Package: flowMerge

Version: 2.28.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowMerge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowMerge_2.28.0.tar.gz

StartedAt: 2018-10-17 02:01:55 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:04:04 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 129.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowMerge.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowMerge.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowMerge_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowMerge.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowMerge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowMerge' version '2.28.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC' 'multicore'

Depends: includes the non-default packages:
  'graph' 'feature' 'flowClust' 'Rgraphviz' 'foreach' 'snow'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'flowMerge' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
Packages in Depends field not imported from:
  'foreach' 'snow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.compMD: no visible global function definition for 'mahalanobis'
initPFlowMerge: no visible global function definition for
  'clusterEvalQ'
mergeClusters: no visible global function definition for '%dopar%'
mergeClusters: no visible global function definition for 'foreach'
mergeClusters: no visible global function definition for '%do%'
pFlowClust : <anonymous>: no visible global function definition for
  'clusterMap'
pFlowClust: no visible global function definition for 'clusterMap'
ptree : <anonymous>: no visible global function definition for 'rgb'
ptree: no visible global function definition for 'subGraph'
ptree : <anonymous>: no visible global function definition for
  'nodeDataDefaults<-'
ptree : <anonymous>: no visible global function definition for
  'nodeData<-'
ptree : <anonymous>: no visible global function definition for
  'subGraph'
ptree : <anonymous>: no visible global function definition for
  'nodeRenderInfo<-'
flagOutliers,flowMerge: no visible global function definition for 'qf'
Undefined global functions or variables:
  %do% %dopar% clusterEvalQ clusterMap foreach mahalanobis nodeData<-
  nodeDataDefaults<- nodeRenderInfo<- qf rgb subGraph
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "mahalanobis", "qf")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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-3.7-bioc/meat/flowMerge.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowMerge_2.28.0.tar.gz && rm -rf flowMerge.buildbin-libdir && mkdir flowMerge.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowMerge.buildbin-libdir flowMerge_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowMerge_2.28.0.zip && rm flowMerge_2.28.0.tar.gz flowMerge_2.28.0.zip
###
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100  397k  100  397k    0     0  6297k      0 --:--:-- --:--:-- --:--:-- 6974k

install for i386

* installing *source* package 'flowMerge' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowMerge'
    finding HTML links ... done
    NENT                                    html  
    checkForRemoteErrors                    html  
    fitPiecewiseLinreg-methods              html  
    fitPiecewiseLinreg                      html  
    flagOutliers-methods                    html  
    flagOutliers                            html  
    flowClust.res                           html  
    flowMerge-class                         html  
    finding level-2 HTML links ... done

    flowMerge-internal                      html  
    flowMerge-package                       html  
    flowObj-class                           html  
    flowObj                                 html  
    initPFlowMerge                          html  
    map                                     html  
    merge-methods                           html  
    merge                                   html  
    mergeClusters                           html  
    mergeClusters2                          html  
    pFlowClust                              html  
    pFlowMerge                              html  
    plot-methods                            html  
    ptree                                   html  
    show-methods                            html  
    split-methods                           html  
    summary-methods                         html  
    updateU                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowMerge' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowMerge' as flowMerge_2.28.0.zip
* DONE (flowMerge)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowMerge' successfully unpacked and MD5 sums checked
In R CMD INSTALL