##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('S4Vectors_0.51.1.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing S4Vectors ────────────────────────────────────────────────────────
✔ Package installed successfully
── S4Vectors session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpbd2lwq/file1c66d75d4120dc/S4Vectors
→ BiocVersion: 3.24
→ Package: S4Vectors
→ PackageVersion: 0.51.1
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/S4Vectors.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpbd2lwq/file1c66d75d4120dc/S4Vectors
→ installDir: /tmp/Rtmpbd2lwq/file1c66d71ed49dd9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on S4Vectors ──────────────────────────────────────────────
* 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...
ℹ Package version 0.51.1; pre-release
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1.0 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...
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 (20%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • S4QuickOverview.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/RleTricks.Rmd
    • vignettes/S4QuickOverview.Rmd
* Checking package installation calls in R code...
* Checking for library/require of S4Vectors...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/aggregate-methods.R (line 104, column 9)
    • ...
    • R/SimpleList-class.R (line 121, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • integer-utils.R (line 479, column 38)
    • ...
    • show-utils.R (line 34, column 65)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/DataFrame-class.R (line 1025, column 5)
    • ...
    • print() in R/TransposedDataFrame-class.R (line 240, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/DataFrame-class.R (line 453, column 29)
    • R/normarg-utils.R (line 366, column 17)
    • R/S4-utils.R (line 284, column 30)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Factor-class.R (line 297, column 22)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • DataFrame-class.R (line 59, column 27)
    • ...
    • DataFrame-class.R (line 1053, column 27)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/normarg-utils.R (line 44, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/Vector-comparison.Rd
ℹ Found @ in vignettes/S4QuickOverview.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/FilterRules-class.R (line 239, column 23)
  • <<- in R/FilterRules-class.R (line 240, column 32)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
  • suppressWarnings() in R/DataFrame-class.R (line 331, column 20)
  • ...
  • suppressWarnings() in R/subsetting-utils.R (line 408, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.276() (R/Rle-class.R): 101 lines
    • ...
    • as.data.frame.DataFrame() (R/DataFrame-class.R): 72 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/DataFrame-combine.Rd
    • ...
    • man/subsetting-utils.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • bindROWS.Rd
  • ...
  • Vector-setops.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • LLint-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • LLint-class.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 (0%) are > 80 characters long.
  First few lines:
    • R/DataFrame-combine.R#L223 stop(wmsg("DataFrames must h ...
    • ...
    • vignettes/S4VectorsOverview.Rmd#L195 ```{r figshiftcorrs, eps=FALSE,
    fig.alig ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3952 lines (17%) are
not.
  First few lines:
    • R/aggregate-methods.R#L61 frequency=N ...
    • ...
    • vignettes/S4VectorsOverview.Rmd#L250 FUN=function(x, y) {var(x, y) ...
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 | ⚠ 3 WARNINGS | ℹ 20 NOTES
ℹ See the S4Vectors.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.