BioC 3.0: CHECK report for RefNet on oaxaca

Package: RefNet

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RefNet_1.2.1.tar.gz

StartedAt: 2015-04-10 02:43:44 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:50:55 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 431.1 seconds

RetCode: 0

Status:  OK

CheckDir: RefNet.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 RefNet_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RefNet.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 ‘RefNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefNet’ version ‘1.2.1’
* 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 ‘RefNet’ can be installed ... [30s/34s] 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [54s/72s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
RefNet-class    13.398  0.095  17.956
providerClasses  8.574  0.091  12.822
interactions     8.479  0.098  12.851
providers        8.442  0.087  12.885
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [35s/44s]
 [35s/45s] OK
* 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

* installing *source* package ‘RefNet’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (RefNet)

name	user	system	elapsed
RefNet-class	13.398	0.095	17.956
detectDuplicateInteractions	0.027	0.001	0.029
interactions	8.479	0.098	12.851
pickBestFromDupGroup	0.024	0.001	0.026
providerClasses	8.574	0.091	12.822
providers	8.442	0.087	12.885
pubmedAbstract	0.073	0.001	0.481