predictionet 1.30.0
Benjamin Haibe-Kains
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/predictionet |
| Branch: RELEASE_3_9 |
| Last Commit: 7e77793 |
| Last Changed Date: 2019-05-02 11:53:31 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf predictionet.buildbin-libdir && mkdir predictionet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh predictionet_1.30.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R predictionet.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=predictionet.buildbin-libdir predictionet_1.30.0.tar.gz'
>>>>>>>
* installing *source* package ‘predictionet’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c foo_mrmr.cpp -o foo_mrmr.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mrnet_adapted.cpp -o mrnet_adapted.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mrnet_adapted2.cpp -o mrnet_adapted2.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable 'found' [-Wunused-variable]
bool found=false;
^
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:377:16: warning: unused variable 'boot_val' [-Wunused-variable]
double *mim, *boot_val;
^
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:560:9: warning: unused variable 'max_val' [-Wunused-variable]
double max_val=-1000;
^
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: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:794:7: warning: unused variable 'ind' [-Wunused-variable]
int ind=0;
^
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: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: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;
^
= nullptr
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: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: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: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: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;
^
= nullptr
25 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.9-bioc/meat/predictionet.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR predictionet.buildbin-libdir/predictionet/libs//predictionet.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "predictionet.buildbin-libdir/predictionet/libs//predictionet.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "predictionet.buildbin-libdir/predictionet/libs//predictionet.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "predictionet.buildbin-libdir/predictionet/libs//predictionet.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "predictionet.buildbin-libdir/predictionet/libs//predictionet.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "predictionet.buildbin-libdir/predictionet/libs//predictionet.so"