BioC 2.12: CHECK report for crlmm on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/crlmm.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.18.0’
* 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 ... [43s/43s] 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 ... [542s/556s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
genotype              247.596  5.536 255.669
crlmm                 202.304  4.376 210.841
snprma                 38.658  2.224  44.702
ListClassConstructors   6.736  0.084   7.270
celfile-utils           3.616  0.648   6.059
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’ [236s/239s]
  Running ‘doRUnit.R’ [244s/245s]
 [481s/484s] 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
** testing if installed package can be loaded
* DONE (crlmm)

name	user	system	elapsed
ListClassConstructors	6.736	0.084	7.270
PredictionRegion-class	0.008	0.000	0.008
batchStatisticAccessors	0.356	0.016	0.409
calculateRBaf	1.352	0.040	1.408
celfile-utils	3.616	0.648	6.059
cnSetExample	1.549	0.060	1.607
constructInf	0.004	0.000	0.007
copynumberAccessors	0.000	0.024	0.024
crlmm	202.304	4.376	210.841
crlmmIllumina	0.640	0.008	0.648
crlmmIlluminaV2	0.008	0.000	0.005
genotype.Illumina	0.012	0.000	0.010
genotype	247.596	5.536	255.669
genotypeInf	0.008	0.000	0.007
genotypes	0.016	0.000	0.017
posteriorProbability	3.528	0.056	3.588
predictionRegion	0.928	0.008	0.936
preprocessInf	0.004	0.000	0.006
readGenCallOutput	0.008	0.000	0.007
readIdatFiles	0.004	0.000	0.005
snprma	38.658	2.224	44.702
validCdfNames	0.008	0.000	0.006
xyplot	0.993	0.044	1.036

BioC 2.12: CHECK report for crlmm on george2

Summary

Command output