BioC 2.11: CHECK report for crlmm on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/crlmm.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'crlmm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crlmm' version '1.16.9'
* 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 'crlmm' 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 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 ... NOTE
calculateRBafCNSet: no visible binding for global variable 'i'
* 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
genotype             161.914 19.222 210.409
crlmm                141.501  8.006 151.926
snprma                29.294  4.162  35.078
posteriorProbability   2.808  1.555   5.141
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'crlmm_unit_tests.R'
  Running 'doRUnit.R'
 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/crlmm.Rcheck/00check.log'
for details.

* installing *source* package 'crlmm' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c gtypeCaller.c -o gtypeCaller.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -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 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c trimmed.c -o trimmed.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
utils.c: In function 'normalizeBAF':
utils.c:178: warning: suggest parentheses around comparison in operand of &
utils.c:180: warning: suggest parentheses around comparison in operand of &
gcc -arch i386 -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-2.11-bioc/meat/crlmm.Rcheck/crlmm/libs/i386
** 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
PredictionRegion-class	0.002	0.001	0.002
batchStatisticAccessors	1.125	0.064	1.220
calculateRBaf	1.673	0.121	1.871
celfile-utils	2.239	0.793	3.281
cnSetExample	1.052	0.137	1.296
constructInf	0	0	0
copynumberAccessors	0	0	0
crlmm	141.501	8.006	151.926
crlmmIllumina	0	0	0
crlmmIlluminaV2	0.001	0.000	0.000
genotype.Illumina	0	0	0
genotype	161.914	19.222	210.409
genotypeInf	0	0	0
genotypes	0.005	0.000	0.006
posteriorProbability	2.808	1.555	5.141
predictionRegion	0.693	0.240	1.084
preprocessInf	0.001	0.000	0.001
readGenCallOutput	0.000	0.000	0.001
readIDAT	0.001	0.000	0.000
readIdatFiles	0	0	0
snprma	29.294	4.162	35.078
validCdfNames	0.001	0.000	0.000
xyplot	0.791	0.088	0.899

Summary

Command output