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BioC 3.3: CHECK report for survcomp on moscato2

This page was generated on 2016-10-13 12:49:50 -0700 (Thu, 13 Oct 2016).

Package 1134/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.22.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/survcomp
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.22.0
Command: rm -rf survcomp.buildbin-libdir survcomp.Rcheck && mkdir survcomp.buildbin-libdir survcomp.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=survcomp.buildbin-libdir survcomp_1.22.0.tar.gz >survcomp.Rcheck\00install.out 2>&1 && cp survcomp.Rcheck\00install.out survcomp-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=survcomp.buildbin-libdir --install="check:survcomp-install.out" --force-multiarch --no-vignettes --timings survcomp_1.22.0.tar.gz
StartedAt: 2016-10-13 09:29:36 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 09:31:48 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 132.0 seconds
RetCode: 0
Status:  OK  
CheckDir: survcomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf survcomp.buildbin-libdir survcomp.Rcheck && mkdir survcomp.buildbin-libdir survcomp.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=survcomp.buildbin-libdir survcomp_1.22.0.tar.gz >survcomp.Rcheck\00install.out 2>&1 && cp survcomp.Rcheck\00install.out survcomp-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=survcomp.buildbin-libdir --install="check:survcomp-install.out" --force-multiarch --no-vignettes --timings survcomp_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/survcomp.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'survcomp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'survcomp' version '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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'
D.index: no visible global function definition for 'complete.cases'
D.index: no visible global function definition for 'coxph'
D.index: no visible global function definition for 'pchisq'
D.index: no visible global function definition for 'qnorm'
censor.time: no visible global function definition for 'complete.cases'
cindex.comp: no visible global function definition for 'cor'
cindex.comp: no visible global function definition for 'pt'
cindex.comp.meta: no visible global function definition for 'cor'
cindex.comp.meta: no visible global function definition for 'pt'
combine.est: no visible global function definition for 'complete.cases'
combine.test: no visible global function definition for 'pchisq'
combine.test: no visible global function definition for 'qnorm'
combine.test: no visible global function definition for 'pnorm'
combine.test: no visible global function definition for 'pt'
concordance.index: no visible global function definition for
  'complete.cases'
concordance.index: no visible global function definition for 'qnorm'
concordance.index: no visible global function definition for 'pnorm'
cvpl: no visible global function definition for 'complete.cases'
cvpl: no visible global function definition for 'coxph'
cvpl: no visible global function definition for 'formula'
cvpl: no visible global function definition for 'predict'
dindex.comp: no visible global function definition for 'cor'
dindex.comp: no visible global function definition for 'pt'
dindex.comp.meta: no visible global function definition for 'cor'
dindex.comp.meta: no visible global function definition for 'pt'
forestplot.surv: no visible global function definition for 'plot.new'
hazard.ratio: no visible global function definition for
  'complete.cases'
hazard.ratio: no visible global function definition for 'coxph'
hazard.ratio: no visible global function definition for 'pchisq'
hazard.ratio: no visible global function definition for 'qnorm'
hr.comp: no visible global function definition for 'cor'
hr.comp: no visible global function definition for 'pt'
hr.comp.meta: no visible global function definition for 'cor'
hr.comp.meta: no visible global function definition for 'pt'
hr.comp2: no visible global function definition for 'cor'
hr.comp2: no visible global function definition for 'pt'
iauc.comp: no visible global function definition for 'complete.cases'
iauc.comp: no visible global function definition for 'wilcox.test'
ibsc.comp: no visible global function definition for 'complete.cases'
ibsc.comp: no visible global function definition for 'wilcox.test'
km.coxph.plot: no visible global function definition for 'par'
km.coxph.plot: no visible global function definition for 'plot'
km.coxph.plot: no visible global function definition for 'survfit'
km.coxph.plot: no visible global function definition for 'title'
km.coxph.plot: no visible global function definition for 'abline'
km.coxph.plot: no visible global function definition for 'legend'
km.coxph.plot: no visible global function definition for 'mtext'
km.coxph.plot: no visible global function definition for 'text'
km.coxph.plot: no visible global function definition for 'axis'
logpl: no visible global function definition for 'complete.cases'
metaplot.surv: no visible global function definition for 'qnorm'
metaplot.surv: no visible global function definition for 'par'
metaplot.surv: no visible global function definition for 'plot'
metaplot.surv: no visible global function definition for 'axis'
metaplot.surv: no visible global function definition for 'abline'
metaplot.surv: no visible global function definition for 'lines'
metaplot.surv: no visible global function definition for 'text'
metaplot.surv: no visible global function definition for 'rect'
metaplot.surv: no visible global function definition for 'polygon'
mrmr.cindex: no visible global function definition for 'complete.cases'
no.at.risk: no visible global function definition for 'survfit'
sbrier.score2proba: no visible global function definition for
  'complete.cases'
sbrier.score2proba: no visible global function definition for 'survfit'
sbrier.score2proba: no visible global function definition for 'Surv'
sbrier.score2proba: no visible global function definition for 'predict'
score2proba: no visible global function definition for 'complete.cases'
score2proba: no visible global function definition for 'coxph'
score2proba: no visible global function definition for 'survfit'
score2proba: no visible global function definition for 'predict'
td.sens.spec: no visible global function definition for
  'complete.cases'
tdrocc: no visible global function definition for 'complete.cases'
test.hetero.est: no visible global function definition for
  'complete.cases'
test.hetero.est: no visible global function definition for 'pchisq'
test.hetero.test: no visible global function definition for 'qnorm'
test.hetero.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  Surv abline axis complete.cases cor coxph formula legend lines mtext
  par pchisq plot plot.new pnorm polygon predict pt qnorm rect survfit
  text title wilcox.test
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "plot.new", "polygon", "rect", "text",
             "title")
  importFrom("stats", "complete.cases", "cor", "formula", "pchisq",
             "pnorm", "predict", "pt", "qnorm", "wilcox.test")
to your NAMESPACE file.
* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.3-bioc/meat/survcomp.buildbin-libdir/survcomp/libs/i386/survcomp.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/survcomp.Rcheck/00check.log'
for details.

