Package: gprege

Version: 1.3.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings gprege_1.3.0.tar.gz

StartedAt: 2013-01-16 03:19:44 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:21:55 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 130.2 seconds

RetCode: 0

Status:  OK

CheckDir: gprege.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/gprege.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 ‘gprege/DESCRIPTION’ ... OK
* this is package ‘gprege’ version ‘1.3.0’
* 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 ‘gprege’ 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 ... NOTE
exhaustivePlot: warning in filled.contour(x = width, y =
  log10(signal/(y_sd - signal)), z = t(C), color = gray.colors, xlab =
  "Lengthscale", ylab = bquote(paste(log[10] ˜ SNR)), nlevels =
  nlevels, main = "Log-marginal likelihood function", plot.axes = {:
  partial argument match of 'color' to 'color.palette'
exhaustivePlot: warning in axis(1): partial argument match of 'color'
  to 'color.palette'
exhaustivePlot: warning in axis(2): partial argument match of 'color'
  to 'color.palette'
exhaustivePlot: warning in points(w, log10(snr), pch = 20): partial
  argument match of 'color' to 'color.palette'
exhaustivePlot: warning in }): partial argument match of 'color' to
  'color.palette'
gprege: warning in close.screen(all = TRUE): partial argument match of
  'all' to 'all.screens'
* 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
demTp63Gp1     15.221  0.080  23.635
exhaustivePlot 14.673  0.016  14.693
gprege         13.352  0.020  13.382
* 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-2.12-bioc/meat/gprege.Rcheck/00check.log’
for details.

* installing *source* package ‘gprege’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘gprege_quick.Rnw’ 
** testing if installed package can be loaded

* DONE (gprege)

name	user	system	elapsed
compareROC	0.080	0.004	0.083
demTp63Gp1	15.221	0.080	23.635
exhaustivePlot	14.673	0.016	14.693
gprege-package	0.000	0.008	0.006
gprege	13.352	0.020	13.382
rocStats	0.256	0.384	0.640