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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('easyRNASeq_2.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing easyRNASeq ───────────────────────────────────────────────────────
✔ Package installed successfully
── easyRNASeq session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpaqostz/file8604b33a6bc/easyRNASeq
→ BiocVersion: 3.24
→ Package: easyRNASeq
→ PackageVersion: 2.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/easyRNASeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpaqostz/file8604b33a6bc/easyRNASeq
→ installDir: /tmp/Rtmpaqostz/file8604b19b2816a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on easyRNASeq ─────────────────────────────────────────────
* 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...
* 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: Coverage,
Normalization
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 (73%).
* 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:
    • easyRNASeq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • easyRNASeq.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/easyRNASeq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of easyRNASeq...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/easyRNASeq-internal-counts.R (line 254, column 3)
    • ...
    • require() in R/easyRNASeq-internal-methods.R (line 387, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/basename-methods.R (line 23, column 15)
    • ...
    • R/ShortRead-methods.R (line 309, column 62)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • easyRNASeq-internal-annotation.R (line 216, column 60)
    • ...
    • ShortRead-methods.R (line 485, column 40)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/easyRNASeq-counts.R (line 229, column 20)
    • ...
    • R/ShortRead-methods.R (line 471, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/easyRNASeq-accessors.R (line 187, column 30)
    • ...
    • R/ShortRead-methods.R (line 517, column 15)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • easyRNASeq-internal-AnnotParam-methods.R (line 46, column 61)
    • easyRNASeq-internal-AnnotParam-methods.R (line 49, column 28)
! WARNING: .Deprecated / .Defunct usage (found 14 times)
  • .Defunct() in R/easyRNASeq-accessors.R (line 125, column 15)
  • ...
  • .Defunct() in R/print-methods.R (line 27, column 13)
* 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 16
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/easyRNASeq-methods.R): 565 lines
    • ...
    • _anonymous_.22() (R/easyRNASeq-internal-AnnotParam-methods.R): 143 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/basename-methods.Rd
    • ...
    • man/show-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • basename-methods.Rd
    • ...
    • ShortRead-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 22% of man
pages use at least one of these tags.
  Found in files:
    • easyRNASeq-annotation-methods.Rd
    • ...
    • ShortRead-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • easyRNASeq-annotation-methods.Rd
    • ...
    • ShortRead-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; 581 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L25 #' \item \code{\link[easyRNASeq:easyRNAS ...
    • ...
    • R/ShortRead-methods.R#L517 warning(paste("The '",.name,"' fil ...
ℹ NOTE: Consider 4 spaces instead of tabs; 161 lines (2%) contain tabs.
  First few lines:
    • R/easyRNASeq-annotation.R#L53 ##' library("RnaSeqTutorial") ...
    • ...
    • R/ShortRead-methods.R#L118 #' } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2299 lines (31%) are
not.
  First few lines:
    • R/AllClasses.R#L38 Class="RNAseq", ...
    • ...
    • vignettes/easyRNASeq.Rnw#L8 Bastian Schiffthaler\footnote{bastian. ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 16 NOTES
ℹ See the easyRNASeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.