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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('iCheck_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing iCheck ───────────────────────────────────────────────────────────
✔ Package installed successfully
── iCheck session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTVv6Xd/fileb30c119ddf978/iCheck
→ BiocVersion: 3.24
→ Package: iCheck
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/iCheck.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTVv6Xd/fileb30c119ddf978/iCheck
→ installDir: /tmp/RtmpTVv6Xd/fileb30c17a473b6c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on iCheck ─────────────────────────────────────────────────
* 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 3.2.0 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: WholeGenome,
GenomeWideAssociation
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 (35%).
* 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:
    • iCheck.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • iCheck.Rnw
* Checking package installation calls in R code...
* Checking for library/require of iCheck...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/genSimData.BayesNormal.R (line 66, column 10)
    • ...
    • R/readData.R (line 106, column 8)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • genSimData.BayesNormal.R (line 33, column 16)
    • ...
    • readData.R (line 849, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/genExprSet.R (line 16, column 5)
    • ...
    • print() in R/readData.R (line 798, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/genExprSet.R (line 55, column 29)
    • ...
    • R/readData.R (line 712, column 21)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/glmWrapper.R (line 17, column 10)
    • ...
    • R/readData.R (line 362, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/readData.R (line 549, column 16)
    • R/readData.R (line 573, column 14)
    • R/readData.R (line 583, column 16)
* 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 28
functions greater than 50 lines.
  The longest 5 functions are:
    • readData.default() (R/readData.R): 431 lines
    • ...
    • pca2DPlot() (R/plotFuncs.R): 156 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/boxPlots.Rd
  • man/densityPlots.Rd
  • man/scatterPlots.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
Warning: 'rgl.init' failed, will use the null device.
See '?rgl.useNULL' for ways to avoid this warning.
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • genExprSet.Rd
* Checking package NEWS...
* 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; 136 lines (2%) are > 80 characters long.
  First few lines:
    • R/glmWrapper.R#L613 cat("Number of significant tests (ra ...
    • ...
    • vignettes/iCheck.Rnw#L632 Likelihood ratio test wrapper. Compare 2 ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/readData.R#L16 hybName=hybName, ...
    • ...
    • man/lmFitWrapper.Rd#L162 Weiliang Qiu <stwxq@channing.harvard.ed ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3298 lines (42%) are
not.
  First few lines:
    • R/genExprSet.R#L6 annotation="lumiHumanAll.db") ...
    • ...
    • vignettes/iCheck.Rnw#L706 fileName = "scatterPlots_sim.ps") ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 20 NOTES
ℹ See the iCheck.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.