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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RPA_1.69.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RPA ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── RPA session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzwqK6W/file123ead614b503b/RPA
→ BiocVersion: 3.24
→ Package: RPA
→ PackageVersion: 1.69.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RPA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpzwqK6W/file123ead614b503b/RPA
→ installDir: /tmp/RtmpzwqK6W/file123ead60c7229d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RPA ────────────────────────────────────────────────────
* 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 3.1.1 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Microbiome,
OneChannel
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of RPA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/n.phylotypes.per.oligo.R (line 11, column 3)
    • ...
    • R/summarize.batch.R (line 54, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • estimate.hyperparameters.R (line 58, column 13)
    • ...
    • toydata.R (line 47, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/online.quantile.R (line 120, column 3)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/estimate.hyperparameters.R (line 61, column 15)
    • ...
    • R/summarize.batches.R (line 66, column 30)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 11 times:
    • T in R/internals.R (line 4, column 103)
    • ...
    • T in R/update.hyperparameters.R (line 62, column 47)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • levelmap.R (line 15, column 24)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/rpa.online.R (line 242, column 5)
    • system() in R/rpa.online.R (line 275, column 7)
* 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 12
functions greater than 50 lines.
  The longest 5 functions are:
    • rpa.online() (R/rpa.online.R): 201 lines
    • ...
    • rpa.fit() (R/rpa.fit.R): 76 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/collect.hyperparameters.Rd
    • ...
    • man/summarize.batch.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calculate.rpa.Rd
    • ...
    • updating.hyperparameters.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:
    • summarize_probedata.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • summarize_probedata.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; 248 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L2 representation(d = "array", mu. ...
    • ...
    • vignettes/RPA.Rmd#L54 * [Probabilistic analysis of probe reli ...
ℹ NOTE: Consider 4 spaces instead of tabs; 189 lines (6%) contain tabs.
  First few lines:
    • R/AllClasses.R#L3 contains = "list") ...
    • ...
    • R/updating.hyperparameters.R#L52 s2s = estimated$tau2)) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 981 lines (31%) are
not.
  First few lines:
    • R/AllClasses.R#L2 representation(d = "array", mu. ...
    • ...
    • vignettes/RPA.Rmd#L54 * [Probabilistic analysis of probe reli ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the RPA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.