##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ShortRead_1.70.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing ShortRead ────────────────────────────────────────────────────────
✔ Package installed successfully
── ShortRead session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxOvd7J/file944075c4b23eb/ShortRead
→ BiocVersion: 3.23
→ Package: ShortRead
→ PackageVersion: 1.70.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ShortRead.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpxOvd7J/file944075c4b23eb/ShortRead
→ installDir: /tmp/RtmpxOvd7J/file944073f44bd37
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ShortRead ──────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpxOvd7J/file944075c4b23eb/ShortRead/man/ShortRead-deprecated.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage,
Alignment, RNASeq, ImmunoOncology
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...
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 (73%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Overview.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ShortRead...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllUtilities.R (line 8, column 14)
    • ...
    • R/spViewPerFeature.R (line 5, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllClasses-Base.R (line 251, column 30)
    • ...
    • SnapshotFunction-helpers.R (line 321, column 34)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllClasses-Base.R (line 339, column 11)
    • ...
    • cat() in R/AllUtilities.R (line 99, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/methods-Misc.R (line 65, column 12)
    • ...
    • R/spViewPerFeature.R (line 39, column 28)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/methods-QualityScore.R (line 65, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • methods-.QA.R (line 9, column 30)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Defunct() in R/methods-ExperimentPath.R (line 33, column 5)
  • .Defunct() in R/methods-SRFilter.R (line 90, column 5)
  • .Defunct() in R/readQseq.R (line 85, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 7 times)
  • <<- in R/methods-FastqSampler.R (line 11, column 17)
  • ...
  • <<- in R/SpTrellis.R (line 74, column 26)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • .qa_SolexaExport_lane() (R/methods-SolexaExportQA.R): 126 lines
    • ...
    • _anonymous_.214() (R/methods-SolexaExportQA.R): 72 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/deprecated.Rd
    • ...
    • man/SRFilterResult-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AlignedDataFrame.Rd
  • ...
  • SRFilter-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • readIntensities.Rd
    • SolexaPath-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • readIntensities.Rd
    • SolexaPath-class.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; 72 lines (0%) are > 80 characters long.
  First few lines:
    • R/methods-.QA.R#L5 "rbind,.QA-method ...
    • ...
    • vignettes/Overview.Rmd#L334 `r Biocpkg("Biostrings")`, `r Biocpkg("B ...
ℹ NOTE: Consider 4 spaces instead of tabs; 122 lines (1%) contain tabs.
  First few lines:
    • R/methods-BowtieQA.R#L8 verbose=FALSE) ...
    • ...
    • man/SRFilterResult-class.Rd#L100 "SRFilterResult")}: logic operations on
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4206 lines (26%) are
not.
  First few lines:
    • R/AllClasses-Base.R#L7 levels=.STRAND_LEVELS) ...
    • ...
    • vignettes/Overview.Rmd#L111 "ERR127302_1_subset.fa ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the ShortRead.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.