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BioC 3.4: CHECK report for ConsensusClusterPlus on moscato1

This page was generated on 2016-09-21 03:42:56 -0700 (Wed, 21 Sep 2016).

Package 247/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ConsensusClusterPlus 1.37.0
Matt Wilkerson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ConsensusClusterPlus
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ConsensusClusterPlus
Version: 1.37.0
Command: rm -rf ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus.Rcheck && mkdir ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus_1.37.0.tar.gz >ConsensusClusterPlus.Rcheck\00install.out 2>&1 && cp ConsensusClusterPlus.Rcheck\00install.out ConsensusClusterPlus-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ConsensusClusterPlus.buildbin-libdir --install="check:ConsensusClusterPlus-install.out" --force-multiarch --no-vignettes --timings ConsensusClusterPlus_1.37.0.tar.gz
StartedAt: 2016-09-20 06:20:19 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:21:05 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 45.3 seconds
RetCode: 0
Status:  OK  
CheckDir: ConsensusClusterPlus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus.Rcheck && mkdir ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus_1.37.0.tar.gz >ConsensusClusterPlus.Rcheck\00install.out 2>&1 && cp ConsensusClusterPlus.Rcheck\00install.out ConsensusClusterPlus-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ConsensusClusterPlus.buildbin-libdir --install="check:ConsensusClusterPlus-install.out" --force-multiarch --no-vignettes --timings ConsensusClusterPlus_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ConsensusClusterPlus.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ConsensusClusterPlus/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ConsensusClusterPlus' version '1.37.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-3.4-bioc/meat/ConsensusClusterPlus.Rcheck/00check.log'
for details.


ConsensusClusterPlus.Rcheck/00install.out:


install for i386

* installing *source* package 'ConsensusClusterPlus' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ConsensusClusterPlus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ConsensusClusterPlus' as ConsensusClusterPlus_1.37.0.zip
* DONE (ConsensusClusterPlus)

ConsensusClusterPlus.Rcheck/examples_i386/ConsensusClusterPlus-Ex.timings:

nameusersystemelapsed
ConsensusClusterPlus2.980.003.05

ConsensusClusterPlus.Rcheck/examples_x64/ConsensusClusterPlus-Ex.timings:

nameusersystemelapsed
ConsensusClusterPlus2.960.002.96