* installing *source* package ‘rtmpt’ ... ** package ‘rtmpt’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘clang version 18.1.4’ using C++ compiler: ‘clang version 18.1.4’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rtmpt/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Quelle.cpp -o Quelle.o Quelle.cpp:65:42: warning: unused variable 'igr' [-Wunused-variable] 65 | int r = cat2resp[daten[x].category], igr = t2group[t] * respno + r, itr = t * respno + r; | ^~~ Quelle.cpp:82:10: warning: unused variable 'igr' [-Wunused-variable] 82 | int igr = t2group[t] * respno + r, itr = t * respno + r; | ^~~ Quelle.cpp:217:31: warning: unused variable 'igr' [-Wunused-variable] 217 | int itr = t * respno + r, igr = t2group[t] * respno + r; | ^~~ Quelle.cpp:234:32: warning: unused variable 'igr' [-Wunused-variable] 234 | int itr = t * respno + r, igr = t2group[t] * respno + r; | ^~~ /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c adaptive_rejection_sampling.cpp -o adaptive_rejection_sampling.o 4 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c additions.cpp -o additions.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c derivatives.cpp -o derivatives.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c diagnosis.cpp -o diagnosis.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c diffusion.cpp -o diffusion.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c gibbs.cpp -o gibbs.o diagnosis.cpp:228:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] 228 | if ((complength == 1) /*&& (PFAD_INDEX(j, k) > -1)*/) { | ~~~~~~~~~~~^~~~ diagnosis.cpp:228:21: note: remove extraneous parentheses around the comparison to silence this warning 228 | if ((complength == 1) /*&& (PFAD_INDEX(j, k) > -1)*/) { | ~ ^ ~ diagnosis.cpp:228:21: note: use '=' to turn this equality comparison into an assignment 228 | if ((complength == 1) /*&& (PFAD_INDEX(j, k) > -1)*/) { | ^~ | = gibbs.cpp:26:11: warning: unused variable 'old_path' [-Wunused-variable] 26 | int old_path = paths[x]; | ^~~~~~~~ gibbs.cpp:61:7: warning: misleading indentation; statement is not part of the previous 'else' [-Wmisleading-indentation] 61 | if (sigi) free(sigi); | ^ gibbs.cpp:53:5: note: previous statement is here 53 | else | ^ gibbs.cpp:592:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 592 | ioff += 1; | ^ gibbs.cpp:586:7: note: previous statement is here 586 | for (int is = 0; is != (NOTHREADS); is++) | ^ diagnosis.cpp:830:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 830 | belege_lambdas_mus(sample, is, lambdas); | ^ diagnosis.cpp:820:7: note: previous statement is here 820 | for (int t = 0; t != indi; t++) | ^ diagnosis.cpp:841:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 841 | for (int ir = 0; ir != respno; ir++) person << std::setw(20) << mlambdas[t * respno + ir]; | ^ diagnosis.cpp:839:9: note: previous statement is here 839 | for (int iz = 0; iz != ift; iz++) | ^ diagnosis.cpp:927:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 927 | Rprintf("Mean motor/encoding times per group [median, 96 and 99%% HDI]\n"); | ^ diagnosis.cpp:914:5: note: previous statement is here 914 | for (int ix = 0; ix != icompg; ix++) | ^ diagnosis.cpp:957:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 957 | Rprintf("Omega^2 [median, 96 and 99%% HDI]\n"); | ^ diagnosis.cpp:944:5: note: previous statement is here 944 | for (int ip = 0; ip != respno; ip++) | ^ diagnosis.cpp:1038:24: warning: unused variable 'pd' [-Wunused-variable] 1038 | double dbar = 0.0, pd = 0.0, pv = 0.0; | ^~ diagnosis.cpp:1275:9: warning: variable 'exit_status' set but not used [-Wunused-but-set-variable] 1275 | int exit_status = 0; | ^ diagnosis.cpp:1505:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 1505 | test(tt1, tt2, "Posterior predictive checks: latencies"); | ^ diagnosis.cpp:1486:5: note: previous statement is here 1486 | for (int ig = 0; ig != igroup; ig++) | ^ diagnosis.cpp:1525:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 1525 | meansout.close(); | ^ diagnosis.cpp:1510:5: note: previous statement is here 1510 | for (int ig = 0; ig != igroup; ig++) | ^ diagnosis.cpp:1291:9: warning: variable 'exit_status' set but not used [-Wunused-but-set-variable] 1291 | int exit_status = 1; | ^ diagnosis.cpp:1292:9: warning: unused variable 'kein' [-Wunused-variable] 1292 | int kein = kerncat * indi, keig = kerncat * igroup; | ^~~~ diagnosis.cpp:1507:9: warning: unused variable 'nq' [-Wunused-variable] 1507 | int nq = 1; | ^~ diagnosis.cpp:1564:9: warning: variable 'exit_status' set but not used [-Wunused-but-set-variable] 1564 | int exit_status = 0; | ^ 3 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c hamiltonian.cpp -o hamiltonian.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c hcubature.cpp -o hcubature.o hcubature.cpp:282:9: warning: unused variable 'kdiv' [-Wunused-variable] 282 | int kdiv = out.kdivide; | ^~~~ 13 warnings generated. /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c invtri.c -o invtri.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c joint.cpp -o joint.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c lkj.cpp -o lkj.o joint.cpp:116:9: warning: unused variable 'sdt' [-Wunused-variable] 116 | int sdt = indi * respno + t; | ^~~ joint.cpp:301:9: warning: unused variable 'iofft' [-Wunused-variable] 301 | int iofft = iavwoff + t * icompg, itfr = 3 * t * ifreemax; | ^~~~~ joint.cpp:401:29: warning: unused variable 'ipl' [-Wunused-variable] 401 | int i = root->index, ipl = i + root->level; | ^~~ joint.cpp:444:8: warning: unused variable 'xn' [-Wunused-variable] 444 | int xn = isigoff + indi; | ^~ lkj.cpp:90:8: warning: variable 'offset2' set but not used [-Wunused-but-set-variable] 90 | int offset2 = nhamil; | ^ 4 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c lnnorm.cpp -o lnnorm.o 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c main.cpp -o main.o main.cpp:670:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 670 | for (int itree = 0; itree != kerntree; itree++) | ^ main.cpp:654:5: note: previous statement is here 654 | for (int itree = 0; itree != kerntree; itree++) | ^ main.cpp:700:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 700 | for (int i = 0; i != 2 * nodemax * datenzahl; i++) tau_by_node[i] = -1; | ^ main.cpp:694:5: note: previous statement is here 694 | for (int im = 0; im != no_patterns; im++) | ^ main.cpp:764:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 764 | for (int i = 0; i != kerncat * zweig * nodemax; i++) drin[i] = -1; | ^ main.cpp:749:5: note: previous statement is here 749 | for (int j = 0; j != kerncat; j++) | ^ main.cpp:773:9: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 773 | for (int j = 0; j!= kerncat; j++) { | ^ main.cpp:768:7: note: previous statement is here 768 | for (int k = 0; k != branch[j]; k++) | ^ main.cpp:790:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 790 | for (int t = 0; t != indi; t++) | ^ main.cpp:785:9: note: previous statement is here 785 | for (int ip = 0; ip != ifree[type]; ip++) | ^ lnnorm.cpp:31:13: warning: variable 'upper' set but not used [-Wunused-but-set-variable] 31 | int upper, lower ; | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c mvtimes.cpp -o mvtimes.o 5 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c onetimes.cpp -o onetimes.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c r_wrapper.cpp -o r_wrapper.