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Package 504/514HostnameOS / ArchBUILDCHECKBUILD BIN
vsn 3.22.0
Wolfgang Huber
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/vsn
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: vsn
Version: 3.22.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch vsn_3.22.0.tar.gz
StartedAt: 2012-03-24 04:47:42 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 04:49:21 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 99.3 seconds
RetCode: 0
Status:  OK 
CheckDir: vsn.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/vsn.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'convergence2.pdf' from 266Kb to 115Kb
  consider running tools::compactPDF() on these files
* 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

vsn.Rcheck/00install.out:

* installing *source* package 'vsn' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c vsn.c -o vsn.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c vsn2.c -o vsn2.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o vsn.so init.o vsn.o vsn2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/vsn.Rcheck/vsn/libs/i386
** 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)

vsn.Rcheck/vsn-Ex.timings:

nameusersystemelapsed
class.vsn0.8470.0810.935
justvsn2.7270.2693.024
kidney0.0480.0060.055
lymphoma0.0730.0040.078
meanSdPlot0.2940.0600.362
normalize.AffyBatch.vsn000
sagmbSimulateData1.6760.0681.765
scalingFactorTransformation000
vsn1.1640.1511.345
vsn20.8010.0840.921
vsn2trsf0.1220.0060.129
vsnLikelihood6.0071.2597.413
vsnPlotPar0.0000.0000.001
vsnh0.0270.0040.031