BioC 2.11: CHECK report for altcdfenvs on moscato1

Package: altcdfenvs

Version: 2.20.0

Command: rm -rf altcdfenvs.buildbin-libdir && mkdir altcdfenvs.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=altcdfenvs.buildbin-libdir altcdfenvs_2.20.0.tar.gz >altcdfenvs-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=altcdfenvs.buildbin-libdir --install="check:altcdfenvs-install.out" --force-multiarch --no-vignettes --timings altcdfenvs_2.20.0.tar.gz && mv altcdfenvs.buildbin-libdir/* altcdfenvs.Rcheck/ && rmdir altcdfenvs.buildbin-libdir

StartedAt: 2013-03-24 23:41:15 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:44:53 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 217.9 seconds

RetCode: 0

Status: OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.20.0'
* 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 whether package 'altcdfenvs' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
removeIndex      17.72   0.01   17.74
matchAffyProbes   8.73   0.21    8.94
CdfEnvAffy-class  7.21   0.06    7.27
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
removeIndex      16.97   0.05   17.02
matchAffyProbes   9.65   0.27   10.02
CdfEnvAffy-class  7.44   0.04    7.48
* 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


install for i386

* installing *source* package 'altcdfenvs' ...
** R
** data
** inst
** preparing package for lazy loading
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for 'toHypergraph' with signature '"CdfEnvAffy"': no definition for class "CdfEnvAffy"
** help
*** installing help indices
** building package indices
** installing vignettes
   'altcdfenvs.Rnw' 
   'modify.Rnw' 
   'ngenomeschips.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'altcdfenvs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'altcdfenvs' as altcdfenvs_2.20.0.zip

* DONE (altcdfenvs)

Summary

Command output