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BioC 2.12: CHECK report for iPAC on petty

This page was generated on 2013-10-09 09:40:12 -0700 (Wed, 09 Oct 2013).

Package 344/671HostnameOS / ArchBUILDCHECKBUILD BIN
iPAC 1.4.2
Gregory Ryslik
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/iPAC
Last Changed Rev: 79467 / Revision: 81334
Last Changed Date: 2013-08-14 20:31:43 -0700 (Wed, 14 Aug 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: iPAC
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iPAC_1.4.2.tar.gz
StartedAt: 2013-10-08 22:50:55 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:11:44 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 1248.2 seconds
RetCode: 0
Status:  OK 
CheckDir: iPAC.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/iPAC.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'iPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iPAC' version '1.4.2'
* 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 'iPAC' can be installed ... [17s/17s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [17m/18m] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
get.Positions        418.731 19.269 443.034
ClusterFind          416.345  1.768 423.149
nmc                   73.800  0.226 103.000
Plot.Protein.Linear   61.489  1.056  63.956
get.AlignedPositions  20.059  1.009  21.887
get.Remapped.Order    16.664  1.259  18.475
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

iPAC.Rcheck/00install.out:

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

iPAC.Rcheck/iPAC-Ex.timings:

nameusersystemelapsed
ClusterFind416.345 1.768423.149
KRAS.Mutations0.0130.0170.030
PIK3CA.Mutations0.0330.0520.086
Plot.Protein.Linear61.489 1.05663.956
get.AASeq0.0100.0060.171
get.AlignedPositions20.059 1.00921.887
get.Positions418.731 19.269443.034
get.Remapped.Order16.664 1.25918.475
get.SingleLetterCode0.0110.0040.016
iPAC-package0.0080.0040.013
nmc 73.800 0.226103.000