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Package 629/671HostnameOS / ArchBUILDCHECKBUILD BIN
survcomp 1.10.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/survcomp
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: survcomp
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch survcomp_1.10.0.tar.gz
StartedAt: 2013-05-01 11:23:43 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 11:24:45 -0700 (Wed, 01 May 2013)
EllapsedTime: 61.4 seconds
RetCode: 0
Status:  OK 
CheckDir: survcomp.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'survcomp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'survcomp' version '1.10.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'survcomp' can be installed ... [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 ... [10s/11s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck/00check.log'
for details.

survcomp.Rcheck/00install.out:

* installing *source* package 'survcomp' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c concordance.index.c -o concordance.index.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
foo_mrmr_ensemble_surv.cpp:13:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if (namat[ind_x+i]==0 && namat[ind_y+i]==0 ) {
                          ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:13:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if (namat[ind_x+i]==0 && namat[ind_y+i]==0 ) {
                                               ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:14:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mean_data_x+=data[ind_x+i];
                                          ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:15:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mean_data_y+=data[ind_y+i];
                                          ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:23:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if(namat[ind_x+i]==0 && namat[ind_y+i]==0){
                         ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:23:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if(namat[ind_x+i]==0 && namat[ind_y+i]==0){
                                              ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:24:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_nom+=(data[ind_x+i]-mean_data_x)*(data[ind_y+i]-mean_data_y);
                                       ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:24:54: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_nom+=(data[ind_x+i]-mean_data_x)*(data[ind_y+i]-mean_data_y);
                                                                   ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:25:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_x+=(data[ind_x+i]-mean_data_x)*(data[ind_x+i]-mean_data_x);
                                         ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:25:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_x+=(data[ind_x+i]-mean_data_x)*(data[ind_x+i]-mean_data_x);
                                                                     ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:26:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_y+=(data[ind_y+i]-mean_data_y)*(data[ind_y+i]-mean_data_y);
                                         ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:26:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_y+=(data[ind_y+i]-mean_data_y)*(data[ind_y+i]-mean_data_y);
                                                                     ^˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:40:15: warning: variable length arrays are a C99 feature [-Wvla]
        double res_ch[lenStrat];
                     ^
foo_mrmr_ensemble_surv.cpp:41:15: warning: variable length arrays are a C99 feature [-Wvla]
        double res_dh[lenStrat];
                     ^
foo_mrmr_ensemble_surv.cpp:48:10: warning: variable length arrays are a C99 feature [-Wvla]
                int ixs[lenStrat];
                       ^
foo_mrmr_ensemble_surv.cpp:64:12: warning: variable length arrays are a C99 feature [-Wvla]
                double xs[Ns];
                         ^
foo_mrmr_ensemble_surv.cpp:72:10: warning: variable length arrays are a C99 feature [-Wvla]
                int cls[Ns];
                       ^
foo_mrmr_ensemble_surv.cpp:80:13: warning: variable length arrays are a C99 feature [-Wvla]
                double sts[Ns];
                          ^
foo_mrmr_ensemble_surv.cpp:88:10: warning: variable length arrays are a C99 feature [-Wvla]
                int ses[Ns];
                       ^
foo_mrmr_ensemble_surv.cpp:96:18: warning: variable length arrays are a C99 feature [-Wvla]
                double weightss[Ns];
                               ^
foo_mrmr_ensemble_surv.cpp:104:13: warning: variable length arrays are a C99 feature [-Wvla]
                double chs[Ns];
                          ^
foo_mrmr_ensemble_surv.cpp:105:13: warning: variable length arrays are a C99 feature [-Wvla]
                double dhs[Ns];
                          ^
foo_mrmr_ensemble_surv.cpp:106:13: warning: variable length arrays are a C99 feature [-Wvla]
                double uhs[Ns];
                          ^
foo_mrmr_ensemble_surv.cpp:107:14: warning: variable length arrays are a C99 feature [-Wvla]
                double rphs[Ns];
                           ^
foo_mrmr_ensemble_surv.cpp:193:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        namat_x = (int*) R_alloc(nvar*size_subset, sizeof(int));
                         ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:194:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        cl2_x = (int*) R_alloc(size_subset, sizeof(int));
                       ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:195:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        se_x = (int*) R_alloc(size_subset, sizeof(int));
                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:196:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        strat_x = (int*) R_alloc(size_subset, sizeof(int));
