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BioC 2.13: CHECK report for motifStack on perceval

This page was generated on 2014-04-05 09:52:56 -0700 (Sat, 05 Apr 2014).

Package 462/750HostnameOS / ArchBUILDCHECKBUILD BIN
motifStack 1.6.5
Jianhong Ou
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/motifStack
Last Changed Rev: 85540 / Revision: 88450
Last Changed Date: 2014-01-15 07:29:07 -0800 (Wed, 15 Jan 2014)
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: motifStack
Version: 1.6.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch motifStack_1.6.5.tar.gz
StartedAt: 2014-04-05 02:51:44 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:57:54 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 370.0 seconds
RetCode: 0
Status:  OK 
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/motifStack.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.6.5’
* 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 ‘motifStack’ can be installed ... [23s/36s] 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘coloredSymbols’ ‘getIC’ ‘getIE’ ‘hex2psrgb’ ‘highlightCol’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/29s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plotMotifLogoStackWithTree 2.821  0.408   5.317
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [24s/31s]
 [25s/32s] OK
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/motifStack.Rcheck/00check.log’
for details.

motifStack.Rcheck/00install.out:

* installing *source* package ‘motifStack’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifStack)

motifStack.Rcheck/motifStack-Ex.timings:

nameusersystemelapsed
DNAmotifAlignment1.2750.0371.556
colorset0.0070.0020.020
motifCloud0.0220.0040.026
motifSignature0.0250.0020.028
motifStack0.0170.0030.019
ouNode-class0.0140.0020.023
pcm-class0.7760.2151.590
pcm-methods0.0270.0050.033
pfm-class0.7260.1781.287
pfm-methods0.0300.0040.086
plotMotifLogo0.8410.2071.928
plotMotifLogoA1.1000.2012.506
plotMotifLogoStack0.8340.2221.617
plotMotifLogoStackWithTree2.8210.4085.317
plotMotifStackWithPhylog0.0290.0050.065
plotMotifStackWithRadialPhylog0.0380.0020.071
readPCM0.0250.0020.064