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###
### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL predictionet
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘predictionet’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c foo_mrmr.cpp -o foo_mrmr.o
foo_mrmr.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr.cpp:13:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   13 |  for( unsigned int i=0; i< size; ++i ) {
      |                         ~^~~~~~
foo_mrmr.cpp:23:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   23 |  for( unsigned int i=0; i< size; ++i ) {
      |                         ~^~~~~~
foo_mrmr.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr.cpp:50:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   50 |  for(unsigned int i=0; i< size_subset; ++i){
      |                        ~^~~~~~~~~~~~~
foo_mrmr.cpp:51:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   51 |   for(unsigned int j=0; j< nvar; ++j){
      |                         ~^~~~~~
foo_mrmr.cpp:57:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   57 |  for(unsigned int i=0; i< nvar; ++i){
      |                        ~^~~~~~
foo_mrmr.cpp:59:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   59 |   for(unsigned int j=i+1; j< nvar; ++j){
      |                           ~^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mrnet_adapted.cpp -o mrnet_adapted.o
mrnet_adapted.cpp: In function ‘SEXPREC* mrnet_adapted(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted.cpp:58:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
   58 |  for(unsigned int i=0;i < *nsample; ++i){
      |                       ~~^~~~~~~~~~
mrnet_adapted.cpp:103:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  103 |    for( int l=0; l<n; ++l )
      |                  ~^~
mrnet_adapted.cpp:131:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  131 |  for(unsigned int j=0; j< *npredn; ++j ) {
      |                        ~^~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mrnet_adapted2.cpp -o mrnet_adapted2.o
mrnet_adapted2.cpp: In function ‘SEXPREC* mrnet_adapted2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted2.cpp:62:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
   62 |  for(unsigned int i=0;i < *nsample; ++i){
      |                       ~~^~~~~~~~~~
mrnet_adapted2.cpp:121:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  121 |    for( int l=0; l<n; ++l )
      |                  ~^~
mrnet_adapted2.cpp:185:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  185 |  for(unsigned int j=0; j< *npredn; ++j ) {
      |                        ~^~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp: In function ‘void remove_equiv_subtrees(tree<int>&, tree<double>&)’:
mrnet_ensemble_standalone.cpp:24:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   24 |  for(unsigned int j=0;j< length_vec;++j){
      |                       ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:42:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   42 |    for(unsigned int j=0;j< length_vec;++j){
      |                         ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:47:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   47 |     for(unsigned int j=0;j< (res.depth(it_main)-1);++j){
      |                          ~^~~~~~~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:60:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   60 |      for(unsigned int j=0;j< length_vec;++j){
      |                           ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:65:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   65 |      for(unsigned int j=0;j< length_vec && equiv;++j){
      |                           ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)’:
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable ‘found’ [-Wunused-variable]
  111 |  bool found=false;
      |       ^~~~~
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, int, int*, int*)’:
mrnet_ensemble_standalone.cpp:223:6: warning: variable ‘to_remove’ set but not used [-Wunused-but-set-variable]
  223 |  int to_remove[number_leafs];
      |      ^~~~~~~~~
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  283 |  int rootdepth=tr.depth(it);
      |      ^~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void build_tree_int(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, int*, int, int)’:
mrnet_ensemble_standalone.cpp:304:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  304 |  int rootdepth=tr.depth(it);
      |      ^~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr_fix(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:384:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  384 |  for(unsigned int i=1;i<= nsamples;++i){
      |                       ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable ‘boot_val’ [-Wunused-variable]
  377 |  double *mim, *boot_val;
      |                ^~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:414:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  414 |  for(unsigned int k=0; k< rep_boot; ++k){
      |                        ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp:417:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  417 |   for(unsigned int i=1;i<= size_boot;++i){
      |                        ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:426:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  426 |  for(unsigned int i=0;i< rep_boot;++i){
      |                       ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp:433:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  433 |  for(unsigned int i=0;i< rep_boot;++i){
      |                       ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int)’:
mrnet_ensemble_standalone.cpp:507:7: warning: unused variable ‘cnt_back’ [-Wunused-variable]
  507 |   int cnt_back=cnt2;
      |       ^~~~~~~~
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable ‘nsub’ [-Wunused-variable]
  442 |  int  nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
      |       ^~~~
mrnet_ensemble_standalone.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
mrnet_ensemble_standalone.cpp:569:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  569 |   for(unsigned int j=0;j< nbvar; j++){
      |                        ~^~~~~~~
mrnet_ensemble_standalone.cpp:558:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
  558 |  unsigned int jmax;
      |               ^~~~
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable ‘max_val’ [-Wunused-variable]
  560 |  double max_val=-1000;
      |         ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void mrmr_ensemble_one_gene(tree<int>&, tree<int>::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)’:
mrnet_ensemble_standalone.cpp:600:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  600 |  for(unsigned int k=0;k< max_elements ;++k){
      |                       ~^~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:658:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  658 |      for (unsigned int i=0;i<max_elements_tmp-1;++i){
      |                            ~^~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:665:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  665 |     for(unsigned int k=0;k< n;++k){
