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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('derfinder_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing derfinder ────────────────────────────────────────────────────────
✔ Package installed successfully
── derfinder session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbrGW1D/file817b611e3365a/derfinder
→ BiocVersion: 3.24
→ Package: derfinder
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/derfinder.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpbrGW1D/file817b611e3365a/derfinder
→ installDir: /tmp/RtmpbrGW1D/file817b61bf49262
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on derfinder ──────────────────────────────────────────────
* 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 3.5.0 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (80%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of derfinder...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/annotateRegions.R (line 95, column 19)
    • ...
    • R/sampleDepth.R (line 112, column 5)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/coverageToExon.R (line 140, column 18)
    • print() in R/coverageToExon.R (line 202, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/analyzeChr.R (line 162, column 17)
    • ...
    • R/sampleDepth.R (line 83, column 17)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/calculatePvalues.R (line 316, column 13)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/Deprecated.R (line 36, column 5)
* 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 23
functions greater than 50 lines.
  The longest 5 functions are:
    • makeGenomicState() (R/makeGenomicState.R): 425 lines
    • ...
    • analyzeChr() (R/analyzeChr.R): 202 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 30% of man
pages use at least one of these tags.
  Found in files:
    • calculatePvalues.Rd
    • ...
    • regionMatrix.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • calculatePvalues.Rd
    • ...
    • regionMatrix.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; 369 lines (5%) are > 80 characters long.
  First few lines:
    • R/analyzeChr.R#L7 #' and annotating with [annotateTranscri ...
    • ...
    • vignettes/derfinder-users-guide.Rmd#L1510 ```{r vignetteBiblio, results =
    'asis', ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (0%) contain tabs.
  First few lines:
    • vignettes/derfinder-users-guide.Rmd#L1363 echo "Creating script for
    chromosome ${ ...
    • ...
    • vignettes/derfinder-users-guide.Rmd#L1406 $call ...
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 12 NOTES
ℹ See the derfinder.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.