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This page was generated on 2021-10-15 15:05:54 -0400 (Fri, 15 Oct 2021).

CHECK results for survcomp on nebbiolo1

To the developers/maintainers of the survcomp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/survcomp.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1873/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.42.0  (landing page)
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/survcomp
git_branch: RELEASE_3_13
git_last_commit: 2b6bd69
git_last_commit_date: 2021-05-19 11:48:05 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: survcomp
Version: 1.42.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings survcomp_1.42.0.tar.gz
StartedAt: 2021-10-14 11:48:16 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:49:04 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 47.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: survcomp.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings survcomp_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/survcomp.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.42.0’
* 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-3.13-bioc/meat/survcomp.Rcheck/00check.log’
for details.



Installation output

survcomp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL survcomp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c concordance.index.c -o concordance.index.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-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 of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   12 |  for( unsigned int i=0; i< size; ++i ) {
      |                         ~^~~~~~
foo_mrmr_ensemble_surv.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   22 |  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]
  106 |   double uhs[Ns];
      |          ^~~
foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
  107 |   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 of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  202 |  for(unsigned int i=0; i< size_subset; ++i){
      |                        ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  203 |   for(unsigned int j=0; j< (nvar-1); ++j){
      |                         ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  214 |  for(unsigned int i=0; i< nvar-1; ++i){
      |                        ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:216:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  216 |   for(unsigned int j=i+1; j< nvar-1; ++j){
      |                           ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable ‘msurv_x’ [-Wunused-variable]
  191 |  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]
  191 |  int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x;
      |                           ^~~~~~~~
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]
  351 |   int cnt_back=cnt2;
      |       ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable ‘nsub’ [-Wunused-variable]
  286 |  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 of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  393 |  for(unsigned int k=0; k< rep_boot; ++k){
      |                        ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  396 |   for(unsigned int i=1;i<= size_boot;++i){
      |                        ~^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  400 |   for( unsigned int i=0; i< size ; ++i ){
      |                          ~^~~~~~
foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  401 |    for( unsigned int j=0; j< size ; ++j ){
      |                           ~^~~~~~
foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  412 |  for(unsigned int i=0;i< rep_boot;++i){
      |                       ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:419:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  419 |  for(unsigned int i=0;i< rep_boot;++i){
      |                       ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable ‘mim’ [-Wunused-variable]
  387 |  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 of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  448 |   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]
  437 |  unsigned int jmax;
      |               ^~~~
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable ‘max_val’ [-Wunused-variable]
  439 |  double max_val=-1000;
      |         ^~~~~~~
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]
  467 |  bool found=false;
      |       ^~~~~
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:593:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  593 |  for(unsigned int i=1;i<= nsamples;++i){
      |                       ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  596 |  for( unsigned int i=0; i< n; ++i ){
      |                         ~^~~
foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  597 |   for( unsigned int j=0; j< n; ++j ){
      |                          ~^~~
foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  604 |  for(unsigned int k=0;k< max_elements ;++k){
      |                       ~^~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  646 |    for (unsigned int i=0;i<=max_depth;++i){
      |                          ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  654 |    for(unsigned int k=0;k< n;++k){
      |                         ~^~~
foo_mrmr_ensemble_surv.cpp:657:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  657 |    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 of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  661 |    for(unsigned int k=0;k< n;++k){
      |                         ~^~~
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable ‘nsamples_boot’ [-Wunused-variable]
  578 |  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]
  578 |  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]
  578 |  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]
  579 |  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]
  579 |  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 of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  786 |  for(unsigned int i=0;i< *npredn;++i){
      |                       ~^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:820:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  820 |    for(unsigned int k=0;k<length_res_old;k++){
      |                         ~^~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:834:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  834 |   for(unsigned int k=0;k<length_res;k++){
      |                        ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:839:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  839 |   if(i==(*npredn-1)){
      |      ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:843:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  843 |    for(unsigned int k=0;k<length_res;k++){
      |                         ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
  801 |   int cnt=1,cnt2=0;
      |             ^~~~
foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  804 |   int rootdepth=res_tree.depth(it_final);
      |       ^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable ‘ind’ [-Wunused-variable]
  817 |   int ind=0;
      |       ^~~
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable ‘res_all’ [-Wunused-variable]
  733 |  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                              ^~~~~~~
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
  733 |  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                                       ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
  734 |  int vec_tmp;
      |      ^~~~~~~
foo_mrmr_ensemble_surv.cpp:859:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  859 |  return Rres;
      |         ^~~~
foo_mrmr_ensemble_surv.cpp:821:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  821 |     res_all[k]=res_old[k];
      |                ~~~~~~~~~^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-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:12:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   12 |  for( unsigned int i=0; i< size; ++i ) {
      |                         ~^~~~~~
foo_mrmr_surv.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   22 |  for( unsigned int i=0; i< size; ++i ) {
      |                         ~^~~~~~
foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr_surv.cpp:49:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   49 |  for(unsigned int i=0; i< size_subset; ++i){
      |                        ~^~~~~~~~~~~~~
foo_mrmr_surv.cpp:50:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   50 |   for(unsigned int j=0; j< nvar; ++j){
      |                         ~^~~~~~
foo_mrmr_surv.cpp:56:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   56 |  for(unsigned int i=0; i< nvar; ++i){
      |                        ~^~~~~~
foo_mrmr_surv.cpp:58:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   58 |   for(unsigned int j=i+1; j< nvar; ++j){
      |                           ~^~~~~~
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]
  146 |   double uhs[Ns];
      |          ^~~
foo_mrmr_surv.cpp:147:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
  147 |   double rphs[Ns];
      |          ^~~~
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_surv.cpp:301:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  301 |  for(unsigned int i=0;i < *nsample; ++i){
      |                       ~~^~~~~~~~~~
foo_mrmr_surv.cpp:341:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  341 |    for( int l=0; l<n; ++l )
      |                  ~^~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c survcomp_init.cpp -o survcomp_init.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-survcomp/00new/survcomp/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survcomp)

Tests output


Example timings

survcomp.Rcheck/survcomp-Ex.timings

nameusersystemelapsed
D.index0.0290.0040.034
balanced.hazard.ratio0.0120.0040.015
bhr.comp0.0100.0010.012
breastCancerData0.4680.0110.478
censor.time0.0010.0000.001
cindex.comp0.0030.0000.002
cindex.comp.meta0.0040.0000.004
combine.est0.0000.0000.001
combine.test0.0000.0000.001
concordance.index0.0010.0050.006
cvpl0.1610.0000.161
dindex.comp0.0110.0010.011
dindex.comp.meta0.0210.0000.020
fisherz0.0010.0000.001
forestplot.surv0.0210.0030.025
getsurv20.0020.0000.003
hazard.ratio0.0120.0000.013
hr.comp0.010.000.01
hr.comp.meta0.0210.0000.021
hr.comp20.0040.0040.008
iauc.comp0.1790.0080.187
ibsc.comp0.1870.0120.199
km.coxph.plot0.0340.0030.037
logpl0.0100.0010.011
mainz7g0.1690.0110.181
metaplot.surv0.0040.0000.003
mrmr.cindex0.0030.0000.004
nki7g0.1630.0070.172
no.at.risk0.0210.0000.020
sbrier.score2proba0.1350.0000.134
score2proba0.0220.0000.022
td.sens.spec0.0020.0000.002
tdrocc0.0720.0070.081
test.hetero.est0.0000.0000.001
test.hetero.test0.0000.0010.000
transbig7g0.1740.0090.184
unt7g0.1660.0150.182
upp7g0.1720.0040.176
vdx7g0.1750.0080.183