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BioC 3.0: CHECK report for motifStack on oaxaca

This page was generated on 2015-04-10 10:06:23 -0700 (Fri, 10 Apr 2015).

Package 575/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.10.2
Jianhong Ou
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/motifStack
Last Changed Rev: 102193 / Revision: 102249
Last Changed Date: 2015-04-09 08:30:19 -0700 (Thu, 09 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: motifStack
Version: 1.10.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch motifStack_1.10.2.tar.gz
StartedAt: 2015-04-10 01:32:52 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:39:07 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 375.1 seconds
RetCode: 0
Status:  OK 
CheckDir: motifStack.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch motifStack_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/motifStack.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 ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.10.2’
* 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 ... [28s/49s] 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’
* 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/25s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [15s/17s]
 [15s/17s] 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
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/motifStack.Rcheck/00check.log’
for details.

motifStack.Rcheck/00install.out:

* installing *source* package ‘motifStack’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
No methods found in "IRanges" for requests: sapply
* DONE (motifStack)

motifStack.Rcheck/motifStack-Ex.timings:

nameusersystemelapsed
DNAmotifAlignment0.6370.0080.878
colorset0.0010.0000.004
motifCloud0.0070.0000.007
motifSignature0.0050.0000.005
motifStack0.0030.0000.004
ouNode-class0.0060.0000.006
pcm-class0.7110.1131.378
pcm-methods0.0110.0020.013
pfm-class0.9240.1021.055
pfm-methods0.0110.0020.013
plotMotifLogo0.7880.1100.976
plotMotifLogoA0.9900.1081.143
plotMotifLogoStack0.7260.1010.894
plotMotifLogoStackWithTree2.6960.2493.228
plotMotifStackWithPhylog0.0070.0000.010
plotMotifStackWithRadialPhylog0.0080.0010.017
readPCM0.0200.0010.036