BioC 2.12: CHECK report for iPAC on george2

Package: iPAC

Version: 1.4.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings iPAC_1.4.2.tar.gz

StartedAt: 2013-10-09 02:43:28 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:07:50 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 1461.6 seconds

RetCode: 0

Status:  OK

CheckDir: iPAC.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/iPAC.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.4.2’
* 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 ... [18s/18s] 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 ... [21m/22m] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
get.Positions        662.213  0.168 672.076
ClusterFind          378.900  1.436 387.003
Plot.Protein.Linear  112.339  0.756 115.769
nmc                   64.004  0.012  64.553
get.AlignedPositions  29.422  0.432  30.488
get.Remapped.Order    29.158  0.024  30.368
* 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	378.900	1.436	387.003
KRAS.Mutations	0.016	0.008	0.026
PIK3CA.Mutations	0.036	0.028	0.065
Plot.Protein.Linear	112.339	0.756	115.769
get.AASeq	0.008	0.004	0.341
get.AlignedPositions	29.422	0.432	30.488
get.Positions	662.213	0.168	672.076
get.Remapped.Order	29.158	0.024	30.368
get.SingleLetterCode	0.008	0.000	0.010
iPAC-package	0.012	0.000	0.011
nmc	64.004	0.012	64.553