BioC 2.12: CHECK report for crlmm on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/crlmm.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'crlmm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crlmm' version '1.17.15'
* 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 'crlmm' can be installed ... [33s/34s] OK
* checking installed package size ... OK
* checking package 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 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 ... [492s/517s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
genotype      202.174 33.584 253.913
crlmm         179.767  6.197 188.486
snprma         31.844  3.036  38.347
celfile-utils   4.563  0.590   5.379
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'crlmm_unit_tests.R' [212s/214s]
  Running 'doRUnit.R' [210s/212s]
 [422s/427s] 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 'crlmm' ...
** 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  -c gtypeCaller.c -o gtypeCaller.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  -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  -c trimmed.c -o trimmed.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  -c utils.c -o utils.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 -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/crlmm.Rcheck/crlmm/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'AffyGW.Rnw' 
   'CopyNumberOverview.Rnw' 
   'IlluminaPreprocessCN.Rnw' 
   'Infrastructure.Rnw' 
   'genotyping.Rnw' 
   'gtypeDownstream.Rnw' 
** testing if installed package can be loaded
* DONE (crlmm)

name	user	system	elapsed
ListClassConstructors	4.418	0.115	4.550
PredictionRegion-class	0.010	0.005	0.015
batchStatisticAccessors	0.954	0.039	0.998
calculateRBaf	1.112	0.067	1.183
celfile-utils	4.563	0.590	5.379
cnSetExample	1.241	0.141	1.383
constructInf	0.003	0.005	0.008
copynumberAccessors	0.007	0.015	0.022
crlmm	179.767	6.197	188.486
crlmmIllumina	0.311	0.075	0.388
crlmmIlluminaV2	0.003	0.005	0.008
genotype.Illumina	0.005	0.012	0.018
genotype	202.174	33.584	253.913
genotypeInf	0.003	0.005	0.008
genotypes	0.009	0.007	0.016
posteriorProbability	3.186	0.737	3.968
predictionRegion	0.752	0.176	0.933
preprocessInf	0.003	0.005	0.007
readGenCallOutput	0.003	0.004	0.007
readIdatFiles	0.003	0.005	0.007
snprma	31.844	3.036	38.347
validCdfNames	0.003	0.005	0.009
xyplot	0.881	0.113	1.104

Summary

Command output