 #' \item \code{protospacer} 23-mer proto ...
    • ...
    • vignettes/crisprScore.Rmd#L401 genome (`protospacers` argument). PAM se
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • R/getDeepHFScores.R#L71 if (.Platform$OS.type=="windows"){ ...
    • R/getDeepHFScores.R#L72 stop("DeepHF is not available for Wind ...
    • R/getDeepHFScores.R#L73 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 390 lines (15%) are
not.
  First few lines:
    • R/getCasRxRFScores.R#L57 directRepea ...
    • ...
    • vignettes/crisprScore.Rmd#L448 pams=pams) ...
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 | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the crisprScore.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.