Package: crlmm

Version: 1.16.9

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings crlmm_1.16.9.tar.gz

StartedAt: 2013-03-25 00:28:35 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:46:14 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 1058.5 seconds

RetCode: 0

Status:  OK

CheckDir: crlmm.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/crlmm.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.16.9’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
genotype 166.374  8.469 181.570
crlmm    141.973  7.992 154.456
snprma    27.958  7.124  36.134
* 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/crlmm.Rcheck/00check.log’
for details.

* installing *source* package ‘crlmm’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-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-2.11-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-2.11-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/lib64 -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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
PredictionRegion-class	0.000	0.000	0.002
batchStatisticAccessors	1.328	0.024	1.447
calculateRBaf	2.005	0.028	2.058
celfile-utils	2.400	0.380	3.411
cnSetExample	0.948	0.028	0.978
constructInf	0	0	0
copynumberAccessors	0	0	0
crlmm	141.973	7.992	154.456
crlmmIllumina	0	0	0
crlmmIlluminaV2	0	0	0
genotype.Illumina	0	0	0
genotype	166.374	8.469	181.570
genotypeInf	0	0	0
genotypes	0.004	0.000	0.004
posteriorProbability	2.428	0.024	2.476
predictionRegion	0.412	0.012	0.426
preprocessInf	0	0	0
readGenCallOutput	0	0	0
readIDAT	0	0	0
readIdatFiles	0	0	0
snprma	27.958	7.124	36.134
validCdfNames	0	0	0
xyplot	0.640	0.008	0.668