BioC 2.12: CHECK report for ARRmNormalization on moscato2

Package: ARRmNormalization

Version: 1.0.0

Command: rm -rf ARRmNormalization.buildbin-libdir && mkdir ARRmNormalization.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ARRmNormalization.buildbin-libdir ARRmNormalization_1.0.0.tar.gz >ARRmNormalization-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=ARRmNormalization.buildbin-libdir --install="check:ARRmNormalization-install.out" --force-multiarch --no-vignettes --timings ARRmNormalization_1.0.0.tar.gz && mv ARRmNormalization.buildbin-libdir/* ARRmNormalization.Rcheck/ && rmdir ARRmNormalization.buildbin-libdir

StartedAt: 2013-10-09 01:02:22 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:10:41 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 499.5 seconds

RetCode: 0

Status:  OK

CheckDir: ARRmNormalization.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/ARRmNormalization.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ARRmNormalization/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ARRmNormalization' version '1.0.0'
* 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 'ARRmNormalization' 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 ... NOTE
getQuantiles: no visible binding for global variable 'ProbesType'
normalizeARRm: no visible binding for global variable 'ProbesType'
* 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' ... [221s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeARRm   127.42  18.08  145.53
getCoefficients  22.25   1.03   23.27
getQuantiles     16.97   0.92   17.92
positionPlots    15.39   0.94   16.33
quantilePlots    14.36   0.70   15.07
** running examples for arch 'x64' ... [243s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
normalizeARRm   146.55  18.47  165.07
getCoefficients  23.43   1.00   24.43
positionPlots    15.99   1.11   17.09
getQuantiles     15.77   0.96   16.74
quantilePlots    15.63   1.08   16.80
* 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 was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/ARRmNormalization.Rcheck/00check.log'
for details.

install for i386

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

install for x64

* installing *source* package 'ARRmNormalization' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ARRmNormalization' as ARRmNormalization_1.0.0.zip
* DONE (ARRmNormalization)