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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('EBarrays_2.76.0.tar.gz','quit-with-status'=TRUE)"
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── Installing EBarrays ─────────────────────────────────────────────────────────
✔ Package installed successfully
── EBarrays session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpx9bMGJ/file7765f457a0861/EBarrays
→ BiocVersion: 3.23
→ Package: EBarrays
→ PackageVersion: 2.76.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/EBarrays.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpx9bMGJ/file7765f457a0861/EBarrays
→ installDir: /tmp/Rtmpx9bMGJ/file7765f72363413
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EBarrays ───────────────────────────────────────────────
* 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 1.8.0 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:
GeneExpression, Microarray
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 that Package field matches directory/tarball name...
* 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: 'Date:' field format is not 'YYYY-MM-DD': 2007/09/20
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* 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:
    • vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of EBarrays...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/em.algorithm.R (line 75, column 19)
    • ...
    • require() in R/plots.R (line 221, column 10)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ebfamily.R (line 188, column 19)
    • ...
    • plots.R (line 371, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ebpatterns.R (line 37, column 13)
    • ...
    • cat() in R/lnnmv-functions.R (line 75, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ebpatterns.R (line 56, column 23)
    • R/ebpatterns.R (line 57, column 27)
    • R/em.algorithm.R (line 15, column 25)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ebfamily.R (line 25, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/em.algorithm.R (line 69, column 34)
* 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 13
functions greater than 50 lines.
  The longest 5 functions are:
    • emfit1() (R/em.algorithm.R): 223 lines
    • ...
    • eb.createFamilyLNN() (R/ebfamily.R): 152 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gould.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • EBarrays-Internal.Rd
    • ebplots.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 88 lines (3%) are > 80 characters long.
  First few lines:
    • R/ebfamily.R#L25 else stop(paste("\n The only f ...
    • ...
    • vignettes/vignette.Rnw#L802 clustering and differential expression i ...
ℹ NOTE: Consider 4 spaces instead of tabs; 11 lines (0%) contain tabs.
  First few lines:
    • man/emfit.Rd#L54 \code{cluster}; if \code{type}=2, fit t ...
    • ...
    • vignettes/vignette.Rnw#L766 nint=2000, xlim=c(-0.1 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1225 lines (36%) are
not.
  First few lines:
    • R/ebfamily.R#L2 representation("character", ...
    • ...
    • vignettes/vignette.Rnw#L771 \label{fig:varsmarg-lnnmv4} ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the EBarrays.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.