BioC 3.0: CHECK report for Rnits on oaxaca

Package: Rnits

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rnits_1.0.0.tar.gz

StartedAt: 2015-04-10 02:58:26 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:00:01 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 94.9 seconds

RetCode: 0

Status:  OK

CheckDir: Rnits.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rnits_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rnits.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rnits/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rnits’ version ‘1.0.0’
* 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 ‘Rnits’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotResults,Rnits: no visible global function definition for ‘aes’
plotResults,Rnits: no visible binding for global variable ‘Time’
plotResults,Rnits: no visible binding for global variable ‘value’
plotResults,Rnits: no visible global function definition for
  ‘geom_point’
plotResults,Rnits: no visible binding for global variable ‘Sample’
plotResults,Rnits: no visible global function definition for
  ‘geom_smooth’
plotResults,Rnits: no visible global function definition for ‘ylab’
plotResults,Rnits: no visible global function definition for ‘theme_bw’
plotResults,Rnits: no visible global function definition for ‘theme’
plotResults,Rnits: no visible global function definition for
  ‘scale_color_brewer’
plotResults,Rnits: no visible global function definition for
  ‘facet_wrap’
* 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 ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
calculateGCV-methods 8.559  0.093   8.723
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rnits.Rcheck/00check.log’
for details.

* installing *source* package ‘Rnits’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘Rnits’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rnits)

name	user	system	elapsed
build.Rnits	1.042	0.031	1.077
calculateGCV-methods	8.559	0.093	8.723
fit-methods	0.581	0.018	0.601
getCID-methods	0.667	0.027	0.694
getFitModel-methods	0.577	0.007	0.586
getLR-methods	0.575	0.018	0.596
getPval-methods	0.560	0.006	0.567
getStat-methods	0.574	0.020	0.594
plotResults-methods	0.661	0.012	0.684
summarizeProbes-methods	0.577	0.008	0.586
summary-methods	0.657	0.011	0.669
timeAlign-methods	2.284	0.194	2.483
topData-methods	0.583	0.016	0.601