##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('consensus_1.31.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing consensus ────────────────────────────────────────────────────────
✔ Package installed successfully
── consensus session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpu1ow7j/file78dc6498c1ed0/consensus
→ BiocVersion: 3.24
→ Package: consensus
→ PackageVersion: 1.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/consensus.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpu1ow7j/file78dc6498c1ed0/consensus
→ installDir: /tmp/Rtmpu1ow7j/file78dc67f72067c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on consensus ──────────────────────────────────────────────
* 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 3.5 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpu1ow7j/file78dc6498c1ed0/consensus/vignettes/consensus.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG, Network
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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • consensus.Rnw
* Checking package installation calls in R code...
* Checking for library/require of consensus...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/fitMandel.R (line 19, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/AllClasses.R (line 25, column 5)
    • print() in R/AllClasses.R (line 37, column 5)
    • print() in R/AllClasses.R (line 49, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotMarginals.R (line 18, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllClasses.R (line 9, column 10)
    • R/fitMandel.R (line 23, column 34)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AllClasses.R (line 24, column 13)
    • R/AllClasses.R (line 36, column 13)
    • R/AllClasses.R (line 48, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • checkMM() (R/AllClasses.R): 52 lines
* Checking man page documentation...
* 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; 90 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L9 stop(paste0("Length of names vector ...
    • ...
    • vignettes/consensus.Rnw#L136 Mandel, J. Analyzing Interlaboratory Dat ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (1%) contain tabs.
  First few lines:
    • man/consensus-package.Rd#L24 data=list(U133A, Huex, Agilent, RNASe ...
    • ...
    • man/plotOneFit.Rd#L33 data=list(U133A, Huex, Agilent, RNASe ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 210 lines (26%) are
not.
  First few lines:
    • R/AllClasses.R#L4 ...
    • ...
    • vignettes/consensus.Rnw#L134 ...
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 15 NOTES
ℹ See the consensus.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.