* 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/bin/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 g++ -std=gnu++20 accepts -g... yes
checking for g++ -std=gnu++20 option to enable C++11 features... none needed
checking for gdal... yes
checking for gdal... yes
checking for gdal-config... /usr/bin/gdal-config
configure: Using gdal-config at /usr/bin/gdal-config
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc 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: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/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;
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ANN.cpp -o ANN.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ANNIndex.cpp -o ANNIndex.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c IndexInterface.cpp -o IndexInterface.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c bd_fix_rad_search.cpp -o bd_fix_rad_search.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c bd_pr_search.cpp -o bd_pr_search.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c bd_search.cpp -o bd_search.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c bd_tree.cpp -o bd_tree.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c brute.cpp -o brute.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_dump.cpp -o kd_dump.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_fix_rad_search.cpp -o kd_fix_rad_search.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_pr_search.cpp -o kd_pr_search.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_search.cpp -o kd_search.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_split.cpp -o kd_split.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_tree.cpp -o kd_tree.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c kd_util.cpp -o kd_util.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c perf.cpp -o perf.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c random_forest_to_strings.cpp -o random_forest_to_strings.o
In file included from /data/localhost/ripley/R/test-dev/Rcpp/include/RcppCommon.h:29,
from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp.h:27,
from random_forest_to_strings.cpp:2:
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#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’
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"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rasterizeHDF.cpp -o rasterizeHDF.o
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c sampling.cpp -o sampling.o
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/webp -DWITH_GZFILEOP -I/usr/include/gdal -I/usr/local/include -I/usr/include/gdal -I. -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c seq_lens_simplify.cpp -o seq_lens_simplify.o
In file included from /data/localhost/ripley/R/R-devel/include/R.h:73,
from random_forest_to_strings.cpp:1:
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h: In function ‘void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {char (&)[8192]}]’:
/data/localhost/ripley/R/R-devel/include/R_ext/Error.h:89:17: warning: infinite recursion detected [-Winfinite-recursion]
89 | #define warning Rf_warning
| ^~~~~~~~~~
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:189:17: note: in expansion of macro ‘warning’
189 | inline void warning(const char* fmt, Args&&... args ) {
| ^~~~~~~
In file included from /data/localhost/ripley/R/test-dev/Rcpp/include/RcppCommon.h:131:
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/exceptions.h:200:19: note: recursive call
200 | Rf_warning("%s", buf);
| ~~~~~~~~~~^~~~~~~~~~~
In file included from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/Module.h:510,
from /data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp.h:70,
from rasterizeHDF.cpp:1:
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h: In instantiation of ‘void Rcpp::class_<Class>::SetFinalizer(finalizer_class*) [with Class = GDALDatasetR; finalizer_class = Rcpp::CppFinalizer<GDALDatasetR>]’:
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:497:13: required from ‘Rcpp::class_<Class>::self& Rcpp::class_<Class>::finalizer(void (*)(Class*)) [with Class = GDALDatasetR; self = Rcpp::class_<GDALDatasetR>]’
497 | SetFinalizer( new FunctionFinalizer<Class>( f ) ) ;
| ^~~~~~~~~~~~
gdal_bindings.h:349:17: required from here
344 | class_<GDALDatasetR>("CPP_GDALDataset")
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
345 | .method("GetRasterBand", &GDALDatasetR::GetRasterBand)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
346 | .method("GetRasterXSize", &GDALDatasetR::GetRasterXSize)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | .method("GetRasterYSize", &GDALDatasetR::GetRasterYSize)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | .method("Close", &GDALDatasetR::Close)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
349 | .finalizer(&GDALDatasetFinalizer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/data/localhost/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:507:42: warning: deleting object of polymorphic class type ‘Rcpp::CppFinalizer<GDALDatasetR>’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
507 | if( ptr->finalizer_pointer ) delete ptr->finalizer_pointer ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -shared -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/lib64 -lgdal -lproj
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/ICESat2VegR/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/ICESat2VegR/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/ICESat2VegR/src'
installing to /data/localhost/ripley/R/packages/tests-devel/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/bin/pypy`
Caused by: Can't use Python at `/usr/bin/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/bin/pypy`
Caused by: Can't use Python at `/usr/bin/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)