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BioC 3.0: CHECK report for coRNAi on perceval

This page was generated on 2015-04-10 09:55:09 -0700 (Fri, 10 Apr 2015).

Package 202/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coRNAi 1.16.0
Elin Axelsson
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/coRNAi
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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

Command output

##############################################################################
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###
### Running command:
###
###   /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.

coRNAi.Rcheck/00install.out:

* 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)

coRNAi.Rcheck/coRNAi-Ex.timings:

nameusersystemelapsed
BoxPlotShorth0.1550.0170.171
InteractGraph0.0010.0000.000
InteractLevelPlot0.8660.0100.909
MainFitPlot0.0230.0020.043
PlotHeatmap0.2550.0240.301
Pplot0.0050.0010.012
cellHTS2df0.1110.0050.116
cortestmatrices7.4380.1847.638
data2graph0.0000.0000.001
df2array0.1240.0150.139
df2fitmatrix0.1690.0120.181
df2lmFit0.2080.0090.216
estmodel0.1260.0030.129
faultyscreen0.0900.0060.096
interactiontable0.0260.0010.026
key0.0040.0010.005
repplots5.6360.3726.425
rlmmain0.2030.0390.285
screen1_raw0.0140.0040.018
screen2_raw0.1110.0070.119
signalplots0.1750.0070.217
tt2matrix0.0030.0000.003
updateDf0.1500.0120.188
weightDf0.0990.0070.106