Install log for 'rEDM'

* installing *source* package ‘rEDM’ ...
** package ‘rEDM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.3’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c CCM.cpp -o CCM.o
In file included from CCM.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c ComputeError.cpp -o ComputeError.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c DataFrame.cpp -o DataFrame.o
In file included from ComputeError.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #define R_NO_REMAP 1
      |         ^
In file included from DataFrame.cpp:1:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Embed.cpp -o Embed.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c EmbedDim.cpp -o EmbedDim.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Multiview.cpp -o Multiview.o
In file included from Embed.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #define R_NO_REMAP 1
      |         ^
In file included from EmbedDim.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #define R_NO_REMAP 1
      |         ^
In file included from Multiview.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c ParameterList.cpp -o ParameterList.o
In file included from ParameterList.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c PredictInterval.cpp -o PredictInterval.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c PredictNL.cpp -o PredictNL.o
1 warning generated.
In file included from PredictInterval.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #define R_NO_REMAP 1
      |         ^
In file included from PredictNL.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c RcppEDMCommon.cpp -o RcppEDMCommon.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
1 warning generated.
In file included from RcppEDMCommon.cpp:14:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c SMap.cpp -o SMap.o
In file included from SMap.cpp:1:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #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 ./cppEDM/src/ -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppThread/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -DR_NO_REMAP -c Simplex.cpp -o Simplex.o
1 warning generated.
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src/cppEDM/src'
rm -f API.o CCM.o Common.o DateTime.o EDM.o EDM_Formatting.o EDM_Neighbors.o Eval.o Multiview.o Parameter.o Simplex.o SMap.o libEDM.a
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src/cppEDM/src'
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src/cppEDM/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c API.cc
In file included from Simplex.cpp:2:
In file included from ./RcppEDMCommon.h:12:
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>:2:9: note: previous definition is here
    2 | #define R_NO_REMAP 1
      |         ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c CCM.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c Common.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c DateTime.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c EDM.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c EDM_Formatting.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c EDM_Neighbors.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c Eval.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c Multiview.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c Parameter.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c Simplex.cc
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3  -fpic -DCCM_THREADED -DUSING_R -c SMap.cc
ar -rcs libEDM.a API.o CCM.o Common.o DateTime.o EDM.o EDM_Formatting.o EDM_Neighbors.o Eval.o Multiview.o Parameter.o Simplex.o SMap.o # AR passed from Makevars
cp libEDM.a ../lib/
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src/cppEDM/src'
/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 rEDM.so CCM.o ComputeError.o DataFrame.o Embed.o EmbedDim.o Multiview.o ParameterList.o PredictInterval.o PredictNL.o RcppEDMCommon.o RcppExports.o SMap.o Simplex.o -L ./cppEDM/lib/ -lEDM -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/rEDM/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/rEDM/src'
installing to /data/gannet/ripley/R/packages/tests-clang/rEDM.Rcheck/00LOCK-rEDM/00new/rEDM/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (rEDM)