Package: phenoTest

Version: 1.7.4

Command: rm -rf phenoTest.buildbin-libdir && mkdir phenoTest.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoTest.buildbin-libdir phenoTest_1.7.4.tar.gz >phenoTest-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=phenoTest.buildbin-libdir --install="check:phenoTest-install.out" --force-multiarch --no-vignettes --timings phenoTest_1.7.4.tar.gz && mv phenoTest.buildbin-libdir/* phenoTest.Rcheck/ && rmdir phenoTest.buildbin-libdir

StartedAt: 2013-03-25 04:07:49 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:15:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 464.7 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/phenoTest.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.7.4'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'phenoTest' can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaData':
  'plot.gseaData'

S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  'plot.gseaSignaturesSign'

S3 methods shown with full name in documentation object 'summary.gseaData':
  'summary.gseaData'

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  'summary.gseaSignificanceSign'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ...
** running examples for arch 'i386' ... [32s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
findCopyNumber      6.74   0.03    6.77
ExpressionPhenoTest 5.88   0.02    5.90
** running examples for arch 'x64' ... [32s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
findCopyNumber      6.58   0.04    6.63
ExpressionPhenoTest 5.93   0.02    5.94
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/phenoTest.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'phenoTest' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'phenoTest.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'phenoTest' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phenoTest' as phenoTest_1.7.4.zip
* DONE (phenoTest)