Package: pathifier

Version: 1.16.0

Command: rm -rf pathifier.buildbin-libdir pathifier.Rcheck && mkdir pathifier.buildbin-libdir pathifier.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathifier.buildbin-libdir pathifier_1.16.0.tar.gz >pathifier.Rcheck\00install.out 2>&1 && cp pathifier.Rcheck\00install.out pathifier-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pathifier.buildbin-libdir --install="check:pathifier-install.out" --force-multiarch --no-vignettes --timings pathifier_1.16.0.tar.gz

StartedAt: 2018-04-12 02:00:50 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:02:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 92.7 seconds

RetCode: 0

Status:  OK

CheckDir: pathifier.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf pathifier.buildbin-libdir pathifier.Rcheck && mkdir pathifier.buildbin-libdir pathifier.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathifier.buildbin-libdir pathifier_1.16.0.tar.gz >pathifier.Rcheck\00install.out 2>&1 && cp pathifier.Rcheck\00install.out pathifier-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pathifier.buildbin-libdir --install="check:pathifier-install.out" --force-multiarch --no-vignettes --timings pathifier_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/pathifier.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 'pathifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathifier' version '1.16.0'
* 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 'pathifier' 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
.getpathway: no visible global function definition for 'var'
.samplings_stdev: no visible binding for global variable 'sd'
.score_pathway: no visible binding for global variable 'sd'
.score_pathway: no visible global function definition for 'aggregate'
.score_pathway: no visible global function definition for 'dist'
quantify_pathways_deregulation: no visible binding for global variable
  'sd'
quantify_pathways_deregulation: no visible global function definition
  for 'prcomp'
Undefined global functions or variables:
  aggregate dist prcomp sd var
Consider adding
  importFrom("stats", "aggregate", "dist", "prcomp", "sd", "var")
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
pathifier-package              14.73   0.01   14.76
quantify_pathways_deregulation 12.46   0.00   12.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
pathifier-package              16.64   0.04   16.86
quantify_pathways_deregulation 14.00   0.03   14.03
* 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/pathifier.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'pathifier' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'pathifier'
    finding HTML links ... done
    KEGG                                    html  
    Sheffer                                 html  
    pathifier-package                       html  
    quantify_pathways_deregulation          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pathifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathifier' as pathifier_1.16.0.zip
* DONE (pathifier)
In R CMD INSTALL
In R CMD INSTALL