BioC 3.2: CHECK report for gprege on perceval

Package: gprege

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gprege_1.14.0.tar.gz

StartedAt: 2015-11-10 05:37:41 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 05:39:32 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 110.8 seconds

RetCode: 0

Status:  OK

CheckDir: gprege.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gprege_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/gprege.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gprege/DESCRIPTION’ ... OK
* this is package ‘gprege’ version ‘1.14.0’
* 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 ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘gptk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
exhaustivePlot: no visible global function definition for ‘gpCreate’
exhaustivePlot: no visible global function definition for
  ‘gpExpandParam’
exhaustivePlot: no visible global function definition for
  ‘gpLogLikelihood’
exhaustivePlot: no visible global function definition for ‘gpPlot’
gprege: no visible global function definition for ‘gpOptions’
gprege: no visible global function definition for ‘gpCreate’
gprege: no visible global function definition for ‘gpExpandParam’
gprege: no visible global function definition for ‘gpOptimise’
gprege: no visible global function definition for ‘gpExtractParam’
gprege: no visible global function definition for ‘gpLogLikelihood’
gprege: no visible global function definition for ‘gpPlot’
gprege: no visible global function definition for ‘gpPosteriorMeanVar’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
demTp63Gp1     15.531  0.091  16.111
exhaustivePlot 15.130  0.067  15.203
gprege         12.386  0.019  12.410
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.075	0.008	0.082
demTp63Gp1	15.531	0.091	16.111
exhaustivePlot	15.130	0.067	15.203
gprege-package	0.000	0.001	0.001
gprege	12.386	0.019	12.410
rocStats	0.394	0.577	0.971