Package: vsn

Version: 3.26.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings vsn_3.26.0.tar.gz

StartedAt: 2013-03-25 05:34:15 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:35:37 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 82.1 seconds

RetCode: 0

Status:  OK

CheckDir: vsn.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/vsn.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vsn/DESCRIPTION’ ... OK
* this is package ‘vsn’ version ‘3.26.0’
* 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 whether package ‘vsn’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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

* installing *source* package ‘vsn’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c vsn.c -o vsn.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c vsn2.c -o vsn2.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o vsn.so init.o vsn.o vsn2.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/vsn.Rcheck/vsn/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘logLik’ from package ‘stats’ in package ‘vsn’
Creating a generic function for ‘coef’ from package ‘stats’ in package ‘vsn’
Creating a generic function for ‘coefficients’ from package ‘stats’ in package ‘vsn’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘convergence2.Rnw’ 
   ‘likelihoodcomputations.Rnw’ 
   ‘vsn.Rnw’ 
** testing if installed package can be loaded

* DONE (vsn)

name	user	system	elapsed
class.vsn	0.932	0.004	0.965
justvsn	2.348	0.012	2.369
kidney	0.044	0.000	0.043
lymphoma	0.032	0.004	0.038
meanSdPlot	0.308	0.008	0.316
normalize.AffyBatch.vsn	0	0	0
sagmbSimulateData	1.132	0.000	1.147
scalingFactorTransformation	0	0	0
vsn	0.868	0.020	0.890
vsn2	0.644	0.000	0.647
vsn2trsf	0.108	0.000	0.111
vsnLikelihood	4.380	0.052	4.436
vsnPlotPar	0	0	0
vsnh	0.012	0.008	0.018