##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('XVector_0.52.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing XVector ──────────────────────────────────────────────────────────
✔ Package installed successfully
── XVector session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpdVqh2J/file9a9b874518a83/XVector
→ BiocVersion: 3.23
→ Package: XVector
→ PackageVersion: 0.52.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/XVector.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpdVqh2J/file9a9b874518a83/XVector
→ installDir: /tmp/RtmpdVqh2J/file9a9b85a8871
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on XVector ────────────────────────────────────────────────
* 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...
ℹ Package version 0.52.0; pre-release
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.0.0 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...
No vignettes found.
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (55%).
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of XVector...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/SharedRaw-class.R (line 87, column 14)
    • ...
    • R/SharedVector-class.R (line 254, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • XDoubleViews-class.R (line 101, column 23)
    • XIntegerViews-class.R (line 101, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/XDoubleViews-class.R (line 50, column 5)
    • ...
    • cat() in R/XIntegerViews-class.R (line 103, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/XDoubleViews-class.R (line 211, column 17)
    • R/XIntegerViews-class.R (line 211, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • SharedRaw-class.R (line 62, column 26)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/compact-methods.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/XVector-class.R (line 130, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • .getFirstObjectInfoFromRda() (R/OnDiskRaw-class.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/intra-range-methods.Rd
    • man/XRawList-comparison.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • XRawList-comparison.Rd
    • XVector-internals.Rd
    • XVectorList-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
  Found in files:
    • XDoubleViews-class.Rd
    • XIntegerViews-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • XDoubleViews-class.Rd
    • XIntegerViews-class.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 23 lines (0%) are > 80 characters long.
  First few lines:
    • R/compact-methods.R#L58 ...
    • ...
    • man/XRawList-comparison.Rd#L44 \S4method{match}{XRawList,XRawList}(x, t
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 551 lines (11%) are
not.
  First few lines:
    • R/compact-methods.R#L28 lkup=lkup, re ...
    • ...
    • man/XVectorList-class.Rd#L46 \code{\link{compact}} ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the XVector.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.