                         ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:198:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        data_x = (double *) R_alloc(nvar*size_subset, sizeof(double));
                            ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:199:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        st_x = (double *) R_alloc(size_subset, sizeof(double));
                          ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:200:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        weights_x = (double *) R_alloc(size_subset, sizeof(double));
                               ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:204:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                               ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:204:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                                                      ^˜˜˜˜˜˜˜˜ ˜
foo_mrmr_ensemble_surv.cpp:204:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                                                                 ^˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:205:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:205:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                                        ^˜˜˜˜˜˜˜˜ ˜
foo_mrmr_ensemble_surv.cpp:205:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                                                   ^˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:215:14: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                mim[(i+1)*(nvar)+(i+1)]=0;
                         ˜ ^˜˜˜
foo_mrmr_ensemble_surv.cpp:217:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp=get_correlation_ensemble(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:217:50: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        tmp=get_correlation_ensemble(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                                                                     ˜^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:217:63: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp=get_correlation_ensemble(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:217:64: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        tmp=get_correlation_ensemble(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                                                                                   ˜^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:222:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[(j+1)*(nvar)+i+1]= -0.5* log (1-tmp);
                                 ˜ ^˜˜˜
foo_mrmr_ensemble_surv.cpp:223:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[(i+1)*(nvar)+j+1]=mim[(j+1)*(nvar)+i+1];
                                 ˜ ^˜˜˜
foo_mrmr_ensemble_surv.cpp:223:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[(i+1)*(nvar)+j+1]=mim[(j+1)*(nvar)+i+1];
                                                       ˜ ^˜˜˜
foo_mrmr_ensemble_surv.cpp:228:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        data_small =(double*) R_alloc(size_subset, sizeof(double));
                              ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
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:301:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mean =(double*) R_alloc(cnt_leafs, sizeof(double));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:302:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sd =(double*) R_alloc(cnt_leafs, sizeof(double));
                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:303:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        to_remove=(int*) R_alloc(cnt_leafs, sizeof(int));
                         ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:312:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        prev_sel=(int*) R_alloc(max_depth, sizeof(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:389:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        ind=(int*) R_alloc(size_boot, sizeof(int));
                   ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:390:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        boot_val =(double*) R_alloc(rep_boot, sizeof(double));
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:391:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mat_info =(double*) R_alloc(((size)*(size )), sizeof(double));
                            ˜˜˜˜˜˜˜  ˜˜˜˜˜˜^˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:402:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                mat_info[i+(size )*j]=0;
                                            ^˜˜˜  ˜
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable 'mim' [-Wunused-variable]
        double *mim, *boot_val, *mat_info;
                ^
foo_mrmr_ensemble_surv.cpp:441:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        jmax=var_target-1;
            ˜˜˜˜˜˜˜˜˜˜˜^˜
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable 'max_val' [-Wunused-variable]
        double max_val=-1000;
               ^
foo_mrmr_ensemble_surv.cpp:473:13: warning: variable length arrays are a C99 feature [-Wvla]
        int vec_old[depth+1];
                   ^
foo_mrmr_ensemble_surv.cpp:474:42: warning: variable length arrays are a C99 feature [-Wvla]
        int mat_res [power((maxnsol+1),(depth))][depth+2];
                                                ^
foo_mrmr_ensemble_surv.cpp:474:14: warning: variable length arrays are a C99 feature [-Wvla]
        int mat_res [power((maxnsol+1),(depth))][depth+2];
                    ^
foo_mrmr_ensemble_surv.cpp:476:15: warning: variable length arrays are a C99 feature [-Wvla]
        int to_remove[number_leafs];
                     ^
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
foo_mrmr_ensemble_surv.cpp:585:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_mean =(double*) R_alloc(n, sizeof(double));
                            ˜˜˜˜˜˜˜ ^
