Package: SRGnet

Version: 1.4.0

Command: rm -rf SRGnet.buildbin-libdir SRGnet.Rcheck && mkdir SRGnet.buildbin-libdir SRGnet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SRGnet.buildbin-libdir SRGnet_1.4.0.tar.gz >SRGnet.Rcheck\00install.out 2>&1 && cp SRGnet.Rcheck\00install.out SRGnet-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SRGnet.buildbin-libdir --install="check:SRGnet-install.out" --force-multiarch --no-vignettes --timings SRGnet_1.4.0.tar.gz

StartedAt: 2018-04-12 03:23:53 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:27:28 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 214.2 seconds

RetCode: 0

Status:  OK

CheckDir: SRGnet.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SRGnet.buildbin-libdir SRGnet.Rcheck && mkdir SRGnet.buildbin-libdir SRGnet.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SRGnet.buildbin-libdir SRGnet_1.4.0.tar.gz >SRGnet.Rcheck\00install.out 2>&1 && cp SRGnet.Rcheck\00install.out SRGnet-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SRGnet.buildbin-libdir --install="check:SRGnet-install.out" --force-multiarch --no-vignettes --timings SRGnet_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SRGnet.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 'SRGnet/DESCRIPTION' ... OK
* this is package 'SRGnet' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'EBcoexpress' 'MASS' 'igraph' 'pvclust' 'gbm' 'limma' 'DMwR'
  'matrixStats' 'Hmisc'
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 'SRGnet' 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
SRGnet: no visible binding for global variable
  'Differentially_expressed_genes'
SRGnet: no visible binding for global variable 'Transcriptomics'
SRGnet: no visible binding for global variable 'PLCRG'
SRGnet: no visible global function definition for 'ebPatterns'
SRGnet: no visible global function definition for 'par'
SRGnet: no visible global function definition for 'boxplot'
SRGnet: no visible global function definition for 'plot'
SRGnet: no visible global function definition for 'predict'
SRGnet: no visible global function definition for 'terrain.colors'
SRGnet: no visible global function definition for 'na.omit'
SRGnet: no visible global function definition for 'write.table'
Undefined global functions or variables:
  Differentially_expressed_genes PLCRG Transcriptomics boxplot
  ebPatterns na.omit par plot predict terrain.colors write.table
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "boxplot", "par", "plot")
  importFrom("stats", "na.omit", "predict")
  importFrom("utils", "write.table")
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 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
SRGnet 44.75   0.25      45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
SRGnet 55.08   0.25   55.33
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/SRGnet.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SRGnet' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'SRGnet'
    finding HTML links ... done
    Differentially_expressed_genes          html  
    PLCRG                                   html  
    SRGnet                                  html  
    Transcriptomics                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SRGnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SRGnet' as SRGnet_1.4.0.zip
* DONE (SRGnet)
In R CMD INSTALL
In R CMD INSTALL