Install log for 'dtwclust'

* installing *source* package ‘dtwclust’ ...
** package ‘dtwclust’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/dtwclust/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/calculators.cpp -o distances/calculators.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/R-gateways.cpp -o distances/R-gateways.o
In file included from distances/R-gateways.cpp:1:
distances/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/lbk.cpp -o distances/lbk.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/soft-dtw.cpp -o distances/soft-dtw.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/lbi.cpp -o distances/lbi.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/logGAK.cpp -o distances/logGAK.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distances/dtw-basic.cpp -o distances/dtw-basic.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c centroids/dba.cpp -o centroids/dba.o
In file included from centroids/dba.cpp:1:
centroids/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c centroids/sdtw-cent.cpp -o centroids/sdtw-cent.o
In file included from centroids/sdtw-cent.cpp:1:
centroids/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c tadpole/tadpole.cpp -o tadpole/tadpole.o
In file included from tadpole/tadpole.cpp:1:
tadpole/R-gateways.h:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    9 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distmat/dtw-lb.cpp -o distmat/dtw-lb.o
In file included from distmat/dtw-lb.cpp:1:
distmat/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distmat/distmat.cpp -o distmat/distmat.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distmat/distmat-loop.cpp -o distmat/distmat-loop.o
In file included from distmat/distmat-loop.cpp:1:
distmat/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c distmat/fillers.cpp -o distmat/fillers.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c init.cpp -o init.o
In file included from init.cpp:1:
In file included from ./dtwclust.h:4:
./centroids/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils/ParallelWorker.cpp -o utils/ParallelWorker.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils/envelope.cpp -o utils/envelope.o
In file included from utils/ParallelWorker.cpp:1:
In file included from utils/ParallelWorker.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
   10 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils/UndirectedGraph.cpp -o utils/UndirectedGraph.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils/R-utils.cpp -o utils/R-utils.o
In file included from utils/R-utils.cpp:1:
utils/R-gateways.h:4:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
    4 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
In file included from distmat/fillers.cpp:10:
In file included from distmat/../utils/ParallelWorker.h:8:
In file included from /data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread.h:9:
/data/gannet/ripley/R/test-clang/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
   10 | #define R_NO_REMAP
      |         ^
<command line>:3:9: note: previous definition is here
    3 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils/KahanSummer.cpp -o utils/KahanSummer.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppParallel/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c utils/utils.cpp -o utils/utils.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o dtwclust.so ./distances/calculators.o ./distances/R-gateways.o ./distances/lbk.o ./distances/soft-dtw.o ./distances/lbi.o ./distances/logGAK.o ./distances/dtw-basic.o ./centroids/dba.o ./centroids/sdtw-cent.o ./tadpole/tadpole.o ./distmat/dtw-lb.o ./distmat/distmat.o ./distmat/distmat-loop.o ./distmat/fillers.o ./init.o ./utils/ParallelWorker.o ./utils/envelope.o ./utils/UndirectedGraph.o ./utils/R-utils.o ./utils/KahanSummer.o ./utils/utils.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/dtwclust/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/dtwclust/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/dtwclust/src'
installing to /data/gannet/ripley/R/packages/tests-clang/dtwclust.Rcheck/00LOCK-dtwclust/00new/dtwclust/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 (dtwclust)