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Package 140/658HostnameOS / ArchBUILDCHECKBUILD BIN
cnvGSA 1.3.0
Robert Ziman
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cnvGSA
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: cnvGSA
Version: 1.3.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cnvGSA_1.3.0.tar.gz
StartedAt: 2013-03-25 00:57:21 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:59:53 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 152.1 seconds
RetCode: 0
Status:  OK 
CheckDir: cnvGSA.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cnvGSA.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cnvGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cnvGSA’ version ‘1.3.0’
* 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 ‘cnvGSA’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
f.add_binned_bhfdr: no visible binding for global variable ‘GsSize’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [112s/114s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cnvGSAFisher 94.026  1.088  97.213
getCnvGenes   5.168  0.080   5.484
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/cnvGSA.Rcheck/00check.log’
for details.

cnvGSA.Rcheck/00install.out:

* installing *source* package ‘cnvGSA’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘cnvGSA’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cnvGSA-vignette.Rnw’ 
** testing if installed package can be loaded
* DONE (cnvGSA)

cnvGSA.Rcheck/cnvGSA-Ex.timings:

nameusersystemelapsed
CnvGSAInput-class0.0120.0040.016
CnvGSAOutput-class2.5960.2562.886
cnvGSAFisher94.026 1.08897.213
cnvGSAexportBurdenStats1.6240.2121.849
getCnvGenes5.1680.0805.484
readGMT1.5160.0121.543
readGVF2.0600.0042.069
readParamsRFile0.0120.0000.014
summary-methods1.6120.1961.828