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BioC 2.13: CHECK report for coRNAi on zin1

This page was generated on 2014-04-05 09:47:55 -0700 (Sat, 05 Apr 2014).

Package 173/750HostnameOS / ArchBUILDCHECKBUILD BIN
coRNAi 1.12.0
Elin Axelsson
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/coRNAi
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: coRNAi
Version: 1.12.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings coRNAi_1.12.0.tar.gz
StartedAt: 2014-04-05 00:32:46 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:36:03 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 196.9 seconds
RetCode: 0
Status:  OK 
CheckDir: coRNAi.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/coRNAi.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... [19s/21s] 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 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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘coRNAi.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cortestmatrices 5.189  0.004   5.199
* 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
BoxPlotShorth0.4160.0080.426
InteractGraph0.2600.0000.261
InteractLevelPlot0.5360.0000.538
MainFitPlot0.0200.0040.023
PlotHeatmap0.1880.0040.192
Pplot0.0120.0000.009
cellHTS2df0.1240.0000.125
cortestmatrices5.1890.0045.199
data2graph0.0040.0000.001
df2array0.1280.0000.130
df2fitmatrix0.1720.0000.171
df2lmFit0.4600.0000.461
estmodel0.1360.0040.138
faultyscreen0.0760.0000.078
interactiontable0.0240.0080.030
key0.0080.0000.008
repplots4.7080.0764.847
rlmmain0.1800.0000.181
screen1_raw0.0080.0040.013
screen2_raw0.1080.0000.108
signalplots0.1600.0000.158
tt2matrix0.0080.0000.007
updateDf0.4240.0000.423
weightDf0.1240.0000.121