BioC 2.12: CHECK report for pint on petty

Package: pint

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pint_1.12.0.tar.gz

StartedAt: 2013-10-08 23:27:24 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:33:36 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 371.9 seconds

RetCode: 0

Status:  OK

CheckDir: pint.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pint.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 'pint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pint' version '1.12.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'pint' can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
File 'pint/R/firstlib.R':
  .onLoad calls:
    packageStartupMessage("\npint Copyright (C) 2008-2012 Olli-Pekka Huovilainen and Leo Lahti.\n\nThis program comes with ABSOLUTELY NO WARRANTY.\nThis is free software, and you are welcome to redistribute it\nunder the FreeBSD license.\nSee the licensing terms for details.\n")

See section 'Good practice' in '?.onAttach'.

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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [236s/239s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
screen                    94.513  1.471  96.884
ChromosomeModels-class    86.168  1.381  88.642
plot                      22.848  0.267  23.329
GeneDependencyModel-class 22.113  0.242  22.951
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (pint)

name	user	system	elapsed
ChromosomeModels-class	86.168	1.381	88.642
GeneDependencyModel-class	22.113	0.242	22.951
fit.byname	0.238	0.011	0.261
get.neighboring.probes	0.004	0.002	0.006
get.neighs	0.005	0.001	0.007
join.top.regions	0.009	0.002	0.012
order.feature.info	0.005	0.003	0.008
pint.data	0.235	0.006	0.243
plot	22.848	0.267	23.329
screen	94.513	1.471	96.884
summarize.region.parameters	0.007	0.003	0.011
window	0.33	0.01	0.34
z.effect	0.236	0.012	0.248