* 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 /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 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_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 /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 /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 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' 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_::SetFinalizer' requested here 497 | SetFinalizer( new FunctionFinalizer( f ) ) ; | ^ ./gdal_bindings.h:349:8: note: in instantiation of member function 'Rcpp::class_::finalizer' requested here 349 | .finalizer(&GDALDatasetFinalizer); | ^ /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 1 warning generated. /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` cause: Can't use Python at `/usr/sbin/pypy` cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer. Downloading cryptography (4.5MiB) Downloading aiohttp (1.7MiB) Downloading botocore (14.9MiB) Downloading h5py (5.2MiB) Downloading google-api-python-client (15.3MiB) Downloaded aiohttp Downloaded cryptography Downloaded h5py Downloaded botocore Downloaded google-api-python-client Installed 55 packages in 1.44s ** 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` cause: Can't use Python at `/usr/sbin/pypy` cause: 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)