BioC 3.5: CHECK report for branchpointer on toluca2

Package: branchpointer

Version: 0.99.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings branchpointer_0.99.11.tar.gz

StartedAt: 2017-04-23 01:09:51 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:15:10 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 319.4 seconds

RetCode: 0

Status:  OK

CheckDir: branchpointer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings branchpointer_0.99.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/branchpointer.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘branchpointer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘branchpointer’ version ‘0.99.11’
* 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 ‘branchpointer’ can be installed ... 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 loading without being on the library search path ... 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
makeRegions           17.282  0.046  17.346
plotBranchpointWindow 13.559  0.113  13.694
predictBranchpoints    8.740  0.057   8.803
predictionsToStats     6.744  0.086   6.836
* 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

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

name	user	system	elapsed
getQueryLoc	2.115	0.010	2.129
gtfToExons	0.869	0.046	0.914
makeRegions	17.282	0.046	17.346
plotBranchpointWindow	13.559	0.113	13.694
plotStructure	0.347	0.002	0.351
predictBranchpoints	8.740	0.057	8.803
predictionsToStats	6.744	0.086	6.836
readQueryFile	0.019	0.001	0.019
snpToQuery	1.934	0.011	4.027