survcomp.Rcheck/00install.out:


install for i386

* installing *source* package 'survcomp' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c concordance.index.c -o concordance.index.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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<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]
   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<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]
  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 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:785:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:819:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res_old;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:833:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int k=0;k<length_res;k++){
                         ^
foo_mrmr_ensemble_surv.cpp:838:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(i==(*npredn-1)){
       ^
foo_mrmr_ensemble_surv.cpp:842:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:800:13: warning: unused variable 'cnt2' [-Wunused-variable]
   int cnt=1,cnt2=0;
             ^
foo_mrmr_ensemble_surv.cpp:803:7: warning: unused variable 'rootdepth' [-Wunused-variable]
   int rootdepth=res_tree.depth(it_final);
       ^
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable 'ind' [-Wunused-variable]
   int ind=0;
       ^
foo_mrmr_ensemble_surv.cpp:732:30: warning: unused variable 'res_all' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                              ^
foo_mrmr_ensemble_surv.cpp:732:39: warning: unused variable 'res_all2' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                       ^
foo_mrmr_ensemble_surv.cpp:733:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
  int vec_tmp;
      ^
foo_mrmr_ensemble_surv.cpp:858:9: warning: 'Rres' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return Rres;
         ^
foo_mrmr_ensemble_surv.cpp:820:25: warning: 'res_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
     res_all[k]=res_old[k];
                         ^
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                          ^
foo_mrmr_surv.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  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 between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                         ^
foo_mrmr_surv.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                          ^
foo_mrmr_surv.cpp:56:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                         ^
foo_mrmr_surv.cpp:58:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   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]
   double uhs[Ns];
          ^
foo_mrmr_surv.cpp:147:10: warning: variable 'rphs' set but not used [-Wunused-but-set-variable]
   double rphs[Ns];
          ^
foo_mrmr_surv.cpp: In function 'SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
foo_mrmr_surv.cpp:300:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                         ^
foo_mrmr_surv.cpp:340:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l<n; ++l )  
                   ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o survcomp.dll tmp.def concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/survcomp.buildbin-libdir/survcomp/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'survcomp' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c concordance.index.c -o concordance.index.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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<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]
   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<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]
  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 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:785:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:819:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res_old;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:833:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int k=0;k<length_res;k++){
                         ^
foo_mrmr_ensemble_surv.cpp:838:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(i==(*npredn-1)){
       ^
foo_mrmr_ensemble_surv.cpp:842:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:800:13: warning: unused variable 'cnt2' [-Wunused-variable]
   int cnt=1,cnt2=0;
             ^
foo_mrmr_ensemble_surv.cpp:803:7: warning: unused variable 'rootdepth' [-Wunused-variable]
   int rootdepth=res_tree.depth(it_final);
       ^
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable 'ind' [-Wunused-variable]
   int ind=0;
       ^
foo_mrmr_ensemble_surv.cpp:732:30: warning: unused variable 'res_all' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                              ^
foo_mrmr_ensemble_surv.cpp:732:39: warning: unused variable 'res_all2' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                       ^
foo_mrmr_ensemble_surv.cpp:733:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
  int vec_tmp;
      ^
foo_mrmr_ensemble_surv.cpp:858:9: warning: 'Rres' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return Rres;
         ^
foo_mrmr_ensemble_surv.cpp:820:25: warning: 'res_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
     res_all[k]=res_old[k];
                         ^
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -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 between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                          ^
foo_mrmr_surv.cpp:22:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  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 between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                         ^
foo_mrmr_surv.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                          ^
foo_mrmr_surv.cpp:56:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                         ^
foo_mrmr_surv.cpp:58:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   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]
   double uhs[Ns];
          ^
foo_mrmr_surv.cpp:147:10: warning: variable 'rphs' set but not used [-Wunused-but-set-variable]
   double rphs[Ns];
          ^
foo_mrmr_surv.cpp: In function 'SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
foo_mrmr_surv.cpp:300:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                         ^
foo_mrmr_surv.cpp:340:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l<n; ++l )  
                   ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o survcomp.dll tmp.def concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/survcomp.buildbin-libdir/survcomp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'survcomp' as survcomp_1.22.0.zip
* DONE (survcomp)

