* installing *source* package ‘higlasso’ ...
** package ‘higlasso’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/higlasso/src'
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_NO_DEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++11 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_NO_DEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include   -fopenmp -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c higlasso.cpp -o higlasso.o
higlasso.cpp:16:17: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   16 |     for (uword j$ = 0; j$ < s; ++j$) {
      |                 ^
higlasso.cpp:16:25: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   16 |     for (uword j$ = 0; j$ < s; ++j$) {
      |                         ^
higlasso.cpp:16:35: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   16 |     for (uword j$ = 0; j$ < s; ++j$) {
      |                                   ^
higlasso.cpp:17:32: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   17 |         for (uword j = 0; j < j$; ++j) {
      |                                ^
higlasso.cpp:19:28: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   19 |             mat Xmk2 = Xm(j$);
      |                            ^
higlasso.cpp:30:20: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   30 |             Xi(j, j$) = C.slice(0);
      |                    ^
higlasso.cpp:40:17: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   40 |     for (uword j$ = 0; j$ < s; ++j$)
      |                 ^
higlasso.cpp:40:25: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   40 |     for (uword j$ = 0; j$ < s; ++j$)
      |                         ^
higlasso.cpp:40:35: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   40 |     for (uword j$ = 0; j$ < s; ++j$)
      |                                   ^
higlasso.cpp:41:32: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   41 |         for (uword j = 0; j < j$; ++j)
      |                                ^
higlasso.cpp:42:21: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   42 |             eta(j, j$) = eta_init(i++);
      |                     ^
higlasso.cpp:68:20: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   68 |             uword p$ = p + Xi(j, k).n_cols;
      |                    ^
higlasso.cpp:69:26: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   69 |             Xt.cols(p,  p$ - 1) = Xi(j, k) * diagmat(kron(beta(j), beta(k)));
      |                          ^
higlasso.cpp:70:18: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   70 |             p = p$;
      |                  ^
higlasso.cpp:79:17: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   79 |     for (uword j$ = 0; j$ < beta.n_elem; ++j$)
      |                 ^
higlasso.cpp:79:25: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   79 |     for (uword j$ = 0; j$ < beta.n_elem; ++j$)
      |                         ^
higlasso.cpp:79:45: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   79 |     for (uword j$ = 0; j$ < beta.n_elem; ++j$)
      |                                             ^
higlasso.cpp:80:32: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   80 |         for (uword j = 0; j < j$; ++j)
      |                                ^
higlasso.cpp:81:30: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   81 |                 Yt += Xi(j, j$) * (eta(j, j$) % kron(beta(j), beta(j$)));
      |                              ^
higlasso.cpp:81:44: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   81 |                 Yt += Xi(j, j$) * (eta(j, j$) % kron(beta(j), beta(j$)));
      |                                            ^
higlasso.cpp:81:69: warning: '$' in identifier [-Wdollar-in-identifier-extension]
   81 |                 Yt += Xi(j, j$) * (eta(j, j$) % kron(beta(j), beta(j$)));
      |                                                                     ^
higlasso.cpp:113:17: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  113 |     for (uword j$ = 0; j$ < beta.n_elem; ++j$) {
      |                 ^
higlasso.cpp:113:25: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  113 |     for (uword j$ = 0; j$ < beta.n_elem; ++j$) {
      |                         ^
higlasso.cpp:113:45: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  113 |     for (uword j$ = 0; j$ < beta.n_elem; ++j$) {
      |                                             ^
higlasso.cpp:114:24: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  114 |         mat Xtj  = Xm(j$);
      |                        ^
higlasso.cpp:115:35: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  115 |         vec Ytj = residuals + Xm(j$) * beta(j$);
      |                                   ^
higlasso.cpp:115:46: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  115 |         vec Ytj = residuals + Xm(j$) * beta(j$);
      |                                              ^
higlasso.cpp:117:37: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  117 |         mat I_pj = eye <mat> (beta(j$).n_elem, beta(j$).n_elem);
      |                                     ^
higlasso.cpp:117:54: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  117 |         mat I_pj = eye <mat> (beta(j$).n_elem, beta(j$).n_elem);
      |                                                      ^
higlasso.cpp:118:32: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  118 |         for (uword k = 0; k < j$; ++k) {
      |                                ^
higlasso.cpp:119:27: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  119 |             Xtj += Xi(k, j$) * diagmat(eta(k, j$)) * kron(beta(k), I_pj);
      |                           ^
higlasso.cpp:119:48: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  119 |             Xtj += Xi(k, j$) * diagmat(eta(k, j$)) * kron(beta(k), I_pj);
