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Package 497/671HostnameOS / ArchBUILDCHECKBUILD BIN
predictionet 1.6.0
Benjamin Haibe-Kains , 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/predictionet
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 N O T   S U P P O R T E D
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: predictionet
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch predictionet_1.6.0.tar.gz
StartedAt: 2013-05-01 09:30:52 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 09:32:12 -0700 (Wed, 01 May 2013)
EllapsedTime: 79.9 seconds
RetCode: 0
Status:  OK 
CheckDir: predictionet.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/predictionet.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 'predictionet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'predictionet' version '1.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'predictionet' can be installed ... [9s/10s] 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 ... 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 ... 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' ... NOTE
The following files should probably not be installed:
  'Makefile'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [7s/7s] 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/predictionet.Rcheck/00check.log'
for details.

predictionet.Rcheck/00install.out:

* installing *source* package 'predictionet' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c foo_mrmr.cpp -o foo_mrmr.o
foo_mrmr.cpp:14:13: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if (namat[ind_x+i]==0 && namat[ind_y+i]==0 ) {
                          ^˜˜˜˜˜
foo_mrmr.cpp:14:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if (namat[ind_x+i]==0 && namat[ind_y+i]==0 ) {
                                               ^˜˜˜˜˜
foo_mrmr.cpp:15:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mean_data_x+=data[ind_x+i];
                                          ^˜˜˜˜˜
foo_mrmr.cpp:16:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mean_data_y+=data[ind_y+i];
                                          ^˜˜˜˜˜
foo_mrmr.cpp:24:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if(namat[ind_x+i]==0 && namat[ind_y+i]==0){
                         ^˜˜˜˜˜
foo_mrmr.cpp:24:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if(namat[ind_x+i]==0 && namat[ind_y+i]==0){
                                              ^˜˜˜˜˜
foo_mrmr.cpp:25:27: 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.cpp:25:55: 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.cpp:26:29: 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.cpp:26:57: 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.cpp:27:29: 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.cpp:27:57: 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.cpp:47:31: 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.cpp:48:34: 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.cpp:52:11: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                               ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr.cpp:52:34: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                                                      ^˜˜˜˜˜˜˜˜ ˜
foo_mrmr.cpp:52:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        data_x[size_subset*j+i]=data[(subset[i])+nsample*j];
                                                                 ^˜˜˜˜˜˜˜
foo_mrmr.cpp:53:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                ^˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr.cpp:53:36: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                                        ^˜˜˜˜˜˜˜˜ ˜
foo_mrmr.cpp:53:47: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        namat_x[size_subset*j+i]=namat[(subset[i])+nsample*j];
                                                                   ^˜˜˜˜˜˜˜
foo_mrmr.cpp:58:9: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                mim[i*nvar+i]=0;
                     ˜^˜˜˜
foo_mrmr.cpp:60:40: 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.cpp:60:41: 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.cpp:60:54: 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.cpp:60:55: 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.cpp:65:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[j*nvar+i]= -0.5* log (1-tmp);
                             ˜^˜˜˜
foo_mrmr.cpp:66:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[i*nvar+j]=mim[j*nvar+i];
                             ˜^˜˜˜
foo_mrmr.cpp:66:24: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        mim[i*nvar+j]=mim[j*nvar+i];
                                           ˜^˜˜˜
28 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mrnet_adapted.cpp -o mrnet_adapted.o
mrnet_adapted.cpp:32:6: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
        n = *nvar;
          ˜ ^˜˜˜˜
mrnet_adapted.cpp:59:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                ind[i]=i;
                      ˜^
mrnet_adapted.cpp:62:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        build_mim_subset(mim, data, namat, n, *nsample, ind, *nsample);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                   ^
mrnet_adapted.cpp:104:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                red[l] += mim[l*n+jmax];
                                              ^˜
mrnet_adapted.cpp:133:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        tmp[i]= res[i+(predn[j]-1)*n];
                                       ˜˜˜˜˜˜˜˜^˜ ˜
