BioC 2.12: CHECK report for survcomp on george2

Package: survcomp

Version: 1.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings survcomp_1.10.0.tar.gz

StartedAt: 2013-10-09 05:12:27 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:13:32 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 64.6 seconds

RetCode: 0

Status:  OK

CheckDir: survcomp.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/survcomp.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 ‘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 ... [7s/8s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [11s/12s] 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/survcomp.Rcheck/00check.log’
for details.

* 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  -Wall -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  -Wall -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
foo_mrmr_ensemble_surv.cpp: In function ‘double get_correlation_ensemble(double*, int*, int, int, int)’:
foo_mrmr_ensemble_surv.cpp:12:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:22:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:106:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘void build_mim_cIndex_subset(double*, double*, int*, int, int, int*, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int*)’:
foo_mrmr_ensemble_surv.cpp:202:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:214:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:216:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable ‘msurv_x’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:191:27: warning: unused variable ‘ustrat_x’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:351:7: warning: unused variable ‘cnt_back’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable ‘nsub’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:393:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:396:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:400:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:401:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:412:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:419:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable ‘mim’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
foo_mrmr_ensemble_surv.cpp:448:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:437:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable ‘max_val’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)’:
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable ‘found’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree<int>&, tree<int>::pre_order_iterator, double*, int*, int, int, int, int, int, int, double, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:593:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:596:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:597:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:604:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:646:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:654:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:657:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:661:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable ‘nsamples_boot’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:578:48: warning: unused variable ‘tmp_val_max_ind’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:578:66: warning: unused variable ‘prev_sel_tmp’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:579:21: warning: unused variable ‘vec_sort’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:579:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-variable]
foo_mrmr_ensemble_surv.cpp: In function ‘SEXPREC* mrmr_cIndex_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_ensemble_surv.cpp:785:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:819:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:833:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:842:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_ensemble_surv.cpp:800:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:803:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable ‘ind’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:732:30: warning: unused variable ‘res_all’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:732:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:733:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
foo_mrmr_ensemble_surv.cpp:858:9: warning: ‘Rres’ may be used uninitialized in this function [-Wuninitialized]
foo_mrmr_ensemble_surv.cpp:820:25: warning: ‘res_old’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
foo_mrmr_surv.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr_surv.cpp:12:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp:22:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr_surv.cpp:49:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp:50:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp:56:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp:58:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int*, int*)’:
foo_mrmr_surv.cpp:146:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
foo_mrmr_surv.cpp:147:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_surv.cpp:300:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
foo_mrmr_surv.cpp:340:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -L/usr/local/lib -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 /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
** testing if installed package can be loaded
* DONE (survcomp)

name	user	system	elapsed
D.index	0.060	0.008	0.070
breastCancerData	2.028	0.068	2.145
censor.time	0.080	0.000	0.079
cindex.comp	0.236	0.000	0.239
cindex.comp.meta	0.024	0.020	0.044
combine.est	0.016	0.004	0.021
combine.test	0.016	0.000	0.017
concordance.index	0.032	0.012	0.043
cvpl	0.356	0.008	0.362
dindex.comp	0.028	0.004	0.032
dindex.comp.meta	0.064	0.000	0.066
fisherz	0.012	0.000	0.012
forestplot.surv	0.116	0.000	0.116
getsurv2	0.028	0.004	0.032
hazard.ratio	0.044	0.000	0.048
hr.comp	0.056	0.000	0.053
hr.comp.meta	0.076	0.000	0.077
hr.comp2	0.044	0.000	0.046
iauc.comp	0.916	0.036	0.948
ibsc.comp	0.440	0.016	0.489
km.coxph.plot	0.092	0.000	0.092
logpl	0.084	0.000	0.083
mainz7g	0.616	0.012	0.626
metaplot.surv	0.048	0.004	0.061
mrmr.cindex	0.120	0.000	0.121
nki7g	0.568	0.012	0.583
no.at.risk	0.128	0.004	0.134
sbrier.score2proba	0.352	0.000	0.365
score2proba	0.104	0.000	0.105
td.sens.spec	0.068	0.000	0.070
tdrocc	0.532	0.004	0.550
test.hetero.est	0.076	0.000	0.074
test.hetero.test	0.048	0.000	0.049
transbig7g	0.528	0.020	0.551
unt7g	0.384	0.016	0.406
upp7g	0.568	0.012	0.606
vdx7g	0.376	0.008	0.384