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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('iClusterPlus_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing iClusterPlus ─────────────────────────────────────────────────────
✔ Package installed successfully
── iClusterPlus session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpw2122p/fileb31ee3169507f/iClusterPlus
→ BiocVersion: 3.24
→ Package: iClusterPlus
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/iClusterPlus.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpw2122p/fileb31ee3169507f/iClusterPlus
→ installDir: /tmp/Rtmpw2122p/fileb31ee72fce27f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on iClusterPlus ───────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1.0 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...
! WARNING: Invalid BiocViews term(s):
  • 'Multi-omics'
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: 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 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • iClusterPlus.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/iClusterPlus.Rnw
* Checking package installation calls in R code...
* Checking for library/require of iClusterPlus...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/tune.iCluster2.R (line 191, column 10)
    • ...
    • R/tune.iCluster2.R (line 232, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CNregions.R (line 87, column 16)
    • ...
    • utility.R (line 34, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/CNregions.R (line 39, column 7)
    • ...
    • cat() in R/tune.iClusterPlus.R (line 88, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CNregions.R (line 26, column 10)
    • ...
    • R/utility.R (line 40, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/plotHeatmap.R (line 37, column 15)
    • R/plotHMBayes.R (line 61, column 19)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/iCluster2.R (line 45, column 14)
    • ...
    • R/tune.iClusterPlus.R (line 30, column 12)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 50 times:
    • T in R/CNregions.R (line 126, column 75)
    • ...
    • F in R/tune.iCluster2.R (line 21, column 27)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/utility.R (line 46, column 14)
* 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 19
functions greater than 50 lines.
  The longest 5 functions are:
    • mcmcBayes() (R/iClusterBayes.R): 269 lines
    • ...
    • tune.iCluster2() (R/tune.iCluster2.R): 139 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • CNregions.Rd
    • ...
    • utility.Rd
* Checking package NEWS...
* 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; 503 lines (12%) are > 80 characters long.
  First few lines:
    • R/CNregions.R#L1 ###04/12: GenomicRanges findOverlaps slo ...
    • ...
    • vignettes/iClusterPlus.Rnw#L74 A fully Bayesian latent variable model f
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 74 lines (2%) contain tabs.
  First few lines:
    • R/CNregions.R#L131 out=rbind(out,outi.medoid) ...
    • ...
    • man/tune.iClusterPlus.Rd#L61 Proc. Natl. Acad. Sci. USA 110(11):4245 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1764 lines (41%) are
not.
  First few lines:
    • R/CNregions.R#L27 ...
    • ...
    • vignettes/iClusterPlus.Rnw#L61 iCluster. PLOS ONE 7(4):e35236.\\ ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the iClusterPlus.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.