BioC 2.12: CHECK report for coRNAi on moscato2

Package: coRNAi

Version: 1.10.1

Command: rm -rf coRNAi.buildbin-libdir && mkdir coRNAi.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coRNAi.buildbin-libdir coRNAi_1.10.1.tar.gz >coRNAi-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=coRNAi.buildbin-libdir --install="check:coRNAi-install.out" --force-multiarch --no-vignettes --timings coRNAi_1.10.1.tar.gz && mv coRNAi.buildbin-libdir/* coRNAi.Rcheck/ && rmdir coRNAi.buildbin-libdir

StartedAt: 2013-10-09 01:43:19 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:48:20 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 300.6 seconds

RetCode: 0

Status:  OK

CheckDir: coRNAi.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/coRNAi.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 'coRNAi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coRNAi' version '1.10.1'
* 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 'coRNAi' 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
interactiontable: warning in topTable(eBayes(ebfit), n =
  length(ebfit@.Data[[6]]), sort = "none", adjust.method = correction):
  partial argument match of 'n' to 'number'
interactiontable: warning in topTable(eBayes(ebfit), n =
  length(ebfit@.Data[[6]]), sort = "none", adjust.method = correction):
  partial argument match of 'sort' to 'sort.by'
* 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' ... NOTE
The following files should probably not be installed:
  'Annotationfile.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... [35s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
repplots        10.62   0.34   10.96
cortestmatrices  8.60   0.00    8.60
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
cortestmatrices 8.93   0.00    8.93
repplots        8.00   0.25    8.40
* 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/coRNAi.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'coRNAi' ...
** 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 'coRNAi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coRNAi' as coRNAi_1.10.1.zip
* DONE (coRNAi)