mrnet_adapted.cpp:138:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        if(res[i+(predn[j]-1)*n]>tmp[n-(*maxparents) - 1]){
                                  ˜˜˜˜˜˜˜˜^˜ ˜
mrnet_adapted.cpp:138:36: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                        if(res[i+(predn[j]-1)*n]>tmp[n-(*maxparents) - 1]){
                                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
mrnet_adapted.cpp:139:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                res_final[i+(predn[j]-1)*n]=res[i+(predn[j]-1)*n];
                                             ˜˜˜˜˜˜˜˜^˜ ˜
mrnet_adapted.cpp:139:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                res_final[i+(predn[j]-1)*n]=res[i+(predn[j]-1)*n];
                                                                   ˜˜˜˜˜˜˜˜^˜ ˜
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mrnet_adapted2.cpp -o mrnet_adapted2.o
mrnet_adapted2.cpp:36:6: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
        n = *nvar;
          ˜ ^˜˜˜˜
mrnet_adapted2.cpp:63:10: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                ind[i]=i;
                      ˜^
mrnet_adapted2.cpp:66:37: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        build_mim_subset(mim, data, namat, n, *nsample, ind, *nsample);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                   ^
mrnet_adapted2.cpp:122:19: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                red[l] += mim[l*n+jmax];
                                              ^˜
mrnet_adapted2.cpp:187:27: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        tmp[i]= res[i+(predn[j]-1)*n];
                                       ˜˜˜˜˜˜˜˜^˜ ˜
mrnet_adapted2.cpp:192:22: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        if(res[i+(predn[j]-1)*n]>tmp[n-(*maxparents) - 1]){
                                  ˜˜˜˜˜˜˜˜^˜ ˜
mrnet_adapted2.cpp:192:36: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
                        if(res[i+(predn[j]-1)*n]>tmp[n-(*maxparents) - 1]){
                                                      ˜ ^˜˜˜˜˜˜˜˜˜˜
mrnet_adapted2.cpp:193:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                res_final[i+(predn[j]-1)*n]=res[i+(predn[j]-1)*n];
                                             ˜˜˜˜˜˜˜˜^˜ ˜
mrnet_adapted2.cpp:193:48: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                                res_final[i+(predn[j]-1)*n]=res[i+(predn[j]-1)*n];
                                                                   ˜˜˜˜˜˜˜˜^˜ ˜
9 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp:15:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec1=(int*) R_alloc(length_vec, sizeof(int));
                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:16:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec2=(int*) R_alloc(length_vec, sizeof(int));
                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:17:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_main =(int*) R_alloc(length_vec, sizeof(int));
                         ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:18:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_main_sorted =(int*) R_alloc(length_vec, sizeof(int));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:19:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec2_sorted=(int*) R_alloc(length_vec, sizeof(int));
                           ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:20:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_main_mean =(double*) R_alloc(length_vec, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:21:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_tmp_mean =(double*) R_alloc(length_vec, sizeof(double));
                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:117:13: warning: variable length arrays are a C99 feature [-Wvla]
        int vec_old[depth+1];
                   ^
mrnet_ensemble_standalone.cpp:118:42: warning: variable length arrays are a C99 feature [-Wvla]
        int mat_res [power((maxnsol+1),(depth))][depth+2];
                                                ^
mrnet_ensemble_standalone.cpp:118:14: warning: variable length arrays are a C99 feature [-Wvla]
        int mat_res [power((maxnsol+1),(depth))][depth+2];
                    ^
mrnet_ensemble_standalone.cpp:120:15: warning: variable length arrays are a C99 feature [-Wvla]
        int to_remove[number_leafs];
                     ^
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
mrnet_ensemble_standalone.cpp:220:13: warning: variable length arrays are a C99 feature [-Wvla]
        int vec_old[depth+1];
                   ^
mrnet_ensemble_standalone.cpp:221:38: warning: variable length arrays are a C99 feature [-Wvla]
        int mat_res [power(maxnsol,(depth))][depth+2];
                                            ^
mrnet_ensemble_standalone.cpp:221:14: warning: variable length arrays are a C99 feature [-Wvla]
        int mat_res [power(maxnsol,(depth))][depth+2];
                    ^
mrnet_ensemble_standalone.cpp:223:15: warning: variable length arrays are a C99 feature [-Wvla]
        int to_remove[number_leafs];
                     ^
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable 'rootdepth' [-Wunused-variable]
        int rootdepth=tr.depth(it);
            ^
mrnet_ensemble_standalone.cpp:304:6: warning: unused variable 'rootdepth' [-Wunused-variable]
        int rootdepth=tr.depth(it);
            ^
mrnet_ensemble_standalone.cpp:380:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        ind=(int*) R_alloc(size_boot, sizeof(int));