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rtimes.cpp -o rtimes.o mvtimes.cpp:1486:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 1486 | gsl_matrix_memcpy(&Xsigi.matrix, cx); | ^ mvtimes.cpp:1482:5: note: previous statement is here 1482 | for (int j = 0; j != nvar; j++) | ^ mvtimes.cpp:1616:9: warning: variable 'acc' set but not used [-Wunused-but-set-variable] 1616 | int acc = 0; | ^ onetimes.cpp:140:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] 140 | if ((complength == 1) /*&& (PFAD_INDEX(j, k) > -1)*/) { | ~~~~~~~~~~~^~~~ onetimes.cpp:140:21: note: remove extraneous parentheses around the comparison to silence this warning 140 | if ((complength == 1) /*&& (PFAD_INDEX(j, k) > -1)*/) { | ~ ^ ~ onetimes.cpp:140:21: note: use '=' to turn this equality comparison into an assignment 140 | if ((complength == 1) /*&& (PFAD_INDEX(j, k) > -1)*/) { | ^~ | = onetimes.cpp:423:11: warning: unknown pragma ignored [-Wunknown-pragmas] 423 | #pragma optimize("", off) | ^ onetimes.cpp:436:11: warning: unknown pragma ignored [-Wunknown-pragmas] 436 | #pragma optimize("", on) | ^ onetimes.cpp:498:9: warning: unused variable 'n' [-Wunused-variable] 498 | int n = (pars->n), m = (pars->m); | ^ onetimes.cpp:676:15: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 676 | lambdas[t] = gsl_vector_get(xsave,icompg); | ^ onetimes.cpp:674:13: note: previous statement is here 674 | for (int ip = 0; ip != ifree[type]; ip++) | ^ onetimes.cpp:578:23: warning: unused variable 'xx' [-Wunused-variable] 578 | gsl_vector* xx = gsl_vector_alloc(icompg + 2); | ^~ onetimes.cpp:787:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 787 | lambdas[t] = gsl_vector_get(xsave,icompg); | ^ onetimes.cpp:785:9: note: previous statement is here 785 | for (int ip = 0; ip != ifree[type]; ip++) | ^ onetimes.cpp:689:19: warning: unused variable 'xx' [-Wunused-variable] 689 | gsl_vector* xx = gsl_vector_alloc(icompg + 2); | ^~ /usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c rtmpt_init.c -o rtmpt_init.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c rwiener.cpp -o rwiener.o 8 warnings generated. 2 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c specifics.cpp -o specifics.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c times.cpp -o times.o times.cpp:122:8: warning: variable 'exit_status' set but not used [-Wunused-but-set-variable] 122 | int exit_status = 0; | ^ 1 warning generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c tools.cpp -o tools.o tools.cpp:60:12: warning: unused variable 'result' [-Wunused-variable] 60 | double result; | ^~~~~~ tools.cpp:290:9: warning: unused variable 'm' [-Wunused-variable] 290 | int m = (irun + 1) * ireps; | ^ tools.cpp:306:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 306 | for (int t = 0; t != indi; t++) | ^ tools.cpp:297:5: note: previous statement is here 297 | for (int ig = 0; ig != igroup; ig++) | ^ tools.cpp:328:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 328 | for (int t = 0; t != indi; t++) | ^ tools.cpp:319:5: note: previous statement is here 319 | for (int ig = 0; ig != igroup; ig++) | ^ tools.cpp:556:11: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation] 556 | jj = (indi + igroup) * icompg + igroup * respno; | ^ tools.cpp:548:9: note: previous statement is here 548 | for (int t = 0; t != indi; t++) | ^ tools.cpp:805:9: warning: unused variable 'pfadlength' [-Wunused-variable] 805 | int pfadlength = (params->pfadlength); | ^~~~~~~~~~ 6 warnings generated. /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/local/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c trait.cpp -o trait.o /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o rtmpt.so Quelle.o adaptive_rejection_sampling.o additions.o derivatives.o diagnosis.o diffusion.o gibbs.o hamiltonian.o hcubature.o invtri.o joint.o lkj.o lnnorm.o main.o mvtimes.o onetimes.o r_wrapper.o rtimes.o rtmpt_init.o rwiener.o specifics.o times.o tools.o trait.o -L/usr/local/lib -lgsl -lgslcblas make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rtmpt/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rtmpt/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rtmpt/src' installing to /data/gannet/ripley/R/packages/tests-clang/rtmpt.Rcheck/00LOCK-rtmpt/00new/rtmpt/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 (rtmpt)