##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('biocViews_1.80.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing biocViews ────────────────────────────────────────────────────────
✔ Package installed successfully
── biocViews session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0xIg9f/file74301232de402/biocViews
→ BiocVersion: 3.23
→ Package: biocViews
→ PackageVersion: 1.80.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biocViews.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp0xIg9f/file74301232de402/biocViews
→ installDir: /tmp/Rtmp0xIg9f/file7430130f592b8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on biocViews ──────────────────────────────────────────────
* 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/Rtmp0xIg9f/file74301232de402/biocViews/man/getCurrentbiocViews.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: BiocViews
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 (30%).
* 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: Evaluate more vignette chunks.
ℹ 6 out of 11 code chunks = 54% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/createReposHtml.Rmd
    • vignettes/HOWTO-BCV.Rmd
* Checking package installation calls in R code...
* Checking for library/require of biocViews...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/build_dbs.R (line 68, column 55)
    • ...
    • R/recommendBiocViews.R (line 398, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • showvoc.R (line 6, column 12)
    • showvoc.R (line 11, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/getPackageNEWS.R (line 121, column 13)
    • ...
    • cat() in R/showvoc.R (line 17, column 2)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getPackageNEWS.R (line 41, column 14)
    • ...
    • R/repository.R (line 823, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/pump.R (line 27, column 17)
    • R/pump.R (line 40, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/getPackageNEWS.R (line 134, column 33)
    • R/getPackageNEWS.R (line 154, column 25)
    • R/repository.R (line 115, column 25)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • htmlValue-methods.R (line 227, column 64)
    • htmlValue-methods.R (line 231, column 60)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/getPackageNEWS.R (line 42, column 9)
    • ...
    • system() in R/repository.R (line 94, 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 14
functions greater than 50 lines.
  The longest 5 functions are:
    • write_VIEWS() (R/repository.R): 240 lines
    • ...
    • readPackageInfo() (R/getPackNames.R): 66 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/build-dbs.Rd
    • ...
    • man/writeTopLevelView.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • extractManuals.Rd
    • ...
    • writeTopLevelView.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:
    • getPackageTitles.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getPackageTitles.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • man/extractNEWS.Rd
    • ...
    • R/getPackageNEWS.R
* 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; 70 lines (2%) are > 80 characters long.
  First few lines:
    • R/dump_concept.R#L1 #' produce character stream for use with ...
    • ...
    • vignettes/HOWTO-BCV.Rmd#L85 3. re-generate the related HTML packages ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 650 lines (19%) are
not.
  First few lines:
    • R/AllClasses.R#L8 representation("Package"="chara ...
    • ...
    • vignettes/createReposHtml.Rmd#L161 dom$addNode(htmlValue(secObj)) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the biocViews.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.