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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('AgiMicroRna_2.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AgiMicroRna ──────────────────────────────────────────────────────
✔ Package installed successfully
── AgiMicroRna session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvbGJv9/file50e302e10be35/AgiMicroRna
→ BiocVersion: 3.24
→ Package: AgiMicroRna
→ PackageVersion: 2.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/AgiMicroRna.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvbGJv9/file50e302e10be35/AgiMicroRna
→ installDir: /tmp/RtmpvbGJv9/file50e30675028f5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AgiMicroRna ────────────────────────────────────────────
* 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 2.10 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...
! WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData, Workflow)
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 (71%).
* 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:
    • AgiMicroRna.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • AgiMicroRna.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/AgiMicroRna.Rnw
* Checking package installation calls in R code...
* Checking for library/require of AgiMicroRna...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/HeatMapMicroRna.R (line 4, column 1)
    • ...
    • require() in R/significantMicroRna.R (line 6, column 9)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AgiMicroRNA-classes.R (line 35, column 33)
    • ...
    • tgsMicroRna.R (line 52, column 43)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AgiMicroRNA-classes.R (line 36, column 25)
    • ...
    • cat() in R/writeEset.R (line 39, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/basicLimma.R (line 30, column 12)
    • ...
    • R/writeEset.R (line 33, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/miRNA.htmlpage.R (line 55, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 15 times:
    • F in R/significantMicroRna.R (line 96, column 60)
    • ...
    • F in R/writeEset.R (line 35, column 23)
* 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 15
functions greater than 50 lines.
  The longest 5 functions are:
    • `significantMicroRna`() (R/significantMicroRna.R): 193 lines
    • ...
    • `cvArray`() (R/cvArray.R): 95 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/dd.micro.Rd
    • man/ddPROC.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/boxplotMicroRna.Rd
    • ...
    • man/writeEset.Rd


✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • basicLimma.Rd
    • ...
    • writeEset.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 31% of man
pages use at least one of these tags.
  Found in files:
    • basicLimma.Rd
    • ...
    • writeEset.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • basicLimma.Rd
    • ...
    • writeEset.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 318 lines (7%) are > 80 characters long.
  First few lines:
    • R/AgiMicroRNA-classes.R#L122 # require(methods, quietly = TRUE ...
    • ...
    • vignettes/AgiMicroRna.Rnw#L887 of the genes that have been analyzed and
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1492 lines (33%) contain tabs.
  First few lines:
    • R/AgiMicroRNA-classes.R#L11 if(is.atomic(x)) { ...
    • ...
    • vignettes/AgiMicroRna.Rnw#L839 verbose=TRUE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 453 lines (10%) are
not.
  First few lines:
    • R/basicLimma.R#L6 if (is.null(nrow(exprs(eset)))) { ...
    • ...
    • vignettes/AgiMicroRna.Rnw#L653 makePLOT=FALSE, ...
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 | ⚠ 6 WARNINGS | ℹ 17 NOTES
ℹ See the AgiMicroRna.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.