BioC 2.13: CHECK report for vsn on perceval

Package: vsn

Version: 3.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch vsn_3.30.0.tar.gz

StartedAt: 2014-04-05 04:55:38 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:57:13 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 94.5 seconds

RetCode: 0

Status:  OK

CheckDir: vsn.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/vsn.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vsn/DESCRIPTION’ ... OK
* this is package ‘vsn’ version ‘3.30.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘vsn’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 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 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘convergence2.Rnw’, ‘likelihoodcomputations.Rnw’, ‘vsn.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [13s/13s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/vsn.Rcheck/00check.log’
for details.

* installing *source* package ‘vsn’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c vsn.c -o vsn.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c vsn2.c -o vsn2.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.13-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
** testing if installed package can be loaded
* DONE (vsn)

name	user	system	elapsed
class.vsn	0.812	0.016	0.829
justvsn	2.132	0.035	2.177
kidney	0.042	0.010	0.052
lymphoma	0.050	0.014	0.064
meanSdPlot	0.169	0.022	0.199
normalize.AffyBatch.vsn	0.006	0.002	0.008
sagmbSimulateData	0.892	0.005	0.907
scalingFactorTransformation	0.011	0.002	0.013
vsn	0.835	0.033	0.886
vsn2	0.630	0.019	0.662
vsn2trsf	0.104	0.016	0.122
vsnLikelihood	3.481	0.558	4.054
vsnPlotPar	0.016	0.002	0.018
vsnh	0.032	0.012	0.045