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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('PROPER_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing PROPER ───────────────────────────────────────────────────────────
✔ Package installed successfully
── PROPER session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8a6to9/file103860388b31dc/PROPER
→ BiocVersion: 3.24
→ Package: PROPER
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/PROPER.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp8a6to9/file103860388b31dc/PROPER
→ installDir: /tmp/Rtmp8a6to9/file1038608263151
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PROPER ─────────────────────────────────────────────────
* 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 3.3 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:
GeneExpression, GeneTarget
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (100%).
* 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:
    • PROPER.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 13 out of 15 code chunks = 86% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • PROPER.Rnw
* Checking package installation calls in R code...
* Checking for library/require of PROPER...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/DEdetection.R (line 11, column 5)
    • ...
    • require() in R/estParam.R (line 34, column 5)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plots.R (line 7, column 19)
    • ...
    • simfuns.R (line 104, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/power.R (line 199, column 5)
    • print() in R/power.R (line 250, column 5)
    • cat() in R/simfuns.R (line 86, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DEdetection.R (line 14, column 12)
    • ...
    • R/simOptions.util.R (line 91, column 9)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/estParam.R (line 58, column 3)
  • set.seed() in R/simfuns.R (line 81, column 5)
  • set.seed() in R/simOptions.2grp.R (line 41, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/estParam.R (line 71, column 6)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • comparePower() (R/power.R): 114 lines
    • runSims() (R/simfuns.R): 82 lines
    • RNAseq.SimOptions.2grp() (R/simOptions.2grp.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/historicalData.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plots.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • comparePower.Rd
    • ...
    • summaryPower.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 70% of man
pages use at least one of these tags.
  Found in files:
    • comparePower.Rd
    • ...
    • summaryPower.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • comparePower.Rd
    • ...
    • summaryPower.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; 115 lines (5%) are > 80 characters long.
  First few lines:
    • R/plots.R#L44 arrows(stratas, power.lo[,j] ...
    • ...
    • vignettes/PROPER.Rnw#L431 \newblock PROPER: Comprehensive Power Ev ...
ℹ NOTE: Consider 4 spaces instead of tabs; 46 lines (2%) contain tabs.
  First few lines:
    • R/simOptions.util.R#L58 lOD=sample(input, ngenes, replace=TRUE ...
    • ...
    • man/runSims.Rd#L32 must be a vector of the same length as ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 368 lines (16%) are
not.
  First few lines:
    • R/estParam.R#L9 n0 <- ncol(x) ...
    • ...
    • vignettes/PROPER.Rnw#L425 expression detection in rna-seq data. ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 17 NOTES
ℹ See the PROPER.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.