* installing *source* package ‘sdnet’ ... ** package ‘sdnet’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-LTO/sdnet/src' g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c cache.cpp -o cache.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c catnet_entropy.cpp -o catnet_entropy.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c catnet_quant.cpp -o catnet_quant.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c catnet_rexport.cpp -o catnet_rexport.o catnet_rexport.cpp: In function ‘SEXPREC* show_catnet(SEXP, SEXP, SEXP, SEXP)’: catnet_rexport.cpp:222:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 222 | sprintf(strbuff, "%s%s, ", strbuff, CHAR(STRING_ELT(pf, 0))); | ^ catnet_rexport.cpp:226:34: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 226 | sprintf(strbuff, "%s\n", strbuff); | ^ catnet_rexport.cpp:233:45: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 233 | sprintf(strbuff, "%s[%d] ", strbuff, nnode); | ^ catnet_rexport.cpp:236:65: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 236 | sprintf(strbuff, "%s%d, ", strbuff, INTEGER_POINTER(pf)[i]-1); | ^ catnet_rexport.cpp:237:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 237 | sprintf(strbuff, "%s\n", strbuff); | ^ catnet_rexport.cpp:240:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 240 | sprintf(strbuff, "%s\n", strbuff); | ^ catnet_rexport.cpp:251:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 251 | sprintf(strbuff, "%s%s, ", strbuff, CHAR(STRING_ELT(pf,i))); | ^ catnet_rexport.cpp:252:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 252 | sprintf(strbuff, "%s\n", strbuff); | ^ gcc -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -flto -c ccnInit.c -o ccnInit.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c pthread.cpp -o pthread.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c rcatnet.cpp -o rcatnet.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c rcatnet_hist.cpp -o rcatnet_hist.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c rcatnet_prob.cpp -o rcatnet_prob.o rcatnet_prob.cpp: In function ‘char* gen_prob_string(int, SEXP, int, SEXP, SEXP, char*)’: rcatnet_prob.cpp:49:104: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] 49 | sprintf(newstr, "%s%s%s %f\n", newstr, str, CHAR(STRING_ELT(pcats, j)), NUMERIC_POINTER(problist)[j]); | ^ g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c rcatnet_sa.cpp -o rcatnet_sa.o rcatnet_sa.cpp: In member function ‘SEXPREC* RCatnetSearchSA::search(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: rcatnet_sa.cpp:267:38: warning: variable ‘ordProb’ set but not used [-Wunused-but-set-variable] 267 | double *matEdgeLiks, *pMatEdgeLiks, ordProb, *newOrdProb, *pDirProbs, | ^~~~~~~ g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c rcatnet_search.cpp -o rcatnet_search.o In file included from rcatnet_search.cpp:33: dag_search_dc.h: In member function ‘int DAGD_SEARCH_DC::search(SEARCH_PARAMETERS*)’: dag_search_dc.h:885:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 885 | if(pcomblist[k]) | ^~ dag_search_dc.h:886:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 886 | CATNET_FREE(pcomblist[k]); pcomblist[k] = paux; | ^~~~~~~~~ In file included from rcatnet_search.cpp:37: dag_search_dc.h: In member function ‘int DAGP_SEARCH_DC::search(SEARCH_PARAMETERS*)’: dag_search_dc.h:885:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 885 | if(pcomblist[k]) | ^~ dag_search_dc.h:886:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 886 | CATNET_FREE(pcomblist[k]); pcomblist[k] = paux; | ^~~~~~~~~ g++ -std=gnu++11 -I"/data/gannet/ripley/R/LTO/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -flto -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o sdnet.so cache.o catnet_entropy.o catnet_quant.o catnet_rexport.o ccnInit.o pthread.o rcatnet.o rcatnet_hist.o rcatnet_prob.o rcatnet_sa.o rcatnet_search.o utils.o catnet_rexport.h:53:6: warning: type of ‘catnetNodeLoglik’ does not match original declaration [-Wlto-type-mismatch] 53 | SEXP catnetNodeLoglik(SEXP cnet, SEXP rNode, SEXP rSamples, SEXP rPerturbations); | ^ catnet_rexport.cpp:741:6: note: type mismatch in parameter 5 741 | SEXP catnetNodeLoglik(SEXP cnet, SEXP rNode, SEXP rSamples, SEXP rPerturbations, SEXP rKlmode) { | ^ catnet_rexport.cpp:741:6: note: type ‘struct SEXPREC *’ should match type ‘void’ catnet_rexport.cpp:741:6: note: ‘catnetNodeLoglik’ was previously declared here catnet_rexport.h:39:6: warning: type of ‘searchSA’ does not match original declaration [-Wlto-type-mismatch] 39 | SEXP searchSA(SEXP rNodeNames, SEXP rSamples, SEXP rPerturbations, | ^ catnet_rexport.cpp:366:6: note: type mismatch in parameter 24 366 | SEXP searchSA(SEXP rNodeNames, SEXP rSamples, SEXP rPerturbations, | ^ catnet_rexport.cpp:366:6: note: type ‘void’ should match type ‘struct SEXPREC *’ catnet_rexport.cpp:366:6: note: ‘searchSA’ was previously declared here catnet_rexport.h:33:6: warning: type of ‘searchOrder’ does not match original declaration [-Wlto-type-mismatch] 33 | SEXP searchOrder(SEXP rSamples, SEXP rPerturbations, | ^ catnet_rexport.cpp:292:6: note: type mismatch in parameter 15 292 | SEXP searchOrder(SEXP rSamples, SEXP rPerturbations, | ^ catnet_rexport.cpp:292:6: note: type ‘struct SEXPREC *’ should match type ‘void’ catnet_rexport.cpp:292:6: note: ‘searchOrder’ was previously declared here catnet_rexport.h:62:6: warning: type of ‘catnetSoftQuant’ does not match original declaration [-Wlto-type-mismatch] 62 | SEXP catnetSoftQuant(SEXP rSamples, SEXP rSampleWeights, SEXP rNumCats, SEXP rLearnset, SEXP rCover, SEXP rMode, SEXP rMaxiter); | ^ catnet_quant.cpp:384:6: note: type mismatch in parameter 8 384 | SEXP catnetSoftQuant(SEXP rSamples, SEXP rSampleWeights, SEXP rNumCats, SEXP rLearnset, SEXP rCover, SEXP rMode, SEXP rMaxiter, SEXP rEps) { | ^ catnet_quant.cpp:384:6: note: type ‘struct SEXPREC *’ should match type ‘void’ catnet_quant.cpp:384:6: note: ‘catnetSoftQuant’ was previously declared here make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-LTO/sdnet/src' installing to /data/gannet/ripley/R/packages/tests-LTO/Libs/sdnet-lib/00LOCK-sdnet/00new/sdnet/libs ** R ** data ** demo ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (sdnet) Time 1:21.44, 69.72 + 2.20