=> Bootstrap dependency digest>=20010302: found digest-20190127
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Building for py39-rpy-2.9.1nb2
(cd /scratch/work/math/py-rpy/work/rpy2-2.9.1/ && /usr/bin/env USETOOLS=no PTHREAD_CFLAGS=\ -pthread\ PTHREAD_LDFLAGS=\ -pthread PTHREAD_LIBS= PTHREADBASE=/usr DL_CFLAGS=\ -pthread\ DL_LDFLAGS=\ -pthread DL_LIBS= NPY_BLAS_LIBS=-lblas NPY_LAPACK_LIBS=-llapack\ -lblas NPY_CBLAS_LIBS=-lcblas\ -lblas PYTHON=/usr/pkg/bin/python3.9 CC=gcc CFLAGS=-O2\ -D_FORTIFY_SOURCE=2\ -I/usr/pkg/include\ -I/usr/include\ -I/usr/pkg/include/python3.9\ -I/usr/include/readline CPPFLAGS=-I/usr/pkg/include\ -I/usr/include\ -I/usr/pkg/include/python3.9\ -I/usr/include/readline CXX=c++ CXXFLAGS=-O2\ -D_FORTIFY_SOURCE=2\ -I/usr/pkg/include\ -I/usr/include\ -I/usr/pkg/include/python3.9\ -I/usr/include/readline COMPILER_RPATH_FLAG=-Wl,-R F77=gfortran FC=gfortran FFLAGS=-O LANG=C LC_ALL=C LC_COLLATE=C LC_CTYPE=C LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-L/usr/pkg/lib\ -Wl,-R/usr/pkg/lib\ -L/usr/lib\ -Wl,-R/usr/lib LINKER_RPATH_FLAG=-R PATH=/scratch/work/math/py-rpy/work/.cwrapper/bin:/scratch/work/math/py-rpy/work/.buildlink/bin:/scratch/work/math/py-rpy/work/.gfortran/bin:/scratch/work/math/py-rpy/work/.gcc/bin:/scratch/work/math/py-rpy/work/.tools/bin:/usr/pkg/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/X11R7/bin PREFIX=/usr/pkg MAKELEVEL=0 CONFIG_SITE= PKG_SYSCONFDIR=/usr/pkg/etc CXXCPP=cpp HOME=/scratch/work/math/py-rpy/work/.home CWRAPPERS_CONFIG_DIR=/scratch/work/math/py-rpy/work/.cwrapper/config CPP=cpp LOCALBASE=/usr/pkg X11BASE=/usr/X11R7 PKGMANDIR=man PKGINFODIR=info PKGGNUDIR=gnu/ MAKECONF=/dev/null OBJECT_FMT=ELF USETOOLS=no BSD_INSTALL_PROGRAM=/usr/bin/install\ -c\ -s\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_SCRIPT=/usr/bin/install\ -c\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_LIB=/usr/bin/install\ -c\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ users\ -m\ 644 BSD_INSTALL_MAN=/usr/bin/install\ -c\ -o\ pbulk\ -g\ users\ -m\ 644 BSD_INSTALL=/usr/bin/install BSD_INSTALL_PROGRAM_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_SCRIPT_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_LIB_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_DATA_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_MAN_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ users\ -m\ 755 BSD_INSTALL_GAME=/usr/bin/install\ -c\ -s\ -o\ pbulk\ -g\ users\ -m\ 2555 BSD_INSTALL_GAME_DATA=/usr/bin/install\ -c\ -o\ pbulk\ -g\ users\ -m\ 664 BSD_INSTALL_GAME_DIR=/usr/bin/install\ -d\ -o\ pbulk\ -g\ users\ -m\ 775 INSTALL_INFO= MAKEINFO=/scratch/work/math/py-rpy/work/.tools/bin/makeinfo FLEX= BISON= ITSTOOL=/scratch/work/math/py-rpy/work/.tools/bin/itstool GDBUS_CODEGEN=/scratch/work/math/py-rpy/work/.tools/bin/gdbus-codegen PKG_CONFIG= PKG_CONFIG_LIBDIR=/scratch/work/math/py-rpy/work/.buildlink/lib/pkgconfig:/scratch/work/math/py-rpy/work/.buildlink/share/pkgconfig PKG_CONFIG_LOG=/scratch/work/math/py-rpy/work/.pkg-config.log PKG_CONFIG_PATH= CWRAPPERS_CONFIG_DIR=/scratch/work/math/py-rpy/work/.cwrapper/config /usr/pkg/bin/python3.9 setup.py build -j3)
R version 4.1.1 (2021-08-10) -- "Kick Things"
/usr/pkg/lib/R/bin/R CMD config --ldflags
/usr/pkg/lib/R/bin/R CMD config --cppflags
Compilation parameters for rpy2's C components:
include_dirs = ['/usr/pkg/lib/R/include']
library_dirs = ['/usr/pkg/lib', '/usr/lib', '/usr/X11R7/lib', '/usr/pkg/lib/R/lib', '/usr/pkg/lib']
libraries = ['R', 'pcre2-8', 'lzma', 'bz2', 'z', 'rt', 'm', 'iconv']
extra_link_args = ['-Wl,--export-dynamic', '-fopenmp', '-Wl,-R/usr/lib', '-Wl,-R/usr/pkg/lib', '-pthread', '-Wl,-R/usr/X11R7/lib', '-Wl,-R/usr/pkg/lib/R/lib', '-Wl,-R/usr/pkg/lib']
running build
running build_py
creating build
creating build/lib.netbsd-9.0-i386-3.9
creating build/lib.netbsd-9.0-i386-3.9/rpy2
copying ./rpy/rpy_classic.py -> build/lib.netbsd-9.0-i386-3.9/rpy2
copying ./rpy/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2
copying ./rpy/tests.py -> build/lib.netbsd-9.0-i386-3.9/rpy2
copying ./rpy/tests_rpy_classic.py -> build/lib.netbsd-9.0-i386-3.9/rpy2
