Package: iPAC

Version: 1.1.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings iPAC_1.1.3.tar.gz

StartedAt: 2013-01-16 03:42:48 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:59:29 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 1001.1 seconds

RetCode: 0

Status:  OK

CheckDir: iPAC.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/iPAC.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iPAC’ version ‘1.1.3’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
get.Positions        381.492  0.948 401.282
ClusterFind          268.745  1.920 287.825
Plot.Protein.Linear   69.096  0.384  74.032
get.AlignedPositions  53.959  0.596  61.290
nmc                   46.955  0.004  46.994
get.Remapped.Order    17.841  0.004  22.168
* 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
   ‘iPAC.Rnw’ 
** testing if installed package can be loaded

* DONE (iPAC)

name	user	system	elapsed
ClusterFind	268.745	1.920	287.825
KRAS.Mutations	0.064	0.000	0.065
PIK3CA.Mutations	0.308	0.016	0.325
Plot.Protein.Linear	69.096	0.384	74.032
get.AASeq	0.004	0.000	0.575
get.AlignedPositions	53.959	0.596	61.290
get.Positions	381.492	0.948	401.282
get.Remapped.Order	17.841	0.004	22.168
get.SingleLetterCode	0.004	0.004	0.008
iPAC-package	0.012	0.000	0.012
nmc	46.955	0.004	46.994