Install log for 'ICESat2VegR'

* installing *source* package ‘ICESat2VegR’ ...
** this is package ‘ICESat2VegR’ version ‘0.0.1’
** package ‘ICESat2VegR’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /usr/sbin/pkg-config
checking pkg-config is at least version 0.15.0... yes
checking the operating system name... Linux
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 the compiler supports GNU C++... yes
checking whether /usr/local/clang23/bin/clang++ -std=gnu++20 accepts -g... yes
checking for /usr/local/clang23/bin/clang++ -std=gnu++20 option to enable C++11 features... none needed
checking for gdal... yes
checking for gdal... yes
checking for gdal-config... /usr/local/clang/bin/gdal-config
configure: Using gdal-config at /usr/local/clang/bin/gdal-config
checking for gcc... /usr/local/clang23/bin/clang-23 -std=gnu23
checking whether the compiler supports GNU C... yes
checking whether /usr/local/clang23/bin/clang-23 -std=gnu23 accepts -g... yes
checking for /usr/local/clang23/bin/clang-23 -std=gnu23 option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking whether GDAL can be linked using only `gdal-config --libs`... yes
checking for proj... yes
checking proj datadir path... /usr/share/proj
checking whether PROJ can be ran using the datadir... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘clang version 23.1.1’
using C++ compiler: ‘clang version 23.1.1’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/ICESat2VegR/src'
if [ -n "/usr/share/proj" ]; then \
	mkdir -p ../inst/proj;\
	cp -R "/usr/share/proj" ../inst/;\
else \
	echo "PROJ_DATADIR is empty. Skipping file copy.";\
fi;
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c ANN.cpp -o ANN.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c ANNIndex.cpp -o ANNIndex.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c IndexInterface.cpp -o IndexInterface.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c bd_fix_rad_search.cpp -o bd_fix_rad_search.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c bd_pr_search.cpp -o bd_pr_search.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c bd_search.cpp -o bd_search.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c bd_tree.cpp -o bd_tree.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c brute.cpp -o brute.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_dump.cpp -o kd_dump.o
kd_dump.cpp:44:14: warning: unused variable 'EPSILON' [-Wunused-const-variable]
   44 | const double    EPSILON                 = 1E-5; // small number for float comparison
      |                 ^~~~~~~
1 warning generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_fix_rad_search.cpp -o kd_fix_rad_search.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_pr_search.cpp -o kd_pr_search.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_search.cpp -o kd_search.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_split.cpp -o kd_split.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_tree.cpp -o kd_tree.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c kd_util.cpp -o kd_util.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c perf.cpp -o perf.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c random_forest_to_strings.cpp -o random_forest_to_strings.o
In file included from random_forest_to_strings.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp.h:27:
In file included from /data/localhost/ripley/R/test-clang/Rcpp/include/RcppCommon.h:29:
/data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages]
   27 |     #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
      |             ^
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c rasterizeHDF.cpp -o rasterizeHDF.o
1 warning generated.
In file included from rasterizeHDF.cpp:1:
In file included from /data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp.h:70:
In file included from /data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp/Module.h:510:
/data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp/module/class.h:507:42: warning: delete called on non-final 'Rcpp::CppFinalizer<GDALDatasetR>' that has virtual functions but non-virtual destructor [-Wdelete-non-abstract-non-virtual-dtor]
  507 |             if( ptr->finalizer_pointer ) delete ptr->finalizer_pointer ;
      |                                          ^
/data/localhost/ripley/R/test-clang/Rcpp/include/Rcpp/module/class.h:497:13: note: in instantiation of member function 'Rcpp::class_<GDALDatasetR>::SetFinalizer' requested here
  497 |             SetFinalizer( new FunctionFinalizer<Class>( f ) ) ;
      |             ^
./gdal_bindings.h:349:8: note: in instantiation of member function 'Rcpp::class_<GDALDatasetR>::finalizer' requested here
  349 |       .finalizer(&GDALDatasetFinalizer);
      |        ^
/usr/local/clang23/bin/clang-23 -std=gnu23 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
1 warning generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c sampling.cpp -o sampling.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/local/clang/include -isystem /usr/local/clang23/include -I/usr/local/clang/include -I/usr/local/clang/include -I. -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -D_LIBCPP_KEEP_TRANSITIVE_INCLUDES_LLVM23   -c seq_lens_simplify.cpp -o seq_lens_simplify.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o ICESat2VegR.so ANN.o ANNIndex.o IndexInterface.o RcppExports.o bd_fix_rad_search.o bd_pr_search.o bd_search.o bd_tree.o brute.o kd_dump.o kd_fix_rad_search.o kd_pr_search.o kd_search.o kd_split.o kd_tree.o kd_util.o perf.o random_forest_to_strings.o rasterizeHDF.o registerDynamicSymbol.o sampling.o seq_lens_simplify.o -L/usr/local/clang/lib64 -lgdal -lproj
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/ICESat2VegR/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/ICESat2VegR/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/ICESat2VegR/src'
installing to /data/localhost/ripley/R/packages/tests-clang/ICESat2VegR.Rcheck/00LOCK-ICESat2VegR/00new/ICESat2VegR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘clip’ in package ‘ICESat2VegR’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  Caused by: Can't use Python at `/usr/sbin/pypy`
  Caused by: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  Caused by: Can't use Python at `/usr/sbin/pypy`
  Caused by: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
** testing if installed package keeps a record of temporary installation path
* DONE (ICESat2VegR)