BioC 3.0: CHECK report for coRNAi on oaxaca

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: 2015-04-09 22:38:46 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:43:12 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 265.8 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-darwin13.4.0 (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 ... [27s/29s] 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’
MainFitPlot: no visible global function definition for ‘locfit’
MainFitPlot: no visible global function definition for ‘lfknots’
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’
* 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 ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cortestmatrices 6.338  0.126   6.526
* 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	0.437	0.009	0.447
InteractGraph	0	0	0
InteractLevelPlot	0.277	0.012	0.290
MainFitPlot	0.019	0.001	0.021
PlotHeatmap	0.509	0.012	0.522
Pplot	0.005	0.001	0.006
cellHTS2df	0.101	0.005	0.106
cortestmatrices	6.338	0.126	6.526
data2graph	0.001	0.000	0.001
df2array	0.088	0.005	0.092
df2fitmatrix	0.146	0.013	0.158
df2lmFit	0.183	0.005	0.190
estmodel	0.394	0.007	0.401
faultyscreen	0.086	0.005	0.090
interactiontable	0.022	0.000	0.023
key	0.003	0.000	0.005
repplots	4.402	0.227	4.803
rlmmain	0.165	0.013	0.182
screen1_raw	0.014	0.004	0.020
screen2_raw	0.135	0.006	0.142
signalplots	0.155	0.008	0.164
tt2matrix	0.003	0.000	0.002
updateDf	0.123	0.005	0.129
weightDf	0.103	0.006	0.108