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CHECK report for ConsensusClusterPlus on celaya2

This page was generated on 2019-10-16 12:47:53 -0400 (Wed, 16 Oct 2019).

Package 335/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ConsensusClusterPlus 1.48.0
Matt Wilkerson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ConsensusClusterPlus
Branch: RELEASE_3_9
Last Commit: 41d3652
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ConsensusClusterPlus
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ConsensusClusterPlus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ConsensusClusterPlus_1.48.0.tar.gz
StartedAt: 2019-10-16 01:44:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:45:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 52.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ConsensusClusterPlus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ConsensusClusterPlus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ConsensusClusterPlus_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ConsensusClusterPlus.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ConsensusClusterPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ConsensusClusterPlus’ version ‘1.48.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ConsensusClusterPlus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  GPL version 2
Standardizable: TRUE
Standardized license specification:
  GPL-2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ALL’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm
  = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F,
  labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk,
  sep = ""), ColSideCol = oc): partial argument match of 'mar' to
  'margins'
ConsensusClusterPlus: warning in heatmap(pc, Colv = NA, Rowv = NA, symm
  = FALSE, scale = "none", col = tmyPal, na.rm = TRUE, labRow = F,
  labCol = F, mar = c(5, 5), main = paste("consensus matrix k=", tk,
  sep = ""), ColSideCol = oc): partial argument match of 'ColSideCol'
  to 'ColSideColors'
ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc),
  Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE,
  labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix
  k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument
  match of 'mar' to 'margins'
ConsensusClusterPlus: warning in heatmap(pc, Colv = as.dendrogram(hc),
  Rowv = NA, symm = FALSE, scale = "none", col = tmyPal, na.rm = TRUE,
  labRow = F, labCol = F, mar = c(5, 5), main = paste("consensus matrix
  k=", tk, sep = ""), ColSideCol = colorList[[1]]): partial argument
  match of 'ColSideCol' to 'ColSideColors'
ConsensusClusterPlus: no visible global function definition for
  ‘bitmap’
ConsensusClusterPlus: no visible global function definition for
  ‘postscript’
calcICL: no visible global function definition for ‘postscript’
calcICL: no visible global function definition for ‘bitmap’
Undefined global functions or variables:
  bitmap postscript
Consider adding
  importFrom("grDevices", "bitmap", "postscript")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ConsensusClusterPlus.Rcheck/00check.log’
for details.



Installation output

ConsensusClusterPlus.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ConsensusClusterPlus
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ConsensusClusterPlus’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ConsensusClusterPlus)

Tests output


Example timings

ConsensusClusterPlus.Rcheck/ConsensusClusterPlus-Ex.timings

nameusersystemelapsed
ConsensusClusterPlus2.6080.3104.188