BioC 2.12: CHECK report for crlmm on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/crlmm.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [42s/44s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
* 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 ... [539s/556s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
genotype              245.551  5.040 259.808
crlmm                 199.664  4.252 208.181
snprma                 39.970  2.156  43.188
ListClassConstructors   7.552  0.048   8.426
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’ [232s/240s]
  Running ‘doRUnit.R’ [236s/241s]
 [469s/481s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/crlmm.Rcheck/00check.log’
for details.

* installing *source* package ‘crlmm’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c gtypeCaller.c -o gtypeCaller.o
gtypeCaller.c: In function ‘gtypeCallerPart1’:
gtypeCaller.c:91:83: warning: variable ‘ptr2ncIndexes’ set but not used [-Wunused-but-set-variable]
gtypeCaller.c: In function ‘gtypeCallerPart2’:
gtypeCaller.c:315:89: warning: variable ‘ptr2trim’ set but not used [-Wunused-but-set-variable]
gtypeCaller.c:314:83: warning: variable ‘ptr2ncIndexes’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘mad_median’:
utils.c:124:15: warning: unused variable ‘n_ignore’ [-Wunused-variable]
utils.c: In function ‘normalizeBAF’:
utils.c:178:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
utils.c:180:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
gcc -std=gnu99 -shared -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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	7.552	0.048	8.426
PredictionRegion-class	0.016	0.004	0.021
batchStatisticAccessors	1.264	0.020	1.345
calculateRBaf	1.420	0.040	1.482
celfile-utils	3.765	0.656	4.601
cnSetExample	1.480	0.108	1.640
constructInf	0.008	0.000	0.006
copynumberAccessors	0.000	0.024	0.024
crlmm	199.664	4.252	208.181
crlmmIllumina	0.004	0.000	0.005
crlmmIlluminaV2	0.008	0.000	0.007
genotype.Illumina	0.016	0.000	0.017
genotype	245.551	5.040	259.808
genotypeInf	0.008	0.000	0.007
genotypes	0.008	0.004	0.014
posteriorProbability	3.669	0.056	4.001
predictionRegion	0.596	0.016	0.614
preprocessInf	0.008	0.000	0.007
readGenCallOutput	0.004	0.000	0.007
readIdatFiles	0.008	0.000	0.007
snprma	39.970	2.156	43.188
validCdfNames	0.004	0.000	0.008
xyplot	1.052	0.004	1.058

Summary

Command output