* installing *source* package ‘gremlin’ ... ** package ‘gremlin’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ using C++ compiler: ‘g++-13 (GCC) 13.2.0’ make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-noRemap/gremlin/src' g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c ai.cc -o ai.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs.c -o cs.o cs.c: In function 'cs_realloc': cs.c:1199:26: warning: pointer 'p' may be used after 'realloc' [-Wuse-after-free] 1199 | return ((*ok) ? pnew : p) ; /* return original p if failure */ | ~~~~~~~~~~~~~~^~~~ cs.c:1197:12: note: call to 'realloc' here 1197 | pnew = realloc (p, CS_MAX (n,1) * size) ; /* realloc the block */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_cbind.c -o cs_cbind.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_chol2inv_ii.c -o cs_chol2inv_ii.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_cov2cor.c -o cs_cov2cor.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_directsum.c -o cs_directsum.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_directsumupdate.c -o cs_directsumupdate.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c cs_droprowcol.cc -o cs_droprowcol.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_inv.c -o cs_inv.o cs_inv.c: In function 'cs_inv': cs_inv.c:52:10: warning: 'icol' may be used uninitialized [-Wmaybe-uninitialized] 52 | if (irow != icol) { | ^ cs_inv.c:7:15: note: 'icol' was declared here 7 | int n, i, icol,irow,j,k,l,ll; | ^~~~ cs_inv.c:52:10: warning: 'irow' may be used uninitialized [-Wmaybe-uninitialized] 52 | if (irow != icol) { | ^ cs_inv.c:7:20: note: 'irow' was declared here 7 | int n, i, icol,irow,j,k,l,ll; | ^~~~ gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerA.c -o cs_kroneckerA.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerAupdate.c -o cs_kroneckerAupdate.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerI.c -o cs_kroneckerI.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_kroneckerIupdate.c -o cs_kroneckerIupdate.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_omega.c -o cs_omega.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_omegaupdate.c -o cs_omegaupdate.o gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cs_schur.c -o cs_schur.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c gradFun.cc -o gradFun.o g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c gremlin.cc -o gremlin.o gremlin.cc: In function 'void ugremlin(double*, int*, int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, int*, int*, int*, int*, int*, int*, int*, double*, int*, double*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, int*, int*, double*, double*, double*, double*, int*, int*, int*)': gremlin.cc:365:5: error: 'error' was not declared in this scope; did you mean 'perror'? 365 | error("FAILED: symbolic Cholesky factorization of Coefficient matrix (`C`)\n"); | ^~~~~ | perror gremlin.cc:586:7: error: 'error' was not declared in this scope; did you mean 'perror'? 586 | error("\nMixed Model Coefficient matrix (C) singular: possibly caused by a bad combination of G and R (co)variance parameters"); | ^~~~~ | perror gremlin.cc:814:9: error: 'error' was not declared in this scope; did you mean 'perror'? 814 | error("\nUnsuccessful tugug calculation: AI algorithm in iteration %i", i); | ^~~~~ | perror gremlin.cc:824:9: error: 'error' was not declared in this scope; did you mean 'perror'? 824 | error("\nUnsuccessful trace calculation: AI algorithm in iteration %i", i); | ^~~~~ | perror gremlin.cc:836:11: error: 'error' was not declared in this scope; did you mean 'perror'? 836 | error("\nUnsuccessful AI algorithm in iteration %i", i); | ^~~~~ | perror gremlin.cc:850:11: error: 'error' was not declared in this scope; did you mean 'perror'? 850 | error("\nUnsuccessful gradient calculation in iteration %i", i); | ^~~~~ | perror gremlin.cc:863:11: error: 'error' was not declared in this scope; did you mean 'perror'? 863 | error("\nUnsuccessful AI algorithm in iteration %i", i); | ^~~~~ | perror gremlin.cc:876:11: error: 'error' was not declared in this scope; did you mean 'perror'? 876 | error("\nUnsuccessful gradient calculation in iteration %i", i); | ^~~~~ | perror gremlin.cc:1053:9: error: 'error' was not declared in this scope; did you mean 'perror'? 1053 | error("\nUnsuccessful tugug calculation: EM algorithm in iteration %i", i); | ^~~~~ | perror gremlin.cc:1058:9: error: 'error' was not declared in this scope; did you mean 'perror'? 1058 | error("\nUnsuccessful trace calculation: EM algorithm in iteration %i", i); | ^~~~~ | perror gremlin.cc:1182:9: error: 'error' was not declared in this scope; did you mean 'perror'? 1182 | error("Unsuccessful AI algorithm at convergence %i\n", i); | ^~~~~ | perror gremlin.cc:1195:9: error: 'error' was not declared in this scope; did you mean 'perror'? 1195 | error("Unsuccessful AI algorithm at convergence %i\n", i); | ^~~~~ | perror make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:200: gremlin.o] Error 1 make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-noRemap/gremlin/src' ERROR: compilation failed for package ‘gremlin’ * removing ‘/data/gannet/ripley/R/packages/tests-noRemap/Libs/gremlin-lib/gremlin’ Command exited with non-zero status 1 Time 0:13.82, 11.01 + 1.16