Package: survcomp

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch survcomp_1.3.1.tar.gz

StartedAt: 2011-06-22 05:41:08 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 05:42:05 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 57.0 seconds

RetCode: 0

Status:  OK

CheckDir: survcomp.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/survcomp.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.3.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘survcomp’ 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘xtable’
* 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c concordance.index.c -o concordance.index.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o survcomp.so concordance.index.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/survcomp.Rcheck/survcomp/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: rpart
Loading required package: MASS
Loading required package: mlbench
Loading required package: nnet
Loading required package: class
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: ‘bootstrap’

The following object(s) are masked from ‘package:prodlim’:

    jackknife

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘survcomp.Rnw’ 
** testing if installed package can be loaded

* DONE (survcomp)

name	user	system	elapsed
D.index	0.028	0.005	0.033
breastCancerData	1.354	0.027	1.393
censor.time	0.001	0.000	0.002
cindex.comp	0.006	0.000	0.007
cindex.comp.meta	0.021	0.001	0.022
combine.est	0.002	0.000	0.003
combine.test	0.001	0.000	0.001
concordance.index	0.006	0.003	0.009
cvpl	0.422	0.002	0.429
dindex.comp	0.027	0.000	0.028
dindex.comp.meta	0.051	0.002	0.053
fisherz	0.001	0.000	0.002
forestplot.surv	0	0	0
getsurv2	0.012	0.000	0.013
hazard.ratio	0.019	0.002	0.021
hr.comp	0.025	0.000	0.026
hr.comp.meta	0.052	0.000	0.052
hr.comp2	0.017	0.000	0.017
iauc.comp	0.910	0.009	0.925
ibsc.comp	0.462	0.003	0.467
km.coxph.plot	0.065	0.002	0.066
logpl	0.043	0.000	0.043
mainz7g	0.296	0.010	0.313
nki7g	0.298	0.009	0.307
no.at.risk	0.055	0.001	0.056
sbrier.score2proba	0.488	0.003	0.511
score2proba	0.046	0.001	0.046
td.sens.spec	0.004	0.000	0.026
tdrocc	0.443	0.002	0.448
test.hetero.est	0.001	0.001	0.001
test.hetero.test	0.001	0.000	0.001
transbig7g	0.288	0.008	0.297
unt7g	0.278	0.008	0.289
upp7g	0.281	0.007	0.290
vdx7g	0.285	0.008	0.293