Package: GeneGeneInteR

Version: 1.4.0

Command: rm -rf GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && mkdir GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.4.0.tar.gz >GeneGeneInteR.Rcheck\00install.out 2>&1 && cp GeneGeneInteR.Rcheck\00install.out GeneGeneInteR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneGeneInteR.buildbin-libdir --install="check:GeneGeneInteR-install.out" --force-multiarch --no-vignettes --timings GeneGeneInteR_1.4.0.tar.gz

StartedAt: 2018-04-12 00:12:35 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:20:25 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 469.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GeneGeneInteR.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && mkdir GeneGeneInteR.buildbin-libdir GeneGeneInteR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneGeneInteR.buildbin-libdir GeneGeneInteR_1.4.0.tar.gz >GeneGeneInteR.Rcheck\00install.out 2>&1 && cp GeneGeneInteR.Rcheck\00install.out GeneGeneInteR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneGeneInteR.buildbin-libdir --install="check:GeneGeneInteR-install.out" --force-multiarch --no-vignettes --timings GeneGeneInteR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneGeneInteR.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 'GeneGeneInteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneGeneInteR' 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 'GeneGeneInteR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcbh357/R.INSTALL1b946ca06493/GeneGeneInteR/man/importFile.Rd:42: missing file link 'GRanges'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneGeneInteR.Rcheck/00install.out' for details.
* 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
CCA.test: no visible global function definition for 'as'
CLD.test: no visible global function definition for 'as'
GBIGM.test: no visible global function definition for 'as'
KCCA.test: no visible global function definition for 'as'
PCA.Std: no visible global function definition for 'as'
PLSPM.test: no visible global function definition for 'as'
imputeSnpMatrix: no visible global function definition for 'as'
snpMatrixScour: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
** 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneGeneInteR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GeneGeneInteR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneGeneInteR'
    finding HTML links ... done
    CCA.test                                html  
    CLD.test                                html  
    GBIGM.test                              html  
    GGI                                     html  
    KCCA.test                               html  
    PCA.test                                html  
    PLSPM.test                              html  
    data.SNP                                html  
    gates.test                              html  
    gene.pair                               html  
    importFile                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcbh357/R.INSTALL1b946ca06493/GeneGeneInteR/man/importFile.Rd:42: missing file link 'GRanges'
    imputeSnpMatrix                         html  
    minP.test                               html  
    plot.GGInetwork                         html  
    print.GGItest                           html  
    selectSnps                              html  
    snpMatrixScour                          html  
    summary.GGInetwork                      html  
    summary.GGItest                         html  
    tProd.test                              html  
    tTS.test                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GeneGeneInteR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneGeneInteR' as GeneGeneInteR_1.4.0.zip
* DONE (GeneGeneInteR)
In R CMD INSTALL
In R CMD INSTALL