Package: survcomp

Version: 1.9.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings survcomp_1.9.2.tar.gz

StartedAt: 2013-01-16 06:41:07 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:41:53 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 45.8 seconds

RetCode: 0

Status:  OK

CheckDir: survcomp.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.9.2’
* 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 ‘survcomp’ can be installed ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... 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 ‘survcomp’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c concordance.index.c -o concordance.index.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
g++ -shared -L/usr/local/lib64 -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck/survcomp/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘survcomp.Rnw’ 
** testing if installed package can be loaded

* DONE (survcomp)

name	user	system	elapsed
D.index	0.064	0.004	0.066
breastCancerData	1.536	0.024	1.562
censor.time	0.056	0.000	0.053
cindex.comp	0.072	0.004	0.078
cindex.comp.meta	0.144	0.004	0.145
combine.est	0.004	0.008	0.014
combine.test	0.008	0.000	0.010
concordance.index	0.016	0.004	0.021
cvpl	0.264	0.000	0.268
dindex.comp	0.028	0.000	0.030
dindex.comp.meta	0.060	0.000	0.059
fisherz	0.012	0.000	0.011
forestplot.surv	0.092	0.004	0.096
getsurv2	0.024	0.000	0.025
hazard.ratio	0.032	0.000	0.033
hr.comp	0.032	0.000	0.032
hr.comp.meta	0.060	0.000	0.059
hr.comp2	0.140	0.000	0.142
iauc.comp	0.748	0.004	0.757
ibsc.comp	0.324	0.004	0.450
km.coxph.plot	0.060	0.004	0.064
logpl	0.064	0.000	0.064
mainz7g	0.360	0.012	0.378
metaplot.surv	0.136	0.000	0.138
mrmr.cindex	0.012	0.004	0.020
nki7g	0.468	0.000	0.468
no.at.risk	0.080	0.000	0.084
sbrier.score2proba	0.296	0.000	0.299
score2proba	0.100	0.000	0.101
td.sens.spec	0.136	0.004	0.141
tdrocc	0.320	0.000	0.319
test.hetero.est	0.016	0.000	0.013
test.hetero.test	0.012	0.000	0.013
transbig7g	0.328	0.012	0.344
unt7g	0.436	0.008	0.444
upp7g	0.420	0.016	0.434
vdx7g	0.308	0.012	0.320