Package: coRNAi

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch coRNAi_1.9.0.tar.gz

StartedAt: 2013-03-24 04:04:12 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 04:08:50 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 277.2 seconds

RetCode: 0

Status:  OK

CheckDir: coRNAi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/coRNAi.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'coRNAi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coRNAi' version '1.9.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'coRNAi' can be installed ... [26s/27s] 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
* 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 ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cortestmatrices 9.017  0.221   9.303
repplots        8.217  0.645   9.129
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/coRNAi.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
BoxPlotShorth	0.268	0.020	0.288
InteractGraph	0.022	0.001	0.023
InteractLevelPlot	0.477	0.031	0.510
MainFitPlot	0.047	0.003	0.051
PlotHeatmap	0.381	0.014	0.406
Pplot	0.015	0.005	0.020
cellHTS2df	0.236	0.031	0.266
cortestmatrices	9.017	0.221	9.303
data2graph	0.006	0.002	0.008
df2array	0.241	0.027	0.272
df2fitmatrix	0.784	0.029	0.817
df2lmFit	0.400	0.018	0.419
estmodel	0.666	0.013	0.682
faultyscreen	0.141	0.012	0.153
interactiontable	0.071	0.005	0.076
key	0.023	0.005	0.029
repplots	8.217	0.645	9.129
rlmmain	0.344	0.043	0.392
screen1_raw	0.022	0.011	0.033
screen2_raw	0.173	0.020	0.194
signalplots	0.299	0.028	0.330
tt2matrix	0.021	0.005	0.026
updateDf	0.275	0.025	0.363
weightDf	0.217	0.012	0.230