                   ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:381:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mim =(double*) R_alloc(size*size, sizeof(double));
                       ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
mrnet_ensemble_standalone.cpp:385:13: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                ind[i-1]=i-1;
                        ˜˜^˜
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable 'boot_val' [-Wunused-variable]
        double *mim, *boot_val;
                      ^
mrnet_ensemble_standalone.cpp:410:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        ind=(int*) R_alloc(size_boot, sizeof(int));
                   ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:411:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mim =(double*) R_alloc(size*size, sizeof(double));
                       ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
mrnet_ensemble_standalone.cpp:412:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        boot_val =(double*) R_alloc(rep_boot, sizeof(double));
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:457:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mean =(double*) R_alloc(cnt_leafs, sizeof(double));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:458:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        sd =(double*) R_alloc(cnt_leafs, sizeof(double));
                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:459:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        to_remove=(int*) R_alloc(cnt_leafs, sizeof(int));
                         ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:468:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        prev_sel=(int*) R_alloc(max_depth, sizeof(int));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:507:7: warning: unused variable 'cnt_back' [-Wunused-variable]
                int cnt_back=cnt2;
                    ^
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable 'nsub' [-Wunused-variable]
        int  nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
             ^
mrnet_ensemble_standalone.cpp:562:17: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        jmax=var_target-1;
            ˜˜˜˜˜˜˜˜˜˜˜^˜
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable 'max_val' [-Wunused-variable]
        double max_val=-1000;
               ^
mrnet_ensemble_standalone.cpp:593:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        res_vec =(double*) R_alloc(n, sizeof(double));
                           ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:594:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_mean =(double*) R_alloc(n, sizeof(double));
                            ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:595:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sd =(double*) R_alloc(n, sizeof(double));
                          ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:596:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sort =(double*) R_alloc(n, sizeof(double));
                            ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:597:40: 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));
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:598:38: 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));
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:604:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        prev_sel=(int*) R_alloc(max_elements, sizeof(int));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:605:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        nsub=(int*) R_alloc(max_elements, sizeof(int));
                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:674:101: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                bootstrap_mrmr(vec_mean[k],vec_sd[k], data,namat,n, rep_boot,nsamples_boot,nsamples,nsub[0],(k+1), max_elements_tmp-1,prev_sel);                                
                                                ˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                                               ˜^˜
mrnet_ensemble_standalone.cpp:678:41: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                                max_mrmr=vec_mean[k];max_mrmr_ind=k;
                                                                                 ˜^
mrnet_ensemble_standalone.cpp:691:29: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                                                        res.append_child(it,k+1); res_mean.append_child(it_mean,vec_mean[k]);
                                                        ˜˜˜                 ˜^˜
mrnet_ensemble_standalone.cpp:586:48: warning: unused variable 'nprev_sel' [-Wunused-variable]
        int  *nsub, *prev_sel,nsamples_boot=nsamples, nprev_sel=0; 
                                                      ^
mrnet_ensemble_standalone.cpp:783:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp_nchildren[cnt-1]=(res_tree.number_of_children(it_final));
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:805:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res_all[length_res_old+k]=res_tmp[k];
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:808:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res_all[length_res_old+k+res_tree.size()+1]=tmp_nchildren[k];
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
mrnet_ensemble_standalone.cpp:777:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable 'rootdepth' [-Wunused-variable]