      |                          ~^~~
mrnet_ensemble_standalone.cpp:668:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  668 |     for(unsigned int k=0;k<max_elements_tmp;++k){
      |                          ~^~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:672:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  672 |     for(unsigned int k=0;k< n;++k){
      |                          ~^~~
mrnet_ensemble_standalone.cpp:677:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  677 |      if(k!=(nsub[0]-1) && vec_mean[k]>max_mrmr){
      |         ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:689:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  689 |      for(unsigned int k=0;k< n;++k){
      |                           ~^~~
mrnet_ensemble_standalone.cpp:586:48: warning: unused variable ‘nprev_sel’ [-Wunused-variable]
  586 |  int  *nsub, *prev_sel,nsamples_boot=nsamples, nprev_sel=0;
      |                                                ^~~~~~~~~
mrnet_ensemble_standalone.cpp:587:10: warning: variable ‘res_vec’ set but not used [-Wunused-but-set-variable]
  587 |  double *res_vec, *vec_mean, *vec_sort, *vec_sd,  *vec_local_max_mean, *vec_local_max_sd;;
      |          ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:760:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  760 |  for(unsigned int i=0;i< *npredn;++i){
      |                       ~^~~~~~~~~
mrnet_ensemble_standalone.cpp:799:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  799 |    for(unsigned int k=0;k<length_res_old;k++){
      |                         ~^~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:813:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  813 |   for(unsigned int k=0;k<length_res;k++){
      |                        ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:819:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  819 |   if(i==(*npredn-1)){
      |      ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:822:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  822 |    for(unsigned int k=0;k<length_res;k++){
      |                         ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:777:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
  777 |   int cnt=1,cnt2=0;
      |             ^~~~
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  780 |   int rootdepth=res_tree.depth(it_final);
      |       ^~~~~~~~~
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable ‘ind’ [-Wunused-variable]
  794 |   int ind=0;
      |       ^~~
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable ‘res_all’ [-Wunused-variable]
  722 |  int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
      |                              ^~~~~~~
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
  722 |  int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
      |                                       ^~~~~~~~
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
  723 |  int vec_tmp;
      |      ^~~~~~~
mrnet_ensemble_standalone.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)’:
mrnet_ensemble_standalone.cpp:860:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  860 |  for(unsigned int k=0;k< max_elements ;++k){
      |                       ~^~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:904:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  904 |    for (unsigned int i=0;i<=max_depth;++i){
      |                          ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:912:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  912 |    for(unsigned int k=0;k< n;++k){
      |                         ~^~~
mrnet_ensemble_standalone.cpp:915:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
  915 |    for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
      |                         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:919:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  919 |    for(unsigned int k=0;k< n;++k){
      |                         ~^~~
mrnet_ensemble_standalone.cpp:848:48: warning: unused variable ‘tmp_val_max_ind’ [-Wunused-variable]
  848 |  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]
  848 |  int  *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
      |                                                                  ^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:849:21: warning: unused variable ‘vec_sort’ [-Wunused-variable]
  849 |  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:849:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-variable]
  849 |  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: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1029:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
 1029 |  for(unsigned int i=0;i< *npredn;++i){
      |                       ~^~~~~~~~~
mrnet_ensemble_standalone.cpp:1066:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1066 |    for(unsigned int k=0;k<length_res_old;k++){
      |                         ~^~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1080:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1080 |   for(unsigned int k=0;k<length_res;k++){
      |                        ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1085:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1085 |   if(i==(*npredn-1)){
      |      ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1089:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1089 |    for(unsigned int k=0;k<length_res;k++){
      |                         ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
 1046 |   int cnt=1,cnt2=0;
      |             ^~~~
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
 1049 |   int rootdepth=res_tree.depth(it_final);
      |       ^~~~~~~~~
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable ‘ind’ [-Wunused-variable]
 1063 |   int ind=0;
      |       ^~~
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable ‘res_all’ [-Wunused-variable]
  992 |  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                              ^~~~~~~
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
  992 |  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                                       ^~~~~~~~
mrnet_ensemble_standalone.cpp:993:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
  993 |  int vec_tmp;
      |      ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:840:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  840 |  return Rres;
      |         ^~~~
mrnet_ensemble_standalone.cpp:800:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  800 |     res_all[k]=res_old[k];
      |                ~~~~~~~~~^
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1105:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1105 |  return Rres;
      |         ^~~~
mrnet_ensemble_standalone.cpp:1067:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1067 |     res_all[k]=res_old[k];
      |                ~~~~~~~~~^
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-predictionet/00new/predictionet/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (predictionet)