BioC 2.12: CHECK report for survcomp on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'survcomp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'survcomp' version '1.10.0'
* 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 'survcomp' can be installed ... [8s/9s] 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 ... NOTE
.extract.all.parents: warning in matrix(0, nc = nsol, nr = (maxparents
  + 1)): partial argument match of 'nr' to 'nrow'
.extract.all.parents: warning in matrix(0, nc = nsol, nr = (maxparents
  + 1)): partial argument match of 'nc' to 'ncol'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [12s/13s] 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck/00check.log'
for details.

* installing *source* package 'survcomp' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c concordance.index.c -o concordance.index.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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
** testing if installed package can be loaded
* DONE (survcomp)

name	user	system	elapsed
D.index	0.075	0.006	0.096
breastCancerData	2.039	0.066	2.109
censor.time	0.050	0.001	0.051
cindex.comp	0.136	0.004	0.140
cindex.comp.meta	0.026	0.006	0.032
combine.est	0.012	0.003	0.014
combine.test	0.009	0.003	0.011
concordance.index	0.022	0.007	0.030
cvpl	0.383	0.015	0.402
dindex.comp	0.038	0.001	0.040
dindex.comp.meta	0.072	0.006	0.091
fisherz	0.009	0.002	0.012
forestplot.surv	0.155	0.007	0.166
getsurv2	0.024	0.003	0.026
hazard.ratio	0.032	0.005	0.038
hr.comp	0.039	0.000	0.039
hr.comp.meta	0.069	0.003	0.074
hr.comp2	0.026	0.002	0.029
iauc.comp	1.154	0.026	1.183
ibsc.comp	0.460	0.022	0.504
km.coxph.plot	0.080	0.003	0.084
logpl	0.071	0.003	0.074
mainz7g	0.640	0.025	0.697
metaplot.surv	0.027	0.001	0.032
mrmr.cindex	0.084	0.001	0.089
nki7g	0.619	0.021	0.677
no.at.risk	0.089	0.001	0.095
sbrier.score2proba	0.364	0.006	0.371
score2proba	0.103	0.002	0.107
td.sens.spec	0.011	0.004	0.038
tdrocc	0.370	0.037	0.595
test.hetero.est	0.010	0.004	0.014
test.hetero.test	0.008	0.002	0.011
transbig7g	0.473	0.025	0.689
unt7g	0.491	0.025	0.550
upp7g	0.604	0.023	0.679
vdx7g	0.574	0.024	0.602

BioC 2.12: CHECK report for survcomp on petty

Summary

Command output