      |                                                ^
higlasso.cpp:120:27: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  120 |             Ytj += Xi(k, j$) * (eta(k, j$) % kron(beta(k), beta(j$)));
      |                           ^
higlasso.cpp:120:41: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  120 |             Ytj += Xi(k, j$) * (eta(k, j$) % kron(beta(k), beta(j$)));
      |                                         ^
higlasso.cpp:120:66: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  120 |             Ytj += Xi(k, j$) * (eta(k, j$) % kron(beta(k), beta(j$)));
      |                                                                  ^
higlasso.cpp:122:25: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  122 |         for (uword l = j$ + 1; l < beta.n_elem; ++l) {
      |                         ^
higlasso.cpp:123:24: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  123 |             Xtj += Xi(j$, l) * diagmat(eta(j$, l)) * kron(I_pj, beta(l));
      |                        ^
higlasso.cpp:123:45: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  123 |             Xtj += Xi(j$, l) * diagmat(eta(j$, l)) * kron(I_pj, beta(l));
      |                                             ^
higlasso.cpp:124:24: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  124 |             Ytj += Xi(j$, l) * (eta(j$, l) % kron(beta(j$), beta(l)));
      |                        ^
higlasso.cpp:124:38: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  124 |             Ytj += Xi(j$, l) * (eta(j$, l) % kron(beta(j$), beta(l)));
      |                                      ^
higlasso.cpp:124:57: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  124 |             Ytj += Xi(j$, l) * (eta(j$, l) % kron(beta(j$), beta(l)));
      |                                                         ^
higlasso.cpp:127:35: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  127 |         vec D = calculate_D(beta(j$), sigma);
      |                                   ^
higlasso.cpp:128:38: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  128 |         vec C = (abs(D) - D) % beta(j$);
      |                                      ^
higlasso.cpp:138:62: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  138 |             vec b = omega * new_beta + (1.0 - omega) * beta(j$);
      |                                                              ^
higlasso.cpp:140:34: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  140 |             Ytj = Ytj_orig - Xm(j$) * b;
      |                                  ^
higlasso.cpp:141:36: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  141 |             for (uword k = 0; k < j$; ++k)
      |                                    ^
higlasso.cpp:142:31: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  142 |                 Ytj -= Xi(k, j$) * (eta(k, j$) % kron(beta(k), b));
      |                               ^
higlasso.cpp:142:45: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  142 |                 Ytj -= Xi(k, j$) * (eta(k, j$) % kron(beta(k), b));
      |                                             ^
higlasso.cpp:143:29: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  143 |             for (uword l = j$ + 1; l < beta.n_elem; ++l)
      |                             ^
higlasso.cpp:144:28: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  144 |                 Ytj -= Xi(j$, l) * (eta(j$, l) % kron(b, beta(l)));
      |                            ^
higlasso.cpp:144:42: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  144 |                 Ytj -= Xi(j$, l) * (eta(j$, l) % kron(b, beta(l)));
      |                                          ^
higlasso.cpp:159:19: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  159 |             beta(j$).fill(0.0);
      |                   ^
higlasso.cpp:165:19: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  165 |             beta(j$) = omega * new_beta + (1.0 - omega) * beta(j$);
      |                   ^
higlasso.cpp:165:65: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  165 |             beta(j$) = omega * new_beta + (1.0 - omega) * beta(j$);
      |                                                                 ^
higlasso.cpp:180:20: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  180 |             uword p$ = p + eta(j, k).n_elem;
      |                    ^
higlasso.cpp:181:26: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  181 |             e.subvec(p, p$ - 1) = eta(j, k);
      |                          ^
higlasso.cpp:182:26: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  182 |             D.subvec(p, p$ - 1) = calculate_D(eta(j, k), sigma);
      |                          ^
higlasso.cpp:183:18: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  183 |             p = p$;
      |                  ^
higlasso.cpp:197:20: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  197 |             uword p$ = p + eta(j, k).n_elem;
      |                    ^
higlasso.cpp:198:42: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  198 |             new_eta(j, k) = e.subvec(p, p$ - 1);
      |                                          ^
higlasso.cpp:199:18: warning: '$' in identifier [-Wdollar-in-identifier-extension]
  199 |             p = p$;
      |                  ^
61 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++11 -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 higlasso.so RcppExports.o higlasso.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/higlasso/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/higlasso/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/higlasso/src'
installing to /data/gannet/ripley/R/packages/tests-clang/higlasso.Rcheck/00LOCK-higlasso/00new/higlasso/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 (higlasso)