BioC 3.2: CHECK report for gprege on zin1

Package: gprege

Version: 1.13.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gprege_1.13.0.tar.gz

StartedAt: 2015-08-24 00:34:02 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:35:19 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 76.5 seconds

RetCode: 0

Status:  OK

CheckDir: gprege.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings gprege_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/gprege.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gprege/DESCRIPTION’ ... OK
* this is package ‘gprege’ version ‘1.13.0’
* 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 ... [4s/4s] 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 ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
exhaustivePlot 11.905  0.020  11.983
demTp63Gp1     11.271  0.035  12.403
gprege          9.548  0.000   9.558
* 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
  ‘/home/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	0.063	0.003	0.066
demTp63Gp1	11.271	0.035	12.403
exhaustivePlot	11.905	0.020	11.983
gprege-package	0	0	0
gprege	9.548	0.000	9.558
rocStats	0.317	0.312	0.629