Package: pint

Version: 1.10.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings pint_1.10.0.tar.gz

StartedAt: 2013-03-25 03:49:45 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:54:56 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 310.7 seconds

RetCode: 0

Status:  OK

CheckDir: pint.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/pint.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pint/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pint’ version ‘1.10.0’
* 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 whether package ‘pint’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... NOTE
findModel,GenomeModels: no visible binding for global variable ‘pIndex’
* 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
screen                    70.849  0.340  80.236
ChromosomeModels-class    66.180  0.392  78.038
plot                      18.425  0.088  22.534
GeneDependencyModel-class 17.885  0.076  19.786
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/pint.Rcheck/00check.log’
for details.

* installing *source* package ‘pint’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘as.data.frame’ from package ‘base’ in package ‘pint’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘depsearch.Rnw’ 
** testing if installed package can be loaded

* DONE (pint)

name	user	system	elapsed
ChromosomeModels-class	66.180	0.392	78.038
GeneDependencyModel-class	17.885	0.076	19.786
fit.byname	0.152	0.000	0.166
get.neighboring.probes	0	0	0
get.neighs	0	0	0
join.top.regions	0	0	0
order.feature.info	0	0	0
pint.data	0.108	0.004	0.112
plot	18.425	0.088	22.534
screen	70.849	0.340	80.236
summarize.region.parameters	0.004	0.000	0.000
window	0.188	0.004	0.223
z.effect	0.112	0.008	0.124