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BioC 3.1: CHECK report for motifStack on petty

This page was generated on 2015-10-09 09:35:16 -0700 (Fri, 09 Oct 2015).

Package 624/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.12.0
Jianhong Ou
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/motifStack
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifStack
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifStack_1.12.0.tar.gz
StartedAt: 2015-10-09 00:28:42 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:40:26 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 703.8 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/motifStack.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.12.0’
* 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 ‘motifStack’ can be installed ... [25s/26s] 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 ... [20s/81s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plotMotifLogoStackWithTree 2.649  0.223  11.042
pcm-class                  0.917  0.168  10.516
pfm2pwm                    0.921  0.049   6.542
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/13s]
 [12s/13s] 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "IRanges" for requests: sapply
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "IRanges" for requests: sapply
* DONE (motifStack)

motifStack.Rcheck/motifStack-Ex.timings:

nameusersystemelapsed
DNAmotifAlignment0.3360.0300.571
colorset0.0010.0000.000
getRankedUniqueMotifs0.0040.0000.004
highlightCol0.0010.0000.001
motifCircos0.0120.0000.086
motifCloud0.0070.0000.006
motifPiles0.0130.0000.038
motifSignature0.0060.0010.006
motifStack0.0030.0000.004
ouNode-class0.0040.0010.003
pcm-class 0.917 0.16810.516
pcm-methods0.0090.0020.011
pfm-class0.9060.1253.226
pfm-methods0.0090.0020.098
pfm2pwm0.9210.0496.542
plotMotifLogo0.8550.1043.780
plotMotifLogoA1.1170.1133.038
plotMotifLogoStack0.8880.1163.043
plotMotifLogoStackWithTree 2.649 0.22311.042
plotMotifStackWithPhylog0.0080.0000.008
plotMotifStackWithRadialPhylog0.0100.0010.044
readPCM0.0150.0010.016