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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('piano_2.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing piano ────────────────────────────────────────────────────────────
✔ Package installed successfully
── piano session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5imP55/fileff9d94a7de92b/piano
→ BiocVersion: 3.24
→ Package: piano
→ PackageVersion: 2.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/piano.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5imP55/fileff9d94a7de92b/piano
→ installDir: /tmp/Rtmp5imP55/fileff9d966827e64
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on piano ──────────────────────────────────────────────────
* 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 3.5 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (21%).
* 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:
    • piano-vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • piano-vignette.Rnw
    • Running_gene-set_analysis_with_piano.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/piano-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of piano...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calcGeneSetStat.R (line 14, column 66)
    • ...
    • writeFilesForKiwi.R (line 52, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/exploreGSAres.R (line 1051, column 11)
    • ...
    • cat() in R/runGSA.r (line 360, column 44)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/diffExp.r (line 225, column 22)
    • ...
    • R/runQC.r (line 377, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/checkLoadArg.r (line 50, column 12)
    • ...
    • R/writeFilesForKiwi.R (line 129, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/print_ArrayData.r (line 37, column 10)
! WARNING: Remove set.seed usage (found 3 times)
  • set.seed() in R/consensusHeatmap.R (line 175, column 7)
  • set.seed() in R/exploreGSAres.R (line 830, column 11)
  • set.seed() in R/exploreGSAres.R (line 851, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressWarnings() in R/exploreGSAres.R (line 1014, column 23)
  • ...
  • suppressWarnings() in R/writeFilesForKiwi.R (line 101, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 29
functions greater than 50 lines.
  The longest 5 functions are:
    • exploreGSAres() (R/exploreGSAres.R): 1081 lines
    • ...
    • runQC() (R/runQC.r): 381 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • exploreGSAres.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • exploreGSAres.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; 1071 lines (12%) are > 80 characters long.
  First few lines:
    • R/calcGeneSetStat.R#L9 geneSetStatistic <- sum(qnorm(sele ...
    • ...
    • vignettes/Running_gene-set_analysis_with_piano.Rmd#L62 Here is the output
    of `sessionInfo()` on ...
ℹ NOTE: Consider 4 spaces instead of tabs; 24 lines (0%) contain tabs.
  First few lines:
    • R/loadMAdata.r#L195 dataNorm <- as.data.frame(exprs(dat ...
    • ...
    • R/loadMAdata.r#L307 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4915 lines (56%) are
not.
  First few lines:
    • R/calcGeneSetStat.R#L2 ...
    • ...
    • vignettes/Running_gene-set_analysis_with_piano.Rmd#L50 nPerm = 500) # set
    to 5 ...
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 | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the piano.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.