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BioC 3.2: CHECK report for motifStack on oaxaca

This page was generated on 2016-04-23 10:26:07 -0700 (Sat, 23 Apr 2016).

Package 671/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.14.0
Jianhong Ou
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/motifStack
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: motifStack
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.14.0.tar.gz
StartedAt: 2016-04-23 02:22:30 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:28:17 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 346.9 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 motifStack_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/motifStack.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.14.0’
* 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 ‘motifStack’ can be installed ... [24s/28s] 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 ... OK
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/14s]
 [13s/15s] 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

Status: OK

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
DNAmotifAlignment0.2380.0050.247
colorset0.0000.0000.001
getRankedUniqueMotifs0.0030.0010.004
highlightCol0.0020.0000.001
mergeMotifs0.5210.0130.626
motifCircos0.0100.0010.012
motifCloud0.0060.0010.009
motifPiles0.0110.0000.014
motifSignature0.0050.0000.008
motifStack0.0030.0000.003
ouNode-class0.0040.0000.004
pcm-class0.6680.1222.028
pcm-methods0.0100.0010.012
pfm-class0.6650.1010.919
pfm-methods0.0100.0010.011
pfm2pwm1.1470.0231.263
plotMotifLogo0.7420.0991.181
plotMotifLogoA1.0310.1261.383
plotMotifLogoStack0.6710.1091.055
plotMotifLogoStackWithTree2.3440.2213.161
plotMotifOverMotif0.9250.0991.110
plotMotifStackWithPhylog0.0070.0010.007
plotMotifStackWithRadialPhylog0.0080.0000.008
readPCM0.0200.0010.021
reorderUPGMAtree0.0040.0000.004