Package: baySeq

Version: 1.7.1

Command: mkdir baySeq.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=baySeq.buildbin-libdir baySeq_1.7.1.tar.gz >baySeq-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=baySeq.buildbin-libdir --install="check:baySeq-install.out" --force-multiarch --no-vignettes --timings baySeq_1.7.1.tar.gz && mv baySeq.buildbin-libdir/* baySeq.Rcheck/ && rmdir baySeq.buildbin-libdir

StartedAt: 2011-07-07 04:10:24 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:28:07 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 1062.8 seconds

RetCode: 0

Status:  OK

CheckDir: baySeq.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/baySeq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'baySeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'baySeq' version '1.7.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'baySeq' can be installed ... OK
* checking installed package size ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
getPosteriors: no visible binding for global variable 'clustAssign'
getPosteriors: no visible binding for global variable 'getPostsEnv'
getPriors.NB: no visible global function definition for
  'estimateCommonDisp'
getPriors.NB: no visible global function definition for
  'estimateTagwiseDisp'
* 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

install for i386

* installing *source* package 'baySeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "rbind" in package "baySeq"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'baySeq.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'baySeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'baySeq' as baySeq_1.7.1.zip

* DONE (baySeq)

name	user	system	elapsed
baySeq-classes	0.03	0.00	0.03
baySeq-package	5.29	0.00	5.29
bimodalSep	0	0	0
getLikelihoods	115.11	0.03	147.13
getPosteriors	0.03	0.00	0.03
getPriors	0.12	0.00	25.49
getTPs	5.45	0.01	5.46
plotMA.CD	0.01	0.00	0.02
plotPosteriors	114.79	0.05	114.88
plotPriors	199.87	0.03	200.13
topCounts	5.21	0.00	5.24