Package: gprege

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gprege_1.4.0.tar.gz

StartedAt: 2013-05-01 06:27:37 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:30:32 -0700 (Wed, 01 May 2013)

EllapsedTime: 175.4 seconds

RetCode: 0

Status:  OK

CheckDir: gprege.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gprege.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gprege/DESCRIPTION' ... OK
* this is package 'gprege' version '1.4.0'
* 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 ... [11s/12s] 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 ... [65s/70s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
demTp63Gp1     19.895  0.207  24.760
exhaustivePlot 19.636  0.133  20.010
gprege         16.890  0.094  17.286
* 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
  '/Users/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
** testing if installed package can be loaded
* DONE (gprege)

name	user	system	elapsed
compareROC	0.294	0.018	0.315
demTp63Gp1	19.895	0.207	24.760
exhaustivePlot	19.636	0.133	20.010
gprege-package	0.007	0.004	0.015
gprege	16.890	0.094	17.286
rocStats	0.628	0.931	1.591