Package: SRGnet

Version: 1.9.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SRGnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SRGnet_1.9.0.tar.gz

StartedAt: 2019-04-09 06:09:47 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:13:09 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 202.1 seconds

RetCode: 0

Status:  OK

CheckDir: SRGnet.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:SRGnet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SRGnet_1.9.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SRGnet.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.9.0'
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
SRGnet 45.75   0.41   46.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
SRGnet 42.22   0.38   42.61
* 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-3.9-bioc/meat/SRGnet.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/SRGnet_1.9.0.tar.gz && rm -rf SRGnet.buildbin-libdir && mkdir SRGnet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SRGnet.buildbin-libdir SRGnet_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SRGnet_1.9.0.zip && rm SRGnet_1.9.0.tar.gz SRGnet_1.9.0.zip
###
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install for i386

* installing *source* package 'SRGnet' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare 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 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 'SRGnet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SRGnet' as SRGnet_1.9.0.zip
* DONE (SRGnet)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SRGnet' successfully unpacked and MD5 sums checked