##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('EDASeq_2.47.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing EDASeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── EDASeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUOOISj/file1acda667b17e01/EDASeq
→ BiocVersion: 3.24
→ Package: EDASeq
→ PackageVersion: 2.47.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/EDASeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUOOISj/file1acda667b17e01/EDASeq
→ installDir: /tmp/RtmpUOOISj/file1acda63eb00b6c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EDASeq ─────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Normalization,
Regression, 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 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: 'Date:' field format is not 'YYYY-MM-DD': 08-30-2011
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (79%).
* 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: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • EDASeq.Rmd
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/getLengthAndGC.R (line 181, column 17)
    • install() in R/getLengthAndGC.R (line 182, column 26)
* Checking for library/require of EDASeq...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/getLengthAndGC.R (line 186, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/functions.R (line 40, column 21)
    • ...
    • R/methods-SeqExpressionSet.R (line 446, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • functions.R (line 24, column 19)
    • ...
    • methods-SeqExpressionSet.R (line 467, column 24)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/methods-SeqExpressionSet.R (line 210, column 19)
    • R/methods-SeqExpressionSet.R (line 391, column 17)
    • R/methods-SeqExpressionSet.R (line 394, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getLengthAndGC.R (line 50, column 16)
    • ...
    • R/methods-FastqFileList.R (line 11, column 23)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Deprecated() in R/methods-SeqExpressionSet.R (line 77, column 13)
  • .Deprecated() in R/methods-SeqExpressionSet.R (line 92, column 20)
* 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:
    • getGeneLengthAndGCContent() (R/getLengthAndGC.R): 152 lines
    • .org2pkg() (R/getLengthAndGC.R): 86 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/barplot-methods.Rd
    • ...
    • man/withinLaneNormalization-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • getGeneLengthAndGCContent.Rd
    • ...
    • plotQuality-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • getGeneLengthAndGCContent.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; 65 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L38 def = function(x, which=c("me ...
    • ...
    • vignettes/EDASeq.Rmd#L513 head(round(normCounts(dataNorm)) - round ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 417 lines (25%) are
not.
  First few lines:
    • R/AllClasses.R#L2 Class = "SeqExpressionSet", ...
    • ...
    • vignettes/EDASeq.Rmd#L539 ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 13 NOTES
ℹ See the EDASeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.