copying ./rpy/situation.py -> build/lib.netbsd-9.0-i386-3.9/rpy2
creating build/lib.netbsd-9.0-i386-3.9/rpy2/rlike
copying ./rpy/rlike/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike
copying ./rpy/rlike/functional.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike
copying ./rpy/rlike/container.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike
copying ./rpy/rlike/indexing.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike
creating build/lib.netbsd-9.0-i386-3.9/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_container.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike/tests
copying ./rpy/rlike/tests/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_functional.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike/tests
copying ./rpy/rlike/tests/test_indexing.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rlike/tests
creating build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface
copying ./rpy/rinterface/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface
creating build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_Device.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpSymbol.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/tests
creating build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/packages_utils.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/packages.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/numpy2ri.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/pandas2ri.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/functions.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/constants.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/methods.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/help.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/language.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/conversion.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/vectors.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/environments.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
copying ./rpy/robjects/robject.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects
creating build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRObject.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPackages.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testHelp.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testRobjects.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testMethods.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testLanguage.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testArray.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFormula.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testFunction.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
copying ./rpy/robjects/tests/testVector.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/tests
creating build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/test_dplyr.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/dplyr.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/grdevices.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/tidyr.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/ggplot2.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
copying ./rpy/robjects/lib/grid.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib
creating build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_dplyr.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib/tests
copying ./rpy/robjects/lib/tests/test_grdevices.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/robjects/lib/tests
creating build/lib.netbsd-9.0-i386-3.9/rpy2/interactive
copying ./rpy/interactive/packages.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/interactive
copying ./rpy/interactive/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/interactive
copying ./rpy/interactive/process_revents.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/interactive
creating build/lib.netbsd-9.0-i386-3.9/rpy2/interactive/tests
copying ./rpy/interactive/tests/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/interactive/tests
