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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('limmaGUI_1.89.0.tar.gz','quit-with-status'=TRUE)"
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── Installing limmaGUI ─────────────────────────────────────────────────────────
✔ Package installed successfully
── limmaGUI session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXNwprh/filec8e51effeaad/limmaGUI
→ BiocVersion: 3.24
→ Package: limmaGUI
→ PackageVersion: 1.89.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/limmaGUI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpXNwprh/filec8e51effeaad/limmaGUI
→ installDir: /tmp/RtmpXNwprh/filec8e517d6b907e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on limmaGUI ───────────────────────────────────────────────
* 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...
* 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (11%).
* 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:
    • extract.Rnw
    • limmaGUI.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 3 out of 3 code chunks = 100% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • limmaGUI.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/extract.Rnw
    • vignettes/limmaGUI.Rnw
* Checking package installation calls in R code...
* Checking for library/require of limmaGUI...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/main.R (line 1, column 19)
    • require() in R/main.R (line 7, column 4)
    • require() in R/main.R (line 36, column 31)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • htmlReport.R (line 446, column 20)
    • ...
    • plot.R (line 3374, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/htmlReport.R (line 231, column 5)
    • ...
    • print() in R/main.R (line 5193, column 27)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plot.R (line 1547, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/zzz.R (line 12, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/main.R (line 307, column 22)
    • ...
    • R/main.R (line 477, column 57)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • plot.R (line 3360, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 123 times)
  • <<- in R/GetBC.R (line 56, column 35)
  • ...
  • <<- in R/PlotOptions.R (line 37, column 26)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 72
functions greater than 50 lines.
  The longest 5 functions are:
    • ExportHTMLreport() (R/htmlReport.R): 899 lines
    • ...
    • OpenALimmaFile() (R/main.R): 448 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/limmaGUI.Rd
Warning in fun(libname, pkgname) : couldn't connect to display ":1.0"
Warning: loading Rplot failed
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • LGchangelog.Rd
    • limmaGUI.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; 2522 lines (19%) are > 80 characters long.
  First few lines:
    • R/GetBC.R#L18 Try(tkgrid(tklabel(tkframe2,text="Choos ...
    • ...
    • vignettes/limmaGUI.Rnw#L23 The limmaGUI Documentation can be access ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6621 lines (50%) contain tabs.
  First few lines:
    • R/GetBC.R#L3 Try(help("backgroundCorrect",help_type= ...
    • ...
    • man/limmaGUI.Rd#L362 \item{ylabel}{GetPlotLabels:arg3} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3372 lines (25%) are
not.
  First few lines:
    • R/htmlReport.R#L4 Try(NumParameterizations <- get("NumPa ...
    • ...
    • vignettes/limmaGUI.Rnw#L42 help.start() ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the limmaGUI.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.