##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('consensusOV_1.35.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing consensusOV ──────────────────────────────────────────────────────
✔ Package installed successfully
── consensusOV session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpOeYuRV/file790ec7fa429f/consensusOV
→ BiocVersion: 3.24
→ Package: consensusOV
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/consensusOV.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpOeYuRV/file790ec7fa429f/consensusOV
→ installDir: /tmp/RtmpOeYuRV/file790ec73db0e11
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on consensusOV ────────────────────────────────────────────
* 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 3.6 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...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
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 (45%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/consensusOV.Rmd
* Checking package installation calls in R code...
* Checking for library/require of consensusOV...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/get.helland.subtypes.R (line 33, column 21)
    • R/get.konecny.subtypes.R (line 33, column 23)
    • R/get.konecny.subtypes.R (line 35, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/get.hao.subtypes.R (line 47, column 24)
    • R/get.hao.subtypes.R (line 51, column 25)
* 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 2
functions greater than 50 lines.
  The longest 5 functions are:
    • dataset.merging() (R/dataset.merging.R): 200 lines
    • get.consensus.subtypes() (R/get.consensus.subtypes.R): 93 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 45 lines (5%) are > 80 characters long.
  First few lines:
    • R/data.R#L7 #' @source \url{http://biorxiv.org/conte ...
    • ...
    • vignettes/consensusOV.Rmd#L134 and `r round(cor(konecny.subtypes$spearm
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 45 lines (5%) contain tabs.
  First few lines:
    • R/get.consensus.subtypes.R#L100 train.expression.matrix[,pair[1]] > t ...
    • ...
    • vignettes/consensusOV.Rmd#L124 rep(colnames(hest), each=nrow(hest))) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 134 lines (16%) are
not.
  First few lines:
    • R/dataset.merging.R#L13 method = c("union", "inter ...
    • ...
    • R/get.verhaak.subtypes.R#L58 return(list(Verhaak.subtypes=subclasse ...
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 | ⚠ 0 WARNINGS | ℹ 13 NOTES
ℹ See the consensusOV.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.