##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('tkWidgets_1.90.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing tkWidgets ────────────────────────────────────────────────────────
✔ Package installed successfully
── tkWidgets session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpN0HBXL/file99dc228613ccd/tkWidgets
→ BiocVersion: 3.23
→ Package: tkWidgets
→ PackageVersion: 1.90.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/tkWidgets.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpN0HBXL/file99dc228613ccd/tkWidgets
→ installDir: /tmp/RtmpN0HBXL/file99dc2493d1780
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on tkWidgets ──────────────────────────────────────────────
* 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 2.0.0 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...
* 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: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • importWizard.Rnw
    • tkWidgets.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • importWizard.Rnw
    • tkWidgets.Rnw
* Checking package installation calls in R code...
* Checking for library/require of tkWidgets...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/eExplorer.R (line 11, column 9)
    • ...
    • require() in R/zzz.R (line 7, column 42)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/argsWidget.R (line 23, column 25)
    • ...
    • R/vExplorer.R (line 158, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • args2XML.R (line 25, column 14)
    • ...
    • widgetRender.R (line 149, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/args2XML.R (line 11, column 18)
    • R/importWizard.R (line 791, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/eExplorer.R (line 12, column 14)
    • R/guess.sep.R (line 26, column 18)
    • R/hasChar.R (line 18, column 14)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/pExplorer.R (line 309, column 26)
    • system() in R/pExplorer.R (line 325, column 4)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 112 times)
  • <<- in R/DPExplorer.R (line 30, column 17)
  • ...
  • <<- in R/widgetRender.R (line 121, column 53)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 33
functions greater than 50 lines.
  The longest 5 functions are:
    • tkphenoData() (R/tkphenoData.R): 475 lines
    • ...
    • pExplorer() (R/pExplorer.R): 215 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • tkMIAME.Rd
  • tkphenoData.Rd
  • tkSampleNames.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; 66 lines (1%) are > 80 characters long.
  First few lines:
    • R/importPhenoData.R#L86 filename <- getName4Data("ph ...
    • ...
    • man/tkSampleNames.Rd#L36 \seealso{\code{\link[Biobase:class.Annot ...
ℹ NOTE: Consider 4 spaces instead of tabs; 11 lines (0%) contain tabs.
  First few lines:
    • R/objectBrowser.R#L292 command = up) ...
    • ...
    • man/fileBrowser.Rd#L45 be specified.  Examples of validity fu ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1666 lines (20%) are
not.
  First few lines:
    • R/appendSepDir.R#L8 toCheck <- list.files(path) ...
    • ...
    • vignettes/tkWidgets.Rnw#L227 \end{center} ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the tkWidgets.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.