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BioC 3.0: CHECK report for Rnits on oaxaca

This page was generated on 2015-04-10 10:09:13 -0700 (Fri, 10 Apr 2015).

Package 763/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rnits 1.0.0
Dipen P. Sangurdekar
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/Rnits
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
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: 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

Command output

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

Rnits.Rcheck/00install.out:

* 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)

Rnits.Rcheck/Rnits-Ex.timings:

nameusersystemelapsed
build.Rnits1.0420.0311.077
calculateGCV-methods8.5590.0938.723
fit-methods0.5810.0180.601
getCID-methods0.6670.0270.694
getFitModel-methods0.5770.0070.586
getLR-methods0.5750.0180.596
getPval-methods0.5600.0060.567
getStat-methods0.5740.0200.594
plotResults-methods0.6610.0120.684
summarizeProbes-methods0.5770.0080.586
summary-methods0.6570.0110.669
timeAlign-methods2.2840.1942.483
topData-methods0.5830.0160.601