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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('genomation_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing genomation ───────────────────────────────────────────────────────
✔ Package installed successfully
── genomation session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpN2VdUP/filea3e5930cea48c/genomation
→ BiocVersion: 3.24
→ Package: genomation
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/genomation.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpN2VdUP/filea3e5930cea48c/genomation
→ installDir: /tmp/RtmpN2VdUP/filea3e5915448dde
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on genomation ─────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: ChipOnChip
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (48%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GenomationManual.Rmd
* Checking package installation calls in R code...
* Checking for library/require of genomation...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotMatrix.R (line 110, column 20)
    • ...
    • R/readData.R (line 92, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • combineScoreMatrixList.R (line 20, column 13)
    • ...
    • scoreMatrixList.R (line 219, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/findFeatureComb.R (line 47, column 20)
    • ...
    • R/scoreMatrixList.R (line 379, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/plotMatrix.R (line 1024, column 15)
    • ...
    • R/scoreMatrixBin.R (line 365, column 20)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/plotMatrix.R (line 415, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • plotMatrix.R (line 95, column 17)
    • ...
    • scoreMatrixList.R (line 193, column 48)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/randomizeFeature.R (line 60, column 51)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/deprecated_defunct.R (line 6, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/patternMatrix.R (line 21, column 18)
  • ...
  • suppressWarnings() in R/scoreMatrix.R (line 125, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • multiHeatMatrix() (R/plotMatrix.R): 422 lines
    • ...
    • ScoreMatrixList() (R/scoreMatrixList.R): 90 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/sub-ScoreMatrix-ANY-ANY-ANY-method.Rd
    • man/sub-ScoreMatrixList-ANY-ANY-ANY-method.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • annotatGrWithGeneParts.Rd
    • ...
    • target.type.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • getRandomEnrichment-methods.Rd
    • ...
    • ScoreMatrixList-methods.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; 528 lines (7%) are > 80 characters long.
  First few lines:
    • R/combineScoreMatrixList.R#L8 #' Combine a scoreMatrix into a scoreMat
    ...
    • ...
    • vignettes/GenomationManual.Rmd#L577 dnase_query <- query(ah,
    c("wgEncodeOpen ...
ℹ NOTE: Consider 4 spaces instead of tabs; 39 lines (1%) contain tabs.
  First few lines:
    • R/plotMatrix.R#L500 max.q3 <- max(unlist(metas) + unlist(q3 ...
    • ...
    • R/readData.R#L90 stringsAsFactors=FALSE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1858 lines (25%) are
not.
  First few lines:
    • R/combineScoreMatrixList.R#L15 y <- list(...) ...
    • ...
    • vignettes/GenomationManual.Rmd#L558 )) ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the genomation.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.