foo_mrmr_ensemble_surv.cpp:586:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sd =(double*) R_alloc(n, sizeof(double));
                          ˜˜˜˜˜˜˜ ^
foo_mrmr_ensemble_surv.cpp:587:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mrmr_vec_sort =(double*) R_alloc(n, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^
foo_mrmr_ensemble_surv.cpp:588:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_local_max_mean =(double*) R_alloc(max_elements, sizeof(double));
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:589:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_local_max_sd =(double*) R_alloc(max_elements, sizeof(double));
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:590:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mat_info =(double*) R_alloc((n*n), sizeof(double));
                            ˜˜˜˜˜˜˜  ˜^˜
foo_mrmr_ensemble_surv.cpp:591:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        ind=(int*) R_alloc(nsamples, sizeof(int));
                   ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:594:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                ind[i-1]=i-1;
                        ˜˜^˜
foo_mrmr_ensemble_surv.cpp:598:16: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mat_info[i+(n)*j]=0;
                                    ^ ˜
foo_mrmr_ensemble_surv.cpp:608:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        prev_sel=(int*) R_alloc(max_elements, sizeof(int));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:609:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        nsub=(int*) R_alloc(max_elements, sizeof(int));
                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:614:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sol_local=(int*) R_alloc(maxnsol, sizeof(int));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:615:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sol_local_mrmr=(double*) R_alloc(maxnsol, sizeof(double));
                                     ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:663:92: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                        vec_mean[k]=mrnet_onegene( mat_info, n,min(cnt,max_elements_tmp),prev_sel, nsub[0], (k+1)); vec_sd[k]=0;
                                                    ˜˜˜˜˜˜˜˜˜˜˜˜˜                                                            ˜^˜
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: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:578:66: 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: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:806:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp_nchildren[cnt-1]=(res_tree.number_of_children(it_final));
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:825:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res_all[length_res_old+k]=res_tmp[k];
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:828:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res_all[length_res_old+k+res_tree.size()+1]=tmp_nchildren[k];
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=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:800:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=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:742:9: warning: implicit conversion loses integer precision: 'time_t' (aka 'long') to 'unsigned int' [-Wshorten-64-to-32]
        srand (time(NULL));
        ˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:802:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res_tmp[0]=res_tree.size();
                          ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:820:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:815:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
96 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
foo_mrmr_surv.cpp:13:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if (namat[ind_x+i]==0 && namat[ind_y+i]==0 ) {
                          ^˜˜˜˜˜
foo_mrmr_surv.cpp:13:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if (namat[ind_x+i]==0 && namat[ind_y+i]==0 ) {
                                               ^˜˜˜˜˜
foo_mrmr_surv.cpp:14:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mean_data_x+=data[ind_x+i];
                                          ^˜˜˜˜˜
foo_mrmr_surv.cpp:15:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mean_data_y+=data[ind_y+i];
                                          ^˜˜˜˜˜
foo_mrmr_surv.cpp:23:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if(namat[ind_x+i]==0 && namat[ind_y+i]==0){
                         ^˜˜˜˜˜
foo_mrmr_surv.cpp:23:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if(namat[ind_x+i]==0 && namat[ind_y+i]==0){
                                              ^˜˜˜˜˜
foo_mrmr_surv.cpp:24:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_nom+=(data[ind_x+i]-mean_data_x)*(data[ind_y+i]-mean_data_y);
                                       ^˜˜˜˜˜
foo_mrmr_surv.cpp:24:54: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_nom+=(data[ind_x+i]-mean_data_x)*(data[ind_y+i]-mean_data_y);
                                                                   ^˜˜˜˜˜
foo_mrmr_surv.cpp:25:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_x+=(data[ind_x+i]-mean_data_x)*(data[ind_x+i]-mean_data_x);
                                         ^˜˜˜˜˜
foo_mrmr_surv.cpp:25:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_x+=(data[ind_x+i]-mean_data_x)*(data[ind_x+i]-mean_data_x);
                                                                     ^˜˜˜˜˜
foo_mrmr_surv.cpp:26:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_y+=(data[ind_y+i]-mean_data_y)*(data[ind_y+i]-mean_data_y);
                                         ^˜˜˜˜˜
foo_mrmr_surv.cpp:26:56: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                correlation_den_y+=(data[ind_y+i]-mean_data_y)*(data[ind_y+i]-mean_data_y);
                                                                     ^˜˜˜˜˜
