BioC 2.11: CHECK report for gprege on moscato1

Package: gprege

Version: 1.2.0

Command: rm -rf gprege.buildbin-libdir && mkdir gprege.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gprege.buildbin-libdir gprege_1.2.0.tar.gz >gprege-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=gprege.buildbin-libdir --install="check:gprege-install.out" --force-multiarch --no-vignettes --timings gprege_1.2.0.tar.gz && mv gprege.buildbin-libdir/* gprege.Rcheck/ && rmdir gprege.buildbin-libdir

StartedAt: 2013-03-25 01:24:35 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:27:54 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 199.7 seconds

RetCode: 0

Status: OK

CheckDir: gprege.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/gprege.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gprege/DESCRIPTION' ... OK
* this is package 'gprege' version '1.2.0'
* 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 'gprege' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
exhaustivePlot 14.06   0.01   14.07
demTp63Gp1     13.62   0.03   18.80
gprege         13.49   0.02   13.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
demTp63Gp1     18.30   0.01   23.43
exhaustivePlot 17.58   0.07   17.64
gprege         15.80   0.00   15.82
* 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
  'D:/biocbld/bbs-2.11-bioc/meat/gprege.Rcheck/00check.log'
for details.


install for i386

* 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

install for x64

* installing *source* package 'gprege' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gprege' as gprege_1.2.0.zip

* DONE (gprege)

Summary

Command output