Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:54 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the survcomp package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/survcomp.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1873/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
survcomp 1.42.0 (landing page) Benjamin Haibe-Kains
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: survcomp |
Version: 1.42.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL survcomp |
StartedAt: 2021-10-14 06:35:39 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 06:35:49 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 10.0 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL survcomp ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘survcomp’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c concordance.index.c -o concordance.index.o 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_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o foo_mrmr_ensemble_surv.cpp: In function ‘double get_correlation_ensemble(double*, int*, int, int, int)’: foo_mrmr_ensemble_surv.cpp:12:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 12 | for( unsigned int i=0; i< size; ++i ) { | ~^~~~~~ foo_mrmr_ensemble_surv.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 22 | for( unsigned int i=0; i< size; ++i ) { | ~^~~~~~ foo_mrmr_ensemble_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’: foo_mrmr_ensemble_surv.cpp:106:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable] 106 | double uhs[Ns]; | ^~~ foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable] 107 | double rphs[Ns]; | ^~~~ foo_mrmr_ensemble_surv.cpp: In function ‘void build_mim_cIndex_subset(double*, double*, int*, int, int, int*, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int*)’: foo_mrmr_ensemble_surv.cpp:202:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 202 | for(unsigned int i=0; i< size_subset; ++i){ | ~^~~~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 203 | for(unsigned int j=0; j< (nvar-1); ++j){ | ~^~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 214 | for(unsigned int i=0; i< nvar-1; ++i){ | ~^~~~~~~~ foo_mrmr_ensemble_surv.cpp:216:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 216 | for(unsigned int j=i+1; j< nvar-1; ++j){ | ~^~~~~~~~ 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: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’: 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: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’: foo_mrmr_ensemble_surv.cpp:393:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 393 | for(unsigned int k=0; k< rep_boot; ++k){ | ~^~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 396 | for(unsigned int i=1;i<= size_boot;++i){ | ~^~~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 400 | for( unsigned int i=0; i< size ; ++i ){ | ~^~~~~~ foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 401 | for( unsigned int j=0; j< size ; ++j ){ | ~^~~~~~ foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 412 | for(unsigned int i=0;i< rep_boot;++i){ | ~^~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:419:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 419 | for(unsigned int i=0;i< rep_boot;++i){ | ~^~~~~~~~~~ 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: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’: foo_mrmr_ensemble_surv.cpp:448:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 448 | for(unsigned int j=0;j< nbvar; j++){ | ~^~~~~~~ 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: In function ‘int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)’: foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable ‘found’ [-Wunused-variable] 467 | bool found=false; | ^~~~~ foo_mrmr_ensemble_surv.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, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’: foo_mrmr_ensemble_surv.cpp:593:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 593 | for(unsigned int i=1;i<= nsamples;++i){ | ~^~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 596 | for( unsigned int i=0; i< n; ++i ){ | ~^~~ foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 597 | for( unsigned int j=0; j< n; ++j ){ | ~^~~ foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 604 | for(unsigned int k=0;k< max_elements ;++k){ | ~^~~~~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 646 | for (unsigned int i=0;i<=max_depth;++i){ | ~^~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 654 | for(unsigned int k=0;k< n;++k){ | ~^~~ foo_mrmr_ensemble_surv.cpp:657:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 657 | for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:661:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 661 | for(unsigned int k=0;k< n;++k){ | ~^~~ 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: In function ‘SEXPREC* mrmr_cIndex_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: foo_mrmr_ensemble_surv.cpp:786:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 786 | for(unsigned int i=0;i< *npredn;++i){ | ~^~~~~~~~~ foo_mrmr_ensemble_surv.cpp:820:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 820 | for(unsigned int k=0;k<length_res_old;k++){ | ~^~~~~~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:834:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 834 | for(unsigned int k=0;k<length_res;k++){ | ~^~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:839:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 839 | if(i==(*npredn-1)){ | ~^~~~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:843:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 843 | for(unsigned int k=0;k<length_res;k++){ | ~^~~~~~~~~~~ foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable ‘cnt2’ [-Wunused-variable] 801 | int cnt=1,cnt2=0; | ^~~~ foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable ‘rootdepth’ [-Wunused-variable] 804 | int rootdepth=res_tree.depth(it_final); | ^~~~~~~~~ foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable ‘ind’ [-Wunused-variable] 817 | 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; | ^~~~~~~ foo_mrmr_ensemble_surv.cpp:859:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized] 859 | return Rres; | ^~~~ foo_mrmr_ensemble_surv.cpp:821:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized] 821 | res_all[k]=res_old[k]; | ~~~~~~~~~^ 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_surv.cpp -o foo_mrmr_surv.o foo_mrmr_surv.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’: foo_mrmr_surv.cpp:12:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 12 | for( unsigned int i=0; i< size; ++i ) { | ~^~~~~~ foo_mrmr_surv.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 22 | for( unsigned int i=0; i< size; ++i ) { | ~^~~~~~ foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’: foo_mrmr_surv.cpp:49:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 49 | for(unsigned int i=0; i< size_subset; ++i){ | ~^~~~~~~~~~~~~ foo_mrmr_surv.cpp:50:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 50 | for(unsigned int j=0; j< nvar; ++j){ | ~^~~~~~ foo_mrmr_surv.cpp:56:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 56 | for(unsigned int i=0; i< nvar; ++i){ | ~^~~~~~ foo_mrmr_surv.cpp:58:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 58 | for(unsigned int j=i+1; j< nvar; ++j){ | ~^~~~~~ foo_mrmr_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int*, int*)’: foo_mrmr_surv.cpp:146:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable] 146 | double uhs[Ns]; | ^~~ foo_mrmr_surv.cpp:147:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable] 147 | double rphs[Ns]; | ^~~~ foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: foo_mrmr_surv.cpp:301:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 301 | for(unsigned int i=0;i < *nsample; ++i){ | ~~^~~~~~~~~~ foo_mrmr_surv.cpp:341:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 341 | for( int l=0; l<n; ++l ) | ~^~ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c survcomp_init.cpp -o survcomp_init.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/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)