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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('FRASER_2.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing FRASER ───────────────────────────────────────────────────────────
✔ Package installed successfully
── FRASER session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpcW6BPh/file9e54531da098e/FRASER
→ BiocVersion: 3.24
→ Package: FRASER
→ PackageVersion: 2.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/FRASER.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpcW6BPh/file9e54531da098e/FRASER
→ installDir: /tmp/RtmpcW6BPh/file9e5451d28eb46
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on FRASER ─────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Alignment,
QualityControl, DataImport
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • FRASER.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • FRASER.Rnw
* Checking package installation calls in R code...
* Checking for library/require of FRASER...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/countRNAseqData.R (line 152, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllGenerics.R (line 184, column 18)
    • ...
    • R/resultAnnotations.R (line 924, column 29)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • find_encoding_dimensions.R (line 343, column 21)
    • plotMethods.R (line 1928, column 58)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/autoencoder.R (line 58, column 13)
    • ...
    • print() in R/updateE.R (line 22, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/countRNAseqData.R (line 562, column 10)
    • ...
    • R/resultAnnotations.R (line 931, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllGenerics.R (line 176, column 19)
    • ...
    • R/saveHDF5Objects.R (line 107, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/annotationOfRanges.R (line 78, column 25)
    • R/countRNAseqData.R (line 1090, column 20)
    • R/plotMethods.R (line 1255, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/beta-binomial-testing.R (line 213, column 25)
  • <<- in R/beta-binomial-testing.R (line 217, column 22)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/annotationOfRanges.R (line 227, column 5)
  • ...
  • suppressWarnings() in R/pvalsNzscore.R (line 405, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 68
functions greater than 50 lines.
  The longest 5 functions are:
    • addPotentialImpactLabels() (R/resultAnnotations.R): 257 lines
    • ...
    • plotCountCorHeatmap.FRASER() (R/plotMethods.R): 186 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • fit.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; 77 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L171 " We assume that all ...
    • ...
    • vignettes/FRASER.Rnw#L772 sample of the whole cohort based on the ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (0%) contain tabs.
  First few lines:
    • R/calculatePSIValue.R#L129 if (file.exists(cacheFile)) file.re ...
    • ...
    • R/saveHDF5Objects.R#L128 ) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 332 lines (2%) are
not.
  First few lines:
    • R/AllGenerics.R#L171 " We assume that all ...
    • ...
    • vignettes/FRASER.Rnw#L830 splicegraph_labels="id") ...
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 18 NOTES
ℹ See the FRASER.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.