Package: coRNAi

Version: 1.9.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings coRNAi_1.9.0.tar.gz

StartedAt: 2013-03-25 01:00:00 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:05:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 329.7 seconds

RetCode: 0

Status:  OK

CheckDir: coRNAi.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/coRNAi.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [31s/32s] 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 ... [44s/46s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cortestmatrices 9.516  0.008  10.054
repplots        8.709  0.360   9.069
* 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
  ‘/home/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	0.288	0.008	0.296
InteractGraph	0.016	0.004	0.023
InteractLevelPlot	0.537	0.000	0.535
MainFitPlot	0.072	0.008	0.081
PlotHeatmap	0.368	0.008	0.382
Pplot	0.020	0.008	0.026
cellHTS2df	0.244	0.004	0.334
cortestmatrices	9.516	0.008	10.054
data2graph	0.008	0.000	0.025
df2array	0.300	0.016	0.368
df2fitmatrix	1.108	0.008	1.132
df2lmFit	1.080	0.012	1.238
estmodel	0.332	0.016	0.399
faultyscreen	0.120	0.008	0.196
interactiontable	0.092	0.000	0.091
key	0.044	0.000	0.044
repplots	8.709	0.360	9.069
rlmmain	1.068	0.004	1.076
screen1_raw	0.044	0.000	0.044
screen2_raw	0.168	0.000	0.168
signalplots	0.312	0.000	0.312
tt2matrix	0.756	0.000	0.758
updateDf	0.284	0.000	0.284
weightDf	0.236	0.004	0.242