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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ConsensusClusterPlus_1.76.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ConsensusClusterPlus ─────────────────────────────────────────────
✔ Package installed successfully
── ConsensusClusterPlus session metadata ───────────────────────────────────────
→ sourceDir: /tmp/RtmpykXiKA/file75adc68588203/ConsensusClusterPlus
→ BiocVersion: 3.23
→ Package: ConsensusClusterPlus
→ PackageVersion: 1.76.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ConsensusClusterPlus.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpykXiKA/file75adc68588203/ConsensusClusterPlus
→ installDir: /tmp/RtmpykXiKA/file75adc67de7614
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ConsensusClusterPlus ───────────────────────────────────
* 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...
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': 2020-4-24
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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:
    • ConsensusClusterPlus.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ConsensusClusterPlus.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/ConsensusClusterPlus.Rnw (chunk no. 3, line 22, column 39)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ConsensusClusterPlus.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ConsensusClusterPlus...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ConsensusClusterPlus.R (line 273, column 12)
    • ...
    • ConsensusClusterPlus.R (line 652, column 18)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ConsensusClusterPlus.R (line 23, column 9)
    • ...
    • R/ConsensusClusterPlus.R (line 663, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ConsensusClusterPlus.R (line 161, column 15)
    • R/ConsensusClusterPlus.R (line 369, column 15)
    • R/ConsensusClusterPlus.R (line 433, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ConsensusClusterPlus.R (line 411, column 19)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 22 times:
    • T in R/ConsensusClusterPlus.R (line 96, column 24)
    • ...
    • F in R/ConsensusClusterPlus.R (line 654, column 53)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ConsensusClusterPlus.R (line 168, column 20)
    • ...
    • ConsensusClusterPlus.R (line 394, column 49)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/ConsensusClusterPlus.R (line 25, column 3)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • ConsensusClusterPlus() (R/ConsensusClusterPlus.R): 210 lines
    • ccRun() (R/ConsensusClusterPlus.R): 176 lines
    • calcICL() (R/ConsensusClusterPlus.R): 90 lines
* Checking man page documentation...
* 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; 171 lines (16%) are > 80 characters long.
  First few lines:
    • R/ConsensusClusterPlus.R#L37 ## if d is a distance matrix, fix ...
    • ...
    • vignettes/ConsensusClusterPlus.Rnw#L253 \item Version 1.51.1 Breif R code
    update ...
ℹ NOTE: Consider 4 spaces instead of tabs; 87 lines (8%) contain tabs.
  First few lines:
    • R/ConsensusClusterPlus.R#L19 corUse="everything" ) { ...
    • ...
    • R/ConsensusClusterPlus.R#L665 text("*",x=xr+0.5,y=maxH,col=myc[cc],ce ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 366 lines (35%) are
not.
  First few lines:
    • R/ConsensusClusterPlus.R#L2 maxK = ...
    • ...
    • vignettes/ConsensusClusterPlus.Rnw#L221 #return(assignment) ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 16 NOTES
ℹ See the ConsensusClusterPlus.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.