##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('edgeR_4.10.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing edgeR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── edgeR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpISkAMi/file779045e94fbb8/edgeR
→ BiocVersion: 3.23
→ Package: edgeR
→ PackageVersion: 4.10.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/edgeR.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpISkAMi/file779045e94fbb8/edgeR
→ installDir: /tmp/RtmpISkAMi/file77904474bef29
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on edgeR ──────────────────────────────────────────────────
* 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 3.6.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpISkAMi/file779045e94fbb8/edgeR/man/dimnames.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpISkAMi/file779045e94fbb8/edgeR/man/nbinomUnitDeviance.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
ChipOnChip, Metabolomics, Cheminformatics, Preprocessing, ExonArray,
OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms,
DataImport
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 that Package field matches directory/tarball name...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* 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 (17%).
* 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:
    • edgeRUsersGuide.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 1 out of 2 code chunks = 50% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • intro.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/edgeRUsersGuide.Rnw
    • vignettes/intro.Rmd
* Checking package installation calls in R code...
* Checking for library/require of edgeR...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/classes.R (line 1, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/meanvar.R (line 47, column 22)
    • R/meanvar.R (line 49, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calcNormFactors.R (line 73, column 34)
    • ...
    • voomLmFit.R (line 242, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/catchKallisto.R (line 18, column 29)
    • ...
    • cat() in R/spliceVariants.R (line 74, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/calcNormFactors.R (line 59, column 45)
    • ...
    • R/processAmplicons.R (line 250, column 47)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/diffSpliceDGE.R (line 284, column 37)
    • ...
    • R/Seurat2PB.R (line 19, column 36)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/processAmplicons.R (line 268, column 22)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/edgeRUsersGuide.R (line 11, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
  • suppressWarnings() in R/calcNormFactors.R (line 65, column 40)
  • ...
  • suppressWarnings() in R/voomLmFit.R (line 285, column 26)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 55
functions greater than 50 lines.
  The longest 5 functions are:
    • voomLmFit() (R/voomLmFit.R): 306 lines
    • ...
    • estimateDisp.default() (R/estimateDisp.R): 193 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • asdataframe.Rd
    • ...
    • voomLmFit.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • catchSalmon.Rd
    • ...
    • Seurat2PB.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • catchSalmon.Rd
    • ...
    • Seurat2PB.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; 2469 lines (14%) are > 80 characters long.
  First few lines:
    • R/adjustedProfileLik.R#L1 adjustedProfileLik <- function(dispersio ...
    • ...
    • vignettes/intro.Rmd#L66 Robinson MD\#, McCarthy DJ\#, Smyth GK ( ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7434 lines (43%) contain tabs.
  First few lines:
    • R/addPriorCount.R#L10 # Check y ...
    • ...
    • vignettes/intro.Rmd#L47 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 673 lines (4%) are
not.
  First few lines:
    • R/estimateTagwiseDisp.R#L74 "movingave" = { ...
    • ...
    • vignettes/intro.Rmd#L17 comment = NA ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 21 NOTES
ℹ See the edgeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.