* installing *source* package ‘Bayesrel’ ...
** package ‘Bayesrel’ successfully unpacked and MD5 sums checked
** using staged installation
Using bundled CSDP
checking for gcc... gcc-13
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-13 accepts -g... yes
checking for gcc-13 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-13 -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++-13 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++-13 -std=gnu++17 accepts -g... (cached) yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Bayesrel/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c BayesrelCpp.cpp -o BayesrelCpp.o
BayesrelCpp.cpp: In function 'arma::dvec csdpArma(int, int, int, const arma::ivec&, const arma::ivec&, const Rcpp::List&, const Rcpp::List&, const arma::dvec&, const arma::cube&, Rcpp::Function, int)':
BayesrelCpp.cpp:31:9: warning: variable 'status' set but not used [-Wunused-but-set-variable]
31 | int status;
| ^~~~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c LowBoundsCpp.cpp -o LowBoundsCpp.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c convertCpp.cpp -o convertCpp.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c customsdpCpp.cpp -o customsdpCpp.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c initArma.cpp -o initArma.o
customsdpCpp.cpp: In function 'int custom_sdpCpp(int, int, blockmatrix&, double*, constraintmatrix*, double, double*, double*, const arma::cube&, arma::dvec&, Rcpp::Function, bool, int)':
customsdpCpp.cpp:423:19: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
423 | for(i=0; i<car.n_rows; i++)
| ~^~~~~~~~~~~
customsdpCpp.cpp:525:14: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized]
525 | return(ret);
| ^
customsdpCpp.cpp:35:7: note: 'ret' was declared here
35 | int ret;
| ^~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -ICsdp/include -DNOSHORTS -DARMA_NO_DEBUG=1 -DARMA_DONT_USE_FORTRAN_HIDDEN_ARGS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -c pfaCpp.cpp -o pfaCpp.o
(cd Csdp/lib && \
(make libsdp.a CC="gcc-13" CFLAGS="-DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include" AR="gcc-ar" RANLIB="gcc-ranlib") && \
touch Csdp.ts)
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Bayesrel/src/Csdp/lib'
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o readprob.o readprob.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o sdp.o sdp.c
sdp.c: In function 'sdp':
sdp.c:724: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
724 | #pragma omp parallel for schedule(dynamic,64) default(none) shared(O,ldam,k,workvec8) private(i,j)
|
sdp.c:769: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
769 | #pragma omp parallel for schedule(dynamic,64) private(i,j) shared(O,k,ldam)
|
sdp.c:118:7: warning: variable 'lastimprove' set but not used [-Wunused-but-set-variable]
118 | int lastimprove=0;
| ^~~~~~~~~~~
sdp.c:107:10: warning: variable 'newdobj' set but not used [-Wunused-but-set-variable]
107 | double newdobj;
| ^~~~~~~
sdp.c:106:10: warning: variable 'newpobj' set but not used [-Wunused-but-set-variable]
106 | double newpobj;
| ^~~~~~~
sdp.c:105:10: warning: variable 'oldmaxrelinfeas' set but not used [-Wunused-but-set-variable]
105 | double oldmaxrelinfeas=1.0e100;
| ^~~~~~~~~~~~~~~
sdp.c:88:10: warning: variable 'oldmu' set but not used [-Wunused-but-set-variable]
88 | double oldmu;
| ^~~~~
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o op_o.o op_o.c
op_o.c: In function 'op_o':
op_o.c:120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
120 | #pragma omp parallel for schedule(dynamic,64) default(none) shared(O,ldam,k) private(j,i)
|
op_o.c:132: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
132 | #pragma omp parallel for schedule(dynamic,64) default(none) shared(k,constraints,byblocks,Zi,X,O,work1, work2, work, ldam) private(j, ii, jj, blocksize, p, q, r, s, ptri, ptrj, blocknum, contrib, Ziblk, Xblk, workblk, work2blk, enti, entj, scale1, scale2, thread_num)
|
op_o.c:428: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
428 | #pragma omp parallel for schedule(dynamic,64) default(none) shared(O,ldam,k) private(j,i)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o psd_feas.o psd_feas.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o op_a.o op_a.c
op_a.c: In function 'op_a':
op_a.c:22: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
22 | #pragma omp parallel for schedule(dynamic,64) default(none) private(i,contrib,ptr,blk,nume,vec,j,p,mat,ent,q) shared(k,constraints,result,X)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o op_at.o op_at.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o Fnorm.o Fnorm.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o calc_pobj.o calc_pobj.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o calc_dobj.o calc_dobj.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o trace_prod.o trace_prod.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o zero_mat.o zero_mat.c
zero_mat.c: In function 'zero_mat':
zero_mat.c:33: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
33 | #pragma omp parallel for schedule(dynamic,64) default(none) shared(A,blk) private(j,i)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o mat_mult.o mat_mult.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o sym_mat.o sym_mat.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o copy_mat.o copy_mat.c
copy_mat.c: In function 'copy_mat':
copy_mat.c:28: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
28 | #pragma omp parallel for schedule(dynamic,64) private(i,j) shared(p,q)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o addscaledmat.o addscaledmat.c
