Package: ConsensusClusterPlus

Version: 1.48.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ConsensusClusterPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ConsensusClusterPlus_1.48.0.tar.gz

StartedAt: 2019-10-16 02:53:10 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:53:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 42.3 seconds

RetCode: 0

Status:  OK

CheckDir: ConsensusClusterPlus.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ConsensusClusterPlus.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ConsensusClusterPlus_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ConsensusClusterPlus.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.48.0'
* 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 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 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/ConsensusClusterPlus.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ConsensusClusterPlus_1.48.0.tar.gz && rm -rf ConsensusClusterPlus.buildbin-libdir && mkdir ConsensusClusterPlus.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ConsensusClusterPlus.buildbin-libdir ConsensusClusterPlus_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ConsensusClusterPlus_1.48.0.zip && rm ConsensusClusterPlus_1.48.0.tar.gz ConsensusClusterPlus_1.48.0.zip
###
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install for i386

* installing *source* package 'ConsensusClusterPlus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ConsensusClusterPlus'
    finding HTML links ... done
    ConsensusClusterPlus                    html  
** 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

install for x64

* installing *source* package 'ConsensusClusterPlus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ConsensusClusterPlus' as ConsensusClusterPlus_1.48.0.zip
* DONE (ConsensusClusterPlus)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ConsensusClusterPlus' successfully unpacked and MD5 sums checked