##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('Rsubread_2.26.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing Rsubread ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Rsubread session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpdHLVFM/file9116941f04f79/Rsubread
→ BiocVersion: 3.23
→ Package: Rsubread
→ PackageVersion: 2.26.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rsubread.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpdHLVFM/file9116941f04f79/Rsubread
→ installDir: /tmp/RtmpdHLVFM/file91169101b5319
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Rsubread ───────────────────────────────────────────────
* 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: ChipOnChip
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...
! 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:
    • Rsubread.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Rsubread.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Rsubread...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • align.R (line 195, column 12)
    • ...
    • sublong.R (line 15, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/align.R (line 21, column 27)
    • ...
    • print() in R/txUnique.R (line 21, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/align.R (line 53, column 66)
    • ...
    • R/subjunc.R (line 34, column 39)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/cellCounts.R (line 74, column 28)
    • ...
    • R/featureCounts.R (line 58, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cellCounts.R (line 954, column 23)
    • ...
    • R/simReads.R (line 99, column 43)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 102 times:
    • T in R/atgcContent.R (line 3, column 62)
    • ...
    • T in R/txUnique.R (line 5, column 78)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • featureCounts.R (line 28, column 67)
    • findCommonVariants.R (line 16, column 20)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/cellCounts.R (line 1071, column 5)
    • system() in R/RsubreadUsersGuide.R (line 4, column 9)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/cellCounts.R (line 1248, column 3)
* 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 14
functions greater than 50 lines.
  The longest 5 functions are:
    • .one.convert.sample_index.id.to.seq() (R/cellCounts.R): 616 lines
    • ...
    • featureCounts() (R/featureCounts.R): 183 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/sublong.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • atgcContent.Rd
    • ...
    • txUnique.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • cellCounts.Rd
    • ...
    • simReads.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cellCounts.Rd
    • ...
    • simReads.Rd
* 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; 1439 lines (29%) are > 80 characters long.
  First few lines:
    • R/align.R#L10 # stop("Summary file ",sumfile," was ...
    • ...
    • vignettes/Rsubread.Rnw#L257 Please post to the Bioconductor Support ...
ℹ NOTE: Consider 4 spaces instead of tabs; 494 lines (10%) contain tabs.
  First few lines:
    • R/atgcContent.R#L3 filename <- .check_and_NormPath(filen ...
    • ...
    • man/sublong.Rd#L20 \item{nthreads}{ an integer giving the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1660 lines (33%) are
not.
  First few lines:
    • R/align.R#L2 opt <- options(show.error.messages = F ...
    • ...
    • vignettes/Rsubread.Rnw#L213 x[1:10,1:10] ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 18 NOTES
ℹ See the Rsubread.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.