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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('QFeatures_1.22.0.tar.gz','quit-with-status'=TRUE)"
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── Installing QFeatures ────────────────────────────────────────────────────────
✔ Package installed successfully
── QFeatures session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpzcj8l5/file87b4d53ae6d1c/QFeatures
→ BiocVersion: 3.23
→ Package: QFeatures
→ PackageVersion: 1.22.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/QFeatures.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpzcj8l5/file87b4d53ae6d1c/QFeatures
→ installDir: /tmp/Rtmpzcj8l5/file87b4d6def804e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on QFeatures ──────────────────────────────────────────────
* 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...
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 that Package field matches directory/tarball name...
* 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 (47%).
* 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:
    • Processing.Rmd
    • ...
    • readQFeatures2.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/readQFeatures2.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/Rtmpzcj8l5/file87b4d53ae6d1c/QFeatures/vignettes/readQFeatures.Rmd
* Checking package installation calls in R code...
* Checking for library/require of QFeatures...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AssayLinks.R (line 213, column 27)
    • ...
    • R/reduce.R (line 139, column 32)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • QFeatures-class.R (line 343, column 28)
    • ...
    • QFeatures-class.R (line 1308, column 24)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AssayLinks.R (line 309, column 50)
    • ...
    • R/readQFeatures.R (line 305, column 38)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/QFeatures-aggregation.R (line 310, column 27)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/QFeatures-longForm.R (line 181, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/QFeatures-aggregation.R (line 297, column 42)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/QFeatures-class.R (line 310, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.260() (R/QFeatures-aggregation.R): 78 lines
    • ...
    • display() (R/display.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AllGenerics.Rd
    • man/QFeatures-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • display.Rd
  • QFeatures-type.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • display.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • display.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; 74 lines (1%) are > 80 characters long.
  First few lines:
    • R/AssayLinks.R#L40 ##' @aliases AssayLinks AssayLink AssayL ...
    • ...
    • vignettes/Visualization.Rmd#L215 ```{r rowdatadisplay, results='markup',
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 558 lines (7%) are
not.
  First few lines:
    • R/AllGenerics.R#L8 function(assayData, colAnnota ...
    • ...
    • vignettes/Visualization.Rmd#L185 colvars = "tag") ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the QFeatures.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.