Package: survcomp

Version: 1.34.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings survcomp_1.34.0.tar.gz

StartedAt: 2019-10-16 05:19:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:20:58 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 60.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: survcomp.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings survcomp_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/survcomp.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-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 ‘1.34.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
concordance:
  function(object, ...)
concordance.index:
  function(x, surv.time, surv.event, cl, weights, comppairs, strat,
           alpha, outx, method, alternative, na.rm)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  concordance.index
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'concordance.index':
  ‘concordance.index’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/survcomp.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL survcomp
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c concordance.index.c -o concordance.index.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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:12:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                         ~^~~~~~
foo_mrmr_ensemble_surv.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                         ~^~~~~~
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]
   double uhs[Ns];
          ^~~
foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
   double rphs[Ns];
          ^~~~
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:202:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                        ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< (nvar-1); ++j){
                         ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar-1; ++i){
                        ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:216:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=i+1; j< nvar-1; ++j){
                           ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable ‘msurv_x’ [-Wunused-variable]
  int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x;
                 ^~~~~~~
foo_mrmr_ensemble_surv.cpp:191:27: warning: unused variable ‘ustrat_x’ [-Wunused-variable]
  int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x;
                           ^~~~~~~~
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_tree(tree&, tree&, 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]
   int cnt_back=cnt2;
       ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable ‘nsub’ [-Wunused-variable]
  int  nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
       ^~~~
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:393:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0; k< rep_boot; ++k){
                        ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int i=1;i<= size_boot;++i){
                        ~^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int i=0; i< size ; ++i ){
                          ~^~~~~~
foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( unsigned int j=0; j< size ; ++j ){
                           ~^~~~~~
foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                       ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:419:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                       ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable ‘mim’ [-Wunused-variable]
  double *mim, *boot_val, *mat_info;
          ^~~
foo_mrmr_ensemble_surv.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
foo_mrmr_ensemble_surv.cpp:448:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0;j< nbvar; j++){
                        ~^~~~~~~
foo_mrmr_ensemble_surv.cpp:437:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
  unsigned int jmax;
               ^~~~
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable ‘max_val’ [-Wunused-variable]
  double max_val=-1000;
         ^~~~~~~
foo_mrmr_ensemble_surv.cpp: In function ‘int verify_equivalentset_nparents(tree&, tree::pre_order_iterator, tree::pre_order_iterator, tree&, int)’:
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable ‘found’ [-Wunused-variable]
  bool found=false;
       ^~~~~
foo_mrmr_ensemble_surv.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree&, tree::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:593:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=1;i<= nsamples;++i){
                       ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< n; ++i ){
                         ~^~~
foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int j=0; j< n; ++j ){
                          ~^~~
foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                       ~^~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0;i<=max_depth;++i){
                          ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                         ~^~~
foo_mrmr_ensemble_surv.cpp:657:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:661:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                         ~^~~
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable ‘nsamples_boot’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
                        ^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:578:48: warning: unused variable ‘tmp_val_max_ind’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
                                                ^~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:578:66: warning: unused variable ‘prev_sel_tmp’ [-Wunused-variable]
  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
                                                                  ^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:579:21: warning: unused variable ‘vec_sort’ [-Wunused-variable]
  double *vec_mean, *vec_sort, *vec_sd,  *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr;
                     ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:579:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-variable]
  double *vec_mean, *vec_sort, *vec_sd,  *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr;
                                                               ^~~~~~~~~~~~~~~~
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:786:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                       ~^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:820:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k

name	user	system	elapsed
D.index	0.026	0.000	0.026
balanced.hazard.ratio	0.013	0.000	0.013
bhr.comp	0.011	0.000	0.011
breastCancerData	0.496	0.003	0.500
censor.time	0	0	0
cindex.comp	0.002	0.000	0.002
cindex.comp.meta	0.004	0.000	0.004
combine.est	0.001	0.000	0.001
combine.test	0.001	0.000	0.000
concordance.index	0.003	0.000	0.003
cvpl	0.159	0.000	0.159
dindex.comp	0.011	0.000	0.011
dindex.comp.meta	0.030	0.000	0.029
fisherz	0.001	0.000	0.001
forestplot.surv	0.034	0.000	0.034
getsurv2	0.002	0.000	0.002
hazard.ratio	0.011	0.000	0.011
hr.comp	0.006	0.003	0.011
hr.comp.meta	0.022	0.000	0.022
hr.comp2	0.008	0.000	0.008
iauc.comp	0.239	0.004	0.242
ibsc.comp	0.331	0.000	0.331
km.coxph.plot	0.055	0.000	0.055
logpl	0.017	0.000	0.017
mainz7g	0.304	0.011	0.316
metaplot.surv	0.005	0.000	0.004
mrmr.cindex	0.003	0.000	0.003
nki7g	0.292	0.003	0.296
no.at.risk	0.014	0.001	0.014
sbrier.score2proba	0.269	0.000	0.269
score2proba	0.025	0.000	0.026
td.sens.spec	0.003	0.000	0.002
tdrocc	0.096	0.011	0.108
test.hetero.est	0.001	0.000	0.000
test.hetero.test	0.000	0.000	0.001
transbig7g	0.196	0.000	0.196
unt7g	0.281	0.003	0.285
upp7g	0.247	0.007	0.255
vdx7g	0.188	0.004	0.191