BioC 2.12: CHECK report for iPAC on petty

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

* 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

* 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)

name	user	system	elapsed
ClusterFind	416.345	1.768	423.149
KRAS.Mutations	0.013	0.017	0.030
PIK3CA.Mutations	0.033	0.052	0.086
Plot.Protein.Linear	61.489	1.056	63.956
get.AASeq	0.010	0.006	0.171
get.AlignedPositions	20.059	1.009	21.887
get.Positions	418.731	19.269	443.034
get.Remapped.Order	16.664	1.259	18.475
get.SingleLetterCode	0.011	0.004	0.016
iPAC-package	0.008	0.004	0.013
nmc	73.800	0.226	103.000