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BioC 2.13: CHECK report for intansv on perceval

This page was generated on 2014-04-05 09:53:10 -0700 (Sat, 05 Apr 2014).

Package 372/750HostnameOS / ArchBUILDCHECKBUILD BIN
intansv 1.2.0
Wen Yao
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/intansv
Last Changed Rev: 87558 / Revision: 88450
Last Changed Date: 2014-03-18 03:49:14 -0700 (Tue, 18 Mar 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: intansv
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch intansv_1.2.0.tar.gz
StartedAt: 2014-04-05 02:07:51 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:18:57 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 666.4 seconds
RetCode: 0
Status:  OK 
CheckDir: intansv.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/intansv.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 ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.2.0’
* 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 ‘intansv’ can be installed ... [37s/39s] 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 ... [303s/307s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneAnnotation  74.503 15.873  92.050
methodsMerge    63.545  2.578  67.149
plotRegion      24.764  0.759  25.858
plotChromosome  23.796  0.755  24.728
svAnnotation    23.032  1.024  24.329
readDelly       21.102  0.636  21.946
readBreakDancer 13.982  0.424  14.678
readPindel       7.952  0.203   8.210
* 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

intansv.Rcheck/00install.out:

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

intansv.Rcheck/intansv-Ex.timings:

nameusersystemelapsed
geneAnnotation74.50315.87392.050
methodsMerge63.545 2.57867.149
plotChromosome23.796 0.75524.728
plotRegion24.764 0.75925.858
readBreakDancer13.982 0.42414.678
readCnvnator1.4680.0161.545
readDelly21.102 0.63621.946
readLumpy2.4050.0632.475
readPindel7.9520.2038.210
readSoftSearch1.1190.0221.143
readSvseq3.4250.0603.494
svAnnotation23.032 1.02424.329