BioC 2.12: CHECK report for coRNAi on petty

Package: coRNAi

Version: 1.10.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch coRNAi_1.10.1.tar.gz

StartedAt: 2013-10-08 22:05:38 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:10:50 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 312.6 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 3.0.1 (2013-05-16)
* 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 '1.10.1'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'coRNAi' can be installed ... [28s/29s] 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 sizes of PDF files under 'inst/doc' ... 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 ... [42s/42s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
cortestmatrices 10.877  0.200  11.221
repplots         8.400  0.483   9.183
* 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
** testing if installed package can be loaded
* DONE (coRNAi)

name	user	system	elapsed
BoxPlotShorth	0.314	0.030	0.344
InteractGraph	0.012	0.001	0.013
InteractLevelPlot	0.509	0.018	0.528
MainFitPlot	0.051	0.003	0.055
PlotHeatmap	0.410	0.017	0.428
Pplot	0.020	0.001	0.022
cellHTS2df	0.258	0.015	0.274
cortestmatrices	10.877	0.200	11.221
data2graph	0.007	0.002	0.009
df2array	0.282	0.021	0.323
df2fitmatrix	0.735	0.019	0.757
df2lmFit	0.753	0.020	0.793
estmodel	0.281	0.023	0.305
faultyscreen	0.146	0.011	0.156
interactiontable	0.052	0.005	0.056
key	0.015	0.002	0.017
repplots	8.400	0.483	9.183
rlmmain	0.782	0.030	0.934
screen1_raw	0.033	0.006	0.038
screen2_raw	0.214	0.011	0.228
signalplots	0.327	0.017	0.347
tt2matrix	0.011	0.004	0.014
updateDf	0.298	0.022	0.324
weightDf	0.240	0.014	0.255