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###
### Running command:
###
### rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.61.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R survcomp.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=survcomp.buildbin-libdir survcomp_1.61.1.tar.gz'
>>>>>>>
* installing *source* package ‘survcomp’ ...
** this is package ‘survcomp’ version ‘1.61.1’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c concordance.index.c -o concordance.index.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
foo_mrmr_ensemble_surv.cpp:40:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
40 | double res_ch[lenStrat];
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:40:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:38:6: note: declared here
38 | int lenStrat = lenS;
| ^
foo_mrmr_ensemble_surv.cpp:41:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
41 | double res_dh[lenStrat];
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:41:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:38:6: note: declared here
38 | int lenStrat = lenS;
| ^
foo_mrmr_ensemble_surv.cpp:48:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
48 | int ixs[lenStrat];
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:48:11: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:38:6: note: declared here
38 | int lenStrat = lenS;
| ^
foo_mrmr_ensemble_surv.cpp:64:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
64 | double xs[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:64:13: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:72:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
72 | int cls[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:72:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:80:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
80 | double sts[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:80:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:88:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
88 | int ses[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:88:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:96:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
96 | double weightss[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:96:19: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:104:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
104 | double chs[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:104:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:105:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
105 | double dhs[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:105:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:106:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
106 | double uhs[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:106:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:107:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
107 | double rphs[Ns];
| ^~
foo_mrmr_ensemble_surv.cpp:107:15: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
46 | int Ns = 0;
| ^
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable 'msurv_x' [-Wunused-variable]
191 | 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]
191 | int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x;
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:351:7: warning: unused variable 'cnt_back' [-Wunused-variable]
351 | int cnt_back=cnt2;
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable 'nsub' [-Wunused-variable]
286 | int nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
| ^~~~
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable 'mim' [-Wunused-variable]
387 | double *mim, *boot_val, *mat_info;
| ^~~
foo_mrmr_ensemble_surv.cpp:437:15: warning: variable 'jmax' set but not used [-Wunused-but-set-variable]
437 | unsigned int jmax;
| ^
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable 'max_val' [-Wunused-variable]
439 | double max_val=-1000;
| ^~~~~~~
foo_mrmr_ensemble_surv.cpp:473:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
473 | int vec_old[depth+1];
| ^~~~~~~
foo_mrmr_ensemble_surv.cpp:473:14: note: read of non-const variable 'depth' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:471:6: note: declared here
471 | int depth=tr.depth(li);
| ^
foo_mrmr_ensemble_surv.cpp:474:43: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
474 | int mat_res [power((maxnsol+1),(depth))][depth+2];
| ^~~~~~~
foo_mrmr_ensemble_surv.cpp:474:43: note: read of non-const variable 'depth' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:471:6: note: declared here
471 | int depth=tr.depth(li);
| ^
foo_mrmr_ensemble_surv.cpp:474:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
474 | int mat_res [power((maxnsol+1),(depth))][depth+2];
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:474:22: note: function parameter 'maxnsol' with unknown value cannot be used in a constant expression
474 | int mat_res [power((maxnsol+1),(depth))][depth+2];
| ^
foo_mrmr_ensemble_surv.cpp:464:146: note: declared here
464 | int verify_equivalentset_nparents (tree<int>& tr, tree<int>::pre_order_iterator it, tree<int>::pre_order_iterator end,tree<double>& tr_mrmr, int maxnsol){
| ^
foo_mrmr_ensemble_surv.cpp:476:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
476 | int to_remove[number_leafs];
| ^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:476:16: note: read of non-const variable 'number_leafs' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:475:6: note: declared here
475 | int number_leafs=power((maxnsol+1),(depth));
| ^
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable 'found' [-Wunused-variable]
467 | bool found=false;
| ^~~~~
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable 'nsamples_boot' [-Wunused-variable]
578 | 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]
578 | 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]
578 | int *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
| ^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:579:21: warning: unused variable 'vec_sort' [-Wunused-variable]
579 | double *vec_mean, *vec_sort, *vec_sd, *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr;
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:579:63: warning: variable 'vec_local_max_sd' set but not used [-Wunused-but-set-variable]
579 | 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:803:13: warning: unused variable 'cnt2' [-Wunused-variable]
803 | int cnt=1,cnt2=0;
| ^~~~
foo_mrmr_ensemble_surv.cpp:806:7: warning: unused variable 'rootdepth' [-Wunused-variable]
806 | int rootdepth=res_tree.depth(it_final);
| ^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:819:7: warning: unused variable 'ind' [-Wunused-variable]
819 | int ind=0;
| ^~~
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable 'res_all' [-Wunused-variable]
733 | int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
| ^~~~~~~
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable 'res_all2' [-Wunused-variable]
733 | int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
734 | int vec_tmp;
| ^~~~~~~
35 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
foo_mrmr_surv.cpp:80:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
80 | double res_ch[lenStrat];
| ^~~~~~~~
foo_mrmr_surv.cpp:80:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_surv.cpp:78:6: note: declared here
78 | int lenStrat = *lenS;
| ^
foo_mrmr_surv.cpp:81:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
81 | double res_dh[lenStrat];
| ^~~~~~~~
foo_mrmr_surv.cpp:81:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_surv.cpp:78:6: note: declared here
78 | int lenStrat = *lenS;
| ^
foo_mrmr_surv.cpp:88:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
88 | int ixs[lenStrat];
| ^~~~~~~~
foo_mrmr_surv.cpp:88:11: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_surv.cpp:78:6: note: declared here
78 | int lenStrat = *lenS;
| ^
foo_mrmr_surv.cpp:104:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
104 | double xs[Ns];
| ^~
foo_mrmr_surv.cpp:104:13: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:112:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
112 | int cls[Ns];
| ^~
foo_mrmr_surv.cpp:112:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:120:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
120 | double sts[Ns];
| ^~
foo_mrmr_surv.cpp:120:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:128:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
128 | int ses[Ns];
| ^~
foo_mrmr_surv.cpp:128:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:136:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
136 | double weightss[Ns];
| ^~
foo_mrmr_surv.cpp:136:19: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:144:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
144 | double chs[Ns];
| ^~
foo_mrmr_surv.cpp:144:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:145:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
145 | double dhs[Ns];
| ^~
foo_mrmr_surv.cpp:145:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:146:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
146 | double uhs[Ns];
| ^~
foo_mrmr_surv.cpp:146:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
foo_mrmr_surv.cpp:147:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
147 | double rphs[Ns];
| ^~
foo_mrmr_surv.cpp:147:15: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
86 | int Ns = 0;
| ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c survcomp_init.cpp -o survcomp_init.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/survcomp.buildbin-libdir/00LOCK-survcomp/00new/survcomp/libs
** R
** data
** 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 (survcomp)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR survcomp.buildbin-libdir/survcomp/libs/survcomp.so
>>>>>>>
>>>>>>> Paths before fix:
survcomp.buildbin-libdir/survcomp/libs/survcomp.so:
survcomp.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!
