BioC 2.12: CHECK report for oligoClasses on moscato2

Package: oligoClasses

Version: 1.21.16

Command: rm -rf oligoClasses.buildbin-libdir && mkdir oligoClasses.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.21.16.tar.gz >oligoClasses-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.21.16.tar.gz && mv oligoClasses.buildbin-libdir/* oligoClasses.Rcheck/ && rmdir oligoClasses.buildbin-libdir

StartedAt: 2013-03-25 03:53:31 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:58:35 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 304.6 seconds

RetCode: 0

Status: OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/oligoClasses.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 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.21.16'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC' 'doMPI' 'doRedis'
* 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 'oligoClasses' 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 ... NOTE
prepare_Rd: SummarizedExperiment-methods.Rd:42-44: Dropping empty section \examples
* 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' ... [33s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
GenomeAnnotatedDataFrame-class 1.07   0.13    10.5
** running examples for arch 'x64' ... [24s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
AssayData-methods 4.93   0.06     5.1
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R' [30s]
 [30s] OK
** running tests for arch 'x64'
  Running 'doRUnit.R' [29s]
 [29s] OK
* checking PDF version of manual ... OK

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


install for i386

* installing *source* package 'oligoClasses' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'oligoClasses'
Creating a generic function for 'close' from package 'base' in package 'oligoClasses'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.21.16.zip
* DONE (oligoClasses)

Summary

Command output