##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('tximeta_1.31.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing tximeta ──────────────────────────────────────────────────────────
✔ Package installed successfully
── tximeta session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxXbHYR/file23e44f4c9561a8/tximeta
→ BiocVersion: 3.24
→ Package: tximeta
→ PackageVersion: 1.31.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/tximeta.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpxXbHYR/file23e44f4c9561a8/tximeta
→ installDir: /tmp/RtmpxXbHYR/file23e44f5f8f1710
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on tximeta ────────────────────────────────────────────────
* 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 4.1.0 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...
! WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData, Workflow)
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...
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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (65%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • rmarkdown
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • tximeta.Rmd
* Checking package installation calls in R code...
* Checking for library/require of tximeta...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/duplicateTxps.R (line 53, column 25)
    • ...
    • R/tximeta.R (line 569, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/addIds.R (line 64, column 11)
    • ...
    • R/tximeta.R (line 506, column 15)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/duplicateTxps.R (line 18, column 11)
    • ...
    • R/tximeta.R (line 555, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 10 times)
  • suppressWarnings() in R/addRanges.R (line 152, column 9)
  • ...
  • suppressMessages() in R/summarizeToGene.R (line 23, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • tximeta() (R/tximeta.R): 213 lines
    • ...
    • getTxDb() (R/get_txome_txpdata.R): 121 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addCDS.Rd
    • ...
    • retrieveCDNA.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • retrieveCDNA.Rd
    • updateMetadata.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • retrieveCDNA.Rd
    • updateMetadata.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; 166 lines (4%) are > 80 characters long.
  First few lines:
    • R/addIds.R#L11 #' @param column the name of the new ID ...
    • ...
    • vignettes/tximeta.Rmd#L789 #gtfFTP <- "ftp://path/to/custom/Drosoph ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/addIds.R#L28 #' library(org.Dm.eg.db) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1201 lines (29%) are
not.
  First few lines:
    • R/addIds.R#L33 missingMetadata(se, summarize=FALSE) ...
    • ...
    • vignettes/tximeta.Rmd#L913 bfcloc <- tempdir() ...
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 v1.49.6 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the tximeta.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.