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Package 180/436HostnameOS / ArchBUILDCHECKBUILD BIN
GGBase 3.11.5
Vince Carey
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGBase
Last Changed Rev: 51105 / Revision: 53255
Last Changed Date: 2010-11-29 08:42:29 -0800 (Mon, 29 Nov 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ WARNINGS ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: GGBase
Version: 3.11.5
Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings GGBase_3.11.5.tar.gz
StartedAt: 2011-02-24 19:57:24 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 20:00:55 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 210.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GGBase.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/GGBase.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.11.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GGBase' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
isCis: no visible global function definition for 'lookUp'
snpsNear: no visible global function definition for 'geneIdType'
snpsNear: no visible global function definition for 'geneIds'
snpLocs.Hs,chrnum-missing: no visible binding for global variable
  'hsSnpLocs'
snpLocs.Hs,chrnum-rsid: no visible binding for global variable
  'hsSnpLocs'
snpLocs.Hs,missing-rsid: no visible binding for global variable
  'hsSnpLocs'
snpLocs.Hs,rsid-ANY: no visible binding for global variable 'hsSnpLocs'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignettes without corresponding PDF:


D:/biocbld/bbs-2.8-bioc/meat/GGBase.Rcheck/00_pkg_src/GGBase/inst/doc/newSNPloc.Rnw
 SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/GGBase.Rcheck/00check.log'
for details

GGBase.Rcheck/00install.out:

* installing *source* package 'GGBase' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GGBase)

GGBase.Rcheck/GGBase-Ex.timings:

nameusersystemelapsed
MAFfilter3.040.063.14
SessionInfo-class000
casting0.020.000.01
featureFilter0.840.060.94
gwSnpScreenResult-class000
make_smlSet0.220.000.21
multiCisTestResult-class000
plot_EvG-methods0.600.020.63
smlSet-class0.170.010.27
smlSummary0.450.000.45
snpLocs.Hs15.50 0.1915.69
snpLocs.Hsapiens1.450.081.69
snpsNear13.98 0.1214.12