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BioC 3.0: CHECK report for RefNet on oaxaca

This page was generated on 2015-04-10 10:08:52 -0700 (Fri, 10 Apr 2015).

Package 737/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefNet 1.2.1
Paul Shannon
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/RefNet
Last Changed Rev: 101772 / Revision: 102249
Last Changed Date: 2015-04-02 07:29:15 -0700 (Thu, 02 Apr 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

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

Command output

##############################################################################
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###
### Running command:
###
###   /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

RefNet.Rcheck/00install.out:

* 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)

RefNet.Rcheck/RefNet-Ex.timings:

nameusersystemelapsed
RefNet-class13.398 0.09517.956
detectDuplicateInteractions0.0270.0010.029
interactions 8.479 0.09812.851
pickBestFromDupGroup0.0240.0010.026
providerClasses 8.574 0.09112.822
providers 8.442 0.08712.885
pubmedAbstract0.0730.0010.481