addscaledmat.c: In function 'addscaledmat':
addscaledmat.c:29: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
29 | #pragma omp parallel for schedule(dynamic,64) default(none) private(i,j) shared(A,B,C,scale,blk)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o user_exit.o user_exit.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o make_i.o make_i.c
make_i.c: In function 'make_i':
make_i.c:25: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
25 | #pragma omp parallel for schedule(dynamic,64) default(none) private(i,j) shared(blk,p,A)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o allocmat.o allocmat.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o initsoln.o initsoln.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o initparams.o initparams.c
initparams.c: In function 'initparams':
initparams.c:34:11: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
34 | int ret = fscanf(paramfile,"%*[^=]%*c%lf",&(params->axtol));
| ^~~
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o add_mat.o add_mat.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o writesol.o writesol.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o readsol.o readsol.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o easysdp.o easysdp.c
easysdp.c: In function 'easy_sdp':
easysdp.c:55:7: warning: variable 'blk' set but not used [-Wunused-but-set-variable]
55 | int blk;
| ^~~
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o writeprob.o writeprob.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o solvesys.o solvesys.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o makefill.o makefill.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o mat_multsp.o mat_multsp.c
mat_multsp.c: In function 'mat_multspb':
mat_multsp.c:169: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
169 | #pragma omp parallel for schedule(dynamic,64) default(none) private(i,j) shared(blk,C,scale2)
|
mat_multsp.c:55:7: warning: unused variable 'thread_num' [-Wunused-variable]
55 | int thread_num;
| ^~~~~~~~~~
mat_multsp.c:54:7: warning: unused variable 'total_threads' [-Wunused-variable]
54 | int total_threads;
| ^~~~~~~~~~~~~
mat_multsp.c: In function 'mat_multspa':
mat_multsp.c:406: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
406 | #pragma omp parallel for default(none) schedule(dynamic,64) private(i,j) shared(blk,C,scale2)
|
mat_multsp.c:291:7: warning: unused variable 'thread_num' [-Wunused-variable]
291 | int thread_num;
| ^~~~~~~~~~
mat_multsp.c:290:7: warning: unused variable 'total_threads' [-Wunused-variable]
290 | int total_threads;
| ^~~~~~~~~~~~~
mat_multsp.c: In function 'mat_multspc':
mat_multsp.c:589: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
589 | #pragma omp parallel for schedule(dynamic,64) default(none) private(i,ii,p,q,temp) shared(ptr,A,B,C,blk,blksize,scale1)
|
mat_multsp.c:630: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
630 | #pragma omp parallel for default(none) schedule(dynamic,64) private(i,j) shared(blk,C,scale2)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o norms.o norms.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o linesearch.o linesearch.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o matvec.o matvec.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o chol.o chol.c
chol.c: In function 'chol_inv':
chol.c:158:10: warning: variable 'scale' set but not used [-Wunused-but-set-variable]
158 | double scale;
| ^~~~~
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o qreig.o qreig.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o tweakgap.o tweakgap.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o freeprob.o freeprob.c
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o packed.o packed.c
packed.c: In function 'store_packed':
packed.c:31: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
31 | #pragma omp parallel for schedule(dynamic,64) private(i,j) shared(p,q,n)
|
packed.c: In function 'store_unpacked':
packed.c:65: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
65 | #pragma omp parallel for schedule(dynamic,64) private(i,j) shared(p,q,n)
|
packed.c: In function 'triu':
packed.c:193: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
193 | #pragma omp parallel for schedule(dynamic,64) private(i,j) shared(A,n)
|
gcc-13 -DDEFINE_FUNCTIONS_LAPACK_BLAS -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -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 -fpic -DNOSHORTS -I../include -c -o sortentries.o sortentries.c
gcc-ar cr libsdp.a readprob.o sdp.o op_o.o psd_feas.o op_a.o op_at.o Fnorm.o calc_pobj.o calc_dobj.o trace_prod.o zero_mat.o mat_mult.o sym_mat.o copy_mat.o addscaledmat.o user_exit.o make_i.o allocmat.o initsoln.o initparams.o add_mat.o writesol.o readsol.o easysdp.o writeprob.o solvesys.o makefill.o mat_multsp.o norms.o linesearch.o matvec.o chol.o qreig.o tweakgap.o freeprob.o packed.o sortentries.o
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Bayesrel/src/Csdp/lib'
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o Bayesrel.so BayesrelCpp.o LowBoundsCpp.o RcppExports.o convertCpp.o customsdpCpp.o initArma.o pfaCpp.o -LCsdp/lib -lsdp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Bayesrel/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Bayesrel/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Bayesrel/src'
installing to /data/gannet/ripley/R/packages/tests-devel/Bayesrel.Rcheck/00LOCK-Bayesrel/00new/Bayesrel/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (Bayesrel)