survcomp.Rcheck/examples_i386/survcomp-Ex.timings:

nameusersystemelapsed
D.index0.030.000.07
breastCancerData0.670.000.67
censor.time000
cindex.comp0.030.000.03
cindex.comp.meta000
combine.est000
combine.test0.020.000.01
concordance.index000
cvpl0.340.000.35
dindex.comp0.020.000.01
dindex.comp.meta0.030.000.03
fisherz000
forestplot.surv0.030.010.05
getsurv2000
hazard.ratio0.020.000.01
hr.comp000
hr.comp.meta0.050.000.05
hr.comp20.010.000.01
iauc.comp0.590.000.60
ibsc.comp0.250.020.56
km.coxph.plot0.040.000.03
logpl0.010.000.01
mainz7g0.30.00.3
metaplot.surv000
mrmr.cindex000
nki7g0.410.030.44
no.at.risk0.030.000.03
sbrier.score2proba0.190.000.19
score2proba0.030.000.03
td.sens.spec000
tdrocc0.380.000.37
test.hetero.est000
test.hetero.test000
transbig7g0.380.000.37
unt7g0.330.020.34
upp7g0.380.010.39
vdx7g0.420.000.42

survcomp.Rcheck/examples_x64/survcomp-Ex.timings:

nameusersystemelapsed
D.index0.030.000.08
breastCancerData0.840.000.84
censor.time0.020.000.02
cindex.comp000
cindex.comp.meta000
combine.est0.010.000.02
combine.test000
concordance.index000
cvpl0.20.00.2
dindex.comp0.020.000.01
dindex.comp.meta0.030.000.03
fisherz000
forestplot.surv0.060.000.07
getsurv20.020.000.01
hazard.ratio000
hr.comp000
hr.comp.meta0.030.000.04
hr.comp2000
iauc.comp0.550.000.54
ibsc.comp0.340.000.34
km.coxph.plot0.230.000.24
logpl0.040.000.03
mainz7g0.410.000.40
metaplot.surv000
mrmr.cindex0.010.000.02
nki7g0.240.000.23
no.at.risk0.010.000.02
sbrier.score2proba0.240.000.23
score2proba0.020.000.01
td.sens.spec000
tdrocc0.160.000.15
test.hetero.est0.010.000.02
test.hetero.test000
transbig7g0.300.000.29
unt7g0.240.000.24
upp7g0.390.000.39
vdx7g0.230.000.23