Package: vsn

Version: 3.22.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings vsn_3.22.0.tar.gz

StartedAt: 2012-03-24 03:06:31 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:07:41 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 69.8 seconds

RetCode: 0

Status:  OK

CheckDir: vsn.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/vsn.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘3.22.0’
* 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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  kidney.RData       83Kb     49Kb       xz
  lymphoma.RData    291Kb    200Kb    bzip2
* 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 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-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c vsn.c -o vsn.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-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 ...
*** tangling vignette sources ...
   ‘convergence2.Rnw’ 
   ‘likelihoodcomputations.Rnw’ 
   ‘vsn.Rnw’ 
** testing if installed package can be loaded

* DONE (vsn)

name	user	system	elapsed
class.vsn	0.932	0.000	0.947
justvsn	2.256	0.020	2.478
kidney	0.040	0.000	0.037
lymphoma	0.040	0.004	0.048
meanSdPlot	0.296	0.016	0.386
normalize.AffyBatch.vsn	0	0	0
sagmbSimulateData	1.052	0.000	1.659
scalingFactorTransformation	0	0	0
vsn	0.936	0.012	0.953
vsn2	0.768	0.000	0.795
vsn2trsf	0.092	0.000	0.092
vsnLikelihood	4.496	0.012	4.538
vsnPlotPar	0	0	0
vsnh	0.016	0.000	0.016