Package: MetaCyto

Version: 1.4.0

Command: rm -rf MetaCyto.buildbin-libdir MetaCyto.Rcheck && mkdir MetaCyto.buildbin-libdir MetaCyto.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MetaCyto.buildbin-libdir MetaCyto_1.4.0.tar.gz >MetaCyto.Rcheck\00install.out 2>&1 && cp MetaCyto.Rcheck\00install.out MetaCyto-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MetaCyto.buildbin-libdir --install="check:MetaCyto-install.out" --force-multiarch --no-vignettes --timings MetaCyto_1.4.0.tar.gz

StartedAt: 2018-04-12 01:15:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:26:56 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 688.0 seconds

RetCode: 0

Status:  OK

CheckDir: MetaCyto.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MetaCyto.buildbin-libdir MetaCyto.Rcheck && mkdir MetaCyto.buildbin-libdir MetaCyto.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MetaCyto.buildbin-libdir MetaCyto_1.4.0.tar.gz >MetaCyto.Rcheck\00install.out 2>&1 && cp MetaCyto.Rcheck\00install.out MetaCyto-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MetaCyto.buildbin-libdir --install="check:MetaCyto-install.out" --force-multiarch --no-vignettes --timings MetaCyto_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MetaCyto.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MetaCyto/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MetaCyto' version '1.4.0'
* 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 'MetaCyto' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
collectData: no visible binding for global variable 'parameter_name'
collectData: no visible binding for global variable 'value'
panelSummary: no visible binding for global variable 'antibodies'
panelSummary: no visible binding for global variable 'value'
plotGA: no visible binding for global variable 'lower'
plotGA: no visible binding for global variable 'upper'
searchCluster : <anonymous>: no visible binding for global variable
  'triS'
Undefined global functions or variables:
  antibodies lower parameter_name triS upper value
* 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
autoCluster.batch   77.44  22.30   99.83
labelCluster        84.66  12.99   97.64
searchCluster.batch 25.18   4.15   29.35
flowSOM.MC          13.14   0.16   13.32
searchCluster        8.60   1.35    9.94
densityPlot          5.53   1.86    7.39
clusterStats         5.45   1.70    7.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
labelCluster        96.73  18.91  115.66
autoCluster.batch   68.56  23.56   92.22
searchCluster.batch 29.04   4.64   33.71
flowSOM.MC          14.13   0.10   14.21
searchCluster        9.65   1.34   11.00
densityPlot          5.36   1.75    7.11
clusterStats         4.94   1.95    6.91
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/MetaCyto.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MetaCyto' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MetaCyto'
    finding HTML links ... done
    autoCluster.batch                       html  
    clusterStats                            html  
    collectData                             html  
    densityPlot                             html  
    fcsInfoParser                           html  
    filterLabels                            html  
    findCutoff                              html  
    flowHC                                  html  
    flowSOM.MC                              html  
    glmAnalysis                             html  
    labelCluster                            html  
    labelSummary                            html  
    markerFinder                            html  
    metaAnalysis                            html  
    nameUpdator                             html  
    panelSummary                            html  
    plotGA                                  html  
    preprocessing                           html  
    preprocessing.batch                     html  
    sampleInfoParser                        html  
    searchCluster                           html  
    searchCluster.batch                     html  
    set2Frame                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MetaCyto' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MetaCyto' as MetaCyto_1.4.0.zip
* DONE (MetaCyto)
In R CMD INSTALL
In R CMD INSTALL