foo_mrmr_surv.cpp:46:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        namat_x = (int*) R_alloc(nvar*size_subset, sizeof(int));
                         ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:47:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        data_x = (double *) R_alloc(nvar*size_subset, sizeof(double));
                            ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:51:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                               ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:51:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                                                      ^˜˜˜˜˜˜˜˜ ˜
foo_mrmr_surv.cpp:51:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                                                                 ^˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:52:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:52:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                                        ^˜˜˜˜˜˜˜˜ ˜
foo_mrmr_surv.cpp:52:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                                                   ^˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:57:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                mim[i*nvar+i]=0;
                     ˜^˜˜˜
foo_mrmr_surv.cpp:59:40: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp=get_correlation(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:59:41: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        tmp=get_correlation(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                                                            ˜^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:59:54: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp=get_correlation(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                              ˜^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:59:55: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        tmp=get_correlation(data_x,namat_x,i*size_subset,j*size_subset,size_subset);
                                                                          ˜^˜˜˜˜˜˜˜˜˜˜
foo_mrmr_surv.cpp:64:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[j*nvar+i]= -0.5* log (1-tmp);
                             ˜^˜˜˜
foo_mrmr_surv.cpp:65:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[i*nvar+j]=mim[j*nvar+i];
                             ˜^˜˜˜
foo_mrmr_surv.cpp:65:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[i*nvar+j]=mim[j*nvar+i];
                                           ˜^˜˜˜
foo_mrmr_surv.cpp:80:15: warning: variable length arrays are a C99 feature [-Wvla]
        double res_ch[lenStrat];
                     ^
foo_mrmr_surv.cpp:81:15: warning: variable length arrays are a C99 feature [-Wvla]
        double res_dh[lenStrat];
                     ^
foo_mrmr_surv.cpp:88:10: warning: variable length arrays are a C99 feature [-Wvla]
                int ixs[lenStrat];
                       ^
foo_mrmr_surv.cpp:104:12: warning: variable length arrays are a C99 feature [-Wvla]
                double xs[Ns];
                         ^
foo_mrmr_surv.cpp:112:10: warning: variable length arrays are a C99 feature [-Wvla]
                int cls[Ns];
                       ^
foo_mrmr_surv.cpp:120:13: warning: variable length arrays are a C99 feature [-Wvla]
                double sts[Ns];
                          ^
foo_mrmr_surv.cpp:128:10: warning: variable length arrays are a C99 feature [-Wvla]
                int ses[Ns];
                       ^
foo_mrmr_surv.cpp:136:18: warning: variable length arrays are a C99 feature [-Wvla]
                double weightss[Ns];
                               ^
foo_mrmr_surv.cpp:144:13: warning: variable length arrays are a C99 feature [-Wvla]
                double chs[Ns];
                          ^
foo_mrmr_surv.cpp:145:13: warning: variable length arrays are a C99 feature [-Wvla]
                double dhs[Ns];
                          ^
foo_mrmr_surv.cpp:146:13: warning: variable length arrays are a C99 feature [-Wvla]
                double uhs[Ns];
                          ^
foo_mrmr_surv.cpp:147:14: warning: variable length arrays are a C99 feature [-Wvla]
                double rphs[Ns];
                           ^
foo_mrmr_surv.cpp:280:6: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
        n = *nvar;
          ˜ ^˜˜˜˜
foo_mrmr_surv.cpp:301:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                ind[i]=i;
                      ˜^
foo_mrmr_surv.cpp:304:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        build_mim_subset(mim, data, namat, n, *nsample, ind, *nsample);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                   ^
foo_mrmr_surv.cpp:341:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                red[l] += mim[l*n+jmax];
                                              ^˜
44 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/survcomp.Rcheck/survcomp/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survcomp)

survcomp.Rcheck/survcomp-Ex.timings:

nameusersystemelapsed
D.index0.0560.0090.075
breastCancerData1.8150.0731.899
censor.time0.0460.0010.047
cindex.comp0.1750.0050.180
cindex.comp.meta0.0290.0070.036
combine.est0.0130.0030.016
combine.test0.0110.0030.014
concordance.index0.0230.0090.032
cvpl0.2880.0080.296
dindex.comp0.0290.0040.034
dindex.comp.meta0.0630.0080.075
fisherz0.0120.0010.014
forestplot.surv0.1270.0040.132
getsurv20.0210.0040.025
hazard.ratio0.0260.0030.029
hr.comp0.0340.0030.038
hr.comp.meta0.0610.0060.068
hr.comp20.0280.0010.029
iauc.comp0.9750.0301.010
ibsc.comp0.3860.0250.502
km.coxph.plot0.0700.0050.089
logpl0.0530.0030.056
mainz7g0.4730.0280.507
metaplot.surv0.0100.0040.014
mrmr.cindex0.0250.0040.029
nki7g0.4380.0220.469
no.at.risk0.0380.0050.044
sbrier.score2proba0.2430.0060.274
score2proba0.0450.0020.048
td.sens.spec0.0170.0020.029
tdrocc0.3900.0370.436
test.hetero.est0.1190.0030.124
test.hetero.test0.0120.0010.013
transbig7g0.6010.0270.637
unt7g0.5620.0180.581
upp7g0.5370.0240.565
vdx7g0.4310.0240.460