* installing *source* package ‘kernlab’ ...
** package ‘kernlab’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.5’
using C++ compiler: ‘clang version 18.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/kernlab/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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c brweight.cpp -o brweight.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c ctable.cpp -o ctable.o
ctable.cpp:60:9: warning: variable 'lcp_idx' set but not used [-Wunused-but-set-variable]
   60 |         UInt32 lcp_idx = 0, lcp_prev_idx = 0;
      |                ^
ctable.cpp:60:22: warning: variable 'lcp_prev_idx' set but not used [-Wunused-but-set-variable]
   60 |         UInt32 lcp_idx = 0, lcp_prev_idx = 0;
      |                             ^
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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c cweight.cpp -o cweight.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dbreakpt.c -o dbreakpt.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dcauchy.c -o dcauchy.o
dcauchy.c:91:29: warning: variable 'nsteps' set but not used [-Wunused-but-set-variable]
   91 |         int search, interp, nbrpt, nsteps = 1, i, inc = 1;
      |                                    ^
1 warning 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    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dgpnrm.c -o dgpnrm.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dgpstep.c -o dgpstep.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dprecond.c -o dprecond.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dprsrch.c -o dprsrch.o
dprsrch.c:93:25: warning: variable 'nsteps' set but not used [-Wunused-but-set-variable]
   93 |         int search = 1, nbrpt, nsteps = 0, i, inc = 1;  
      |                                ^
1 warning 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    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dspcg.c -o dspcg.o
dspcg.c:115:44: warning: variable 'iters' set but not used [-Wunused-but-set-variable]
  115 |         int i, j, nfaces, nfree, inc = 1, infotr, iters = 0, itertr;
      |                                                   ^
dspcg.c:116:40: warning: variable 'alpha' set but not used [-Wunused-but-set-variable]
  116 |         double gfnorm, gfnormf, stol = 1e-16, alpha;
      |                                               ^
2 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    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dtron.c -o dtron.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dtrpcg.c -o dtrpcg.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c dtrqsol.c -o dtrqsol.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c esa.cpp -o esa.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c expdecayweight.cpp -o expdecayweight.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c inductionsort.cpp -o inductionsort.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c init.c -o 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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c kspectrumweight.cpp -o kspectrumweight.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c lcp.cpp -o lcp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c misc.c -o misc.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c msufsort.cpp -o msufsort.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c solvebqp.c -o solvebqp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c stringk.c -o stringk.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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c stringkernel.cpp -o stringkernel.o
In file included from stringkernel.cpp:53:
./stringkernel.h:106:7: warning: private field '_verb' is not used [-Wunused-private-field]
  106 |   int _verb;
      |       ^
/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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c svm.cpp -o svm.o
1 warning generated.
svm.cpp:1474:6: warning: variable 'iter' set but not used [-Wunused-but-set-variable]
 1474 |         int iter = 0, counter = min(l*2, 2000) + 1;
      |             ^
svm.cpp:1549:9: warning: variable 'obj' set but not used [-Wunused-but-set-variable]
 1549 |         double obj = 0;
      |                ^
svm.cpp:1556:6: warning: variable 'nSV' set but not used [-Wunused-but-set-variable]
 1556 |         int nSV = 0, nFREE = 0;
      |             ^
svm.cpp:1556:15: warning: variable 'nFREE' set but not used [-Wunused-but-set-variable]
 1556 |         int nSV = 0, nFREE = 0;
      |                      ^
svm.cpp:1857:6: warning: variable 'iter' set but not used [-Wunused-but-set-variable]
 1857 |         int iter = 0;
      |             ^
svm.cpp:2152:6: warning: 'Solver_B_linear::Solve' hides overloaded virtual function [-Woverloaded-virtual]
 2152 |         int Solve(int l, svm_node * const * x_, double *b_, schar *y_,
      |             ^
svm.cpp:1709:15: note: hidden overloaded virtual function 'Solver_B::Solve' declared here: different number of parameters (11 vs 12)
 1709 |         virtual void Solve(int l, const Kernel& Q, double *b_, schar *y_,
      |                      ^
svm.cpp:2431:7: warning: 'Solver_MB::Solve' hides overloaded virtual function [-Woverloaded-virtual]
 2431 |         void Solve(int l, const Kernel& Q, double lin, double *alpha_,
      |              ^
svm.cpp:1709:15: note: hidden overloaded virtual function 'Solver_B::Solve' declared here: different number of parameters (11 vs 12)
 1709 |         virtual void Solve(int l, const Kernel& Q, double *b_, schar *y_,
      |                      ^
svm.cpp:2665:6: warning: variable 'iter' set but not used [-Wunused-but-set-variable]
 2665 |         int iter = 0;
      |             ^
svm.cpp:3626:7: warning: variable 'totaliter' set but not used [-Wunused-but-set-variable]
 3626 |                 int totaliter = 0;
      |                     ^
svm.cpp:3715:7: warning: variable 'totaliter' set but not used [-Wunused-but-set-variable]
 3715 |                 int totaliter = 0;
      |                     ^
svm.cpp:3758:9: warning: variable 'sum_alpha' set but not used [-Wunused-but-set-variable]
 3758 |         double sum_alpha = 0;
      |                ^
svm.cpp:3888:17: warning: variable 's' set but not used [-Wunused-but-set-variable]
 3888 |     const char* s;
      |                 ^
svm.cpp:4110:11: warning: variable 'sum_alpha' set but not used [-Wunused-but-set-variable]
 4110 |           double sum_alpha = 0;
      |                  ^
svm.cpp:4189:17: warning: variable 's' set but not used [-Wunused-but-set-variable]
 4189 |     const char* s;
      |                 ^
/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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c wkasailcp.cpp -o wkasailcp.o
14 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    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c wmsufsort.cpp -o wmsufsort.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 kernlab.so brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o init.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -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/kernlab/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/kernlab/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/kernlab/src'
installing to /data/gannet/ripley/R/packages/tests-clang/kernlab.Rcheck/00LOCK-kernlab/00new/kernlab/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘pattern’ in package ‘kernlab’
** 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 (kernlab)