                int rootdepth=res_tree.depth(it_final);
                    ^
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
                                    ^
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable 'res_all2' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
                                             ^
mrnet_ensemble_standalone.cpp:728:9: warning: implicit conversion loses integer precision: 'time_t' (aka 'long') to 'unsigned int' [-Wshorten-64-to-32]
        srand (time(NULL));
        ˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:779:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res_tmp[0]=res_tree.size();
                          ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:800:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:793:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
mrnet_ensemble_standalone.cpp:853:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_mean =(double*) R_alloc(n, sizeof(double));
                            ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:854:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sd =(double*) R_alloc(n, sizeof(double));
                          ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:855:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        mrmr_vec_sort =(double*) R_alloc(n, sizeof(double));
                                 ˜˜˜˜˜˜˜ ^
mrnet_ensemble_standalone.cpp:856:40: 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));
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:857:38: 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));
                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:864:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        prev_sel=(int*) R_alloc(max_elements, sizeof(int));
                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:865:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        nsub=(int*) R_alloc(max_elements, sizeof(int));
                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:870:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sol_local=(int*) R_alloc(maxnsol, sizeof(int));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:871:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        vec_sol_local_mrmr=(double*) R_alloc(maxnsol, sizeof(double));
                                     ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:921:104: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                                        bootstrap_mrmr_fix(vec_mean[k],vec_sd[k], data,namat,n, rep_boot,nsamples_boot,nsamples,nsub[0],(k+1), min(cnt,max_elements_tmp),prev_sel);             
                                        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                                                                               ˜^˜
mrnet_ensemble_standalone.cpp:849:21: 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;
                           ^
mrnet_ensemble_standalone.cpp:848:48: 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; 
                                                      ^
mrnet_ensemble_standalone.cpp:848:66: 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; 
                                                                        ^
mrnet_ensemble_standalone.cpp:1052:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
                        tmp_nchildren[cnt-1]=(res_tree.number_of_children(it_final));
                                            ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1072:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res_all[length_res_old+k]=res_tmp[k];
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1075:12: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        res_all[length_res_old+k+res_tree.size()+1]=tmp_nchildren[k];
                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable 'rootdepth' [-Wunused-variable]
                int rootdepth=res_tree.depth(it_final);
                    ^
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
mrnet_ensemble_standalone.cpp:993:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable 'res_all2' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                             ^
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                    ^
mrnet_ensemble_standalone.cpp:998:9: warning: implicit conversion loses integer precision: 'time_t' (aka 'long') to 'unsigned int' [-Wshorten-64-to-32]
        srand (time(NULL));
        ˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1048:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
                res_tmp[0]=res_tree.size();
                          ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1067:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1062:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
82 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 predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/predictionet.Rcheck/predictionet/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (predictionet)

predictionet.Rcheck/predictionet-Ex.timings:

nameusersystemelapsed
adj.get.hops0.0420.0040.115
adj.remove.cycles0.1110.0040.115
data.discretize0.5620.0200.591
expO.colon.ras0.0130.0010.015
jorissen.colon.ras0.0160.0010.019
net2pred0.3520.0160.371
netinf0.2260.0190.248
netinf.cv0.6870.0390.738
netinf.predict0.1560.0110.168
netinf2gml0.6100.0220.644
pred.score0.0300.0050.034
predictionet.press.statistic0.6780.0170.699
predictionet.stability.cv0.5380.0140.553