BioC 2.12: CHECK report for crlmm on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/crlmm.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.18.0'
* 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 'crlmm' can be installed ... [37s/38s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [536s/564s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
genotype              215.818 34.469 272.148
crlmm                 203.105  5.942 214.004
snprma                 35.097  3.032  38.468
celfile-utils           4.716  0.595   5.481
ListClassConstructors   4.982  0.113   5.168
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'crlmm_unit_tests.R' [231s/234s]
  Running 'doRUnit.R' [231s/234s]
 [462s/469s] 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 -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
** testing if installed package can be loaded
* DONE (crlmm)

name	user	system	elapsed
ListClassConstructors	4.982	0.113	5.168
PredictionRegion-class	0.482	0.005	0.489
batchStatisticAccessors	0.515	0.050	0.570
calculateRBaf	1.128	0.066	1.202
celfile-utils	4.716	0.595	5.481
cnSetExample	1.323	0.163	1.494
constructInf	0.002	0.004	0.007
copynumberAccessors	0.006	0.011	0.018
crlmm	203.105	5.942	214.004
crlmmIllumina	0.002	0.004	0.006
crlmmIlluminaV2	0.003	0.005	0.007
genotype.Illumina	0.005	0.009	0.014
genotype	215.818	34.469	272.148
genotypeInf	0.002	0.003	0.007
genotypes	0.011	0.005	0.015
posteriorProbability	3.575	0.638	4.385
predictionRegion	0.670	0.086	0.765
preprocessInf	0.002	0.004	0.007
readGenCallOutput	0.002	0.004	0.006
readIdatFiles	0.003	0.005	0.007
snprma	35.097	3.032	38.468
validCdfNames	0.002	0.004	0.006
xyplot	1.200	0.124	1.350

BioC 2.12: CHECK report for crlmm on petty

Summary

Command output