BioC 3.0: CHECK report for coRNAi on perceval

Package: coRNAi

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch coRNAi_1.16.0.tar.gz

StartedAt: 2015-04-10 00:23:57 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:30:25 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 388.0 seconds

RetCode: 0

Status:  OK

CheckDir: coRNAi.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch coRNAi_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/coRNAi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.16.0’
* 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 ... [33s/46s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘cellHTS2’ ‘limma’ ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘moMatrix’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BoxPlotShorth: no visible binding for global variable ‘shorth’
cellHTS2df: no visible global function definition for ‘fData’
cellHTS2df: no visible global function definition for ‘Data’
df2lmFit: no visible global function definition for ‘lmFit’
estpart: no visible binding for global variable ‘shorth’
interactiontable: no visible global function definition for ‘topTable’
interactiontable: no visible global function definition for ‘eBayes’
MainFitPlot: no visible global function definition for ‘locfit’
MainFitPlot: no visible global function definition for ‘lfknots’
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/35s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cortestmatrices 7.438  0.184   7.638
repplots        5.636  0.372   6.425
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.155	0.017	0.171
InteractGraph	0.001	0.000	0.000
InteractLevelPlot	0.866	0.010	0.909
MainFitPlot	0.023	0.002	0.043
PlotHeatmap	0.255	0.024	0.301
Pplot	0.005	0.001	0.012
cellHTS2df	0.111	0.005	0.116
cortestmatrices	7.438	0.184	7.638
data2graph	0.000	0.000	0.001
df2array	0.124	0.015	0.139
df2fitmatrix	0.169	0.012	0.181
df2lmFit	0.208	0.009	0.216
estmodel	0.126	0.003	0.129
faultyscreen	0.090	0.006	0.096
interactiontable	0.026	0.001	0.026
key	0.004	0.001	0.005
repplots	5.636	0.372	6.425
rlmmain	0.203	0.039	0.285
screen1_raw	0.014	0.004	0.018
screen2_raw	0.111	0.007	0.119
signalplots	0.175	0.007	0.217
tt2matrix	0.003	0.000	0.003
updateDf	0.150	0.012	0.188
weightDf	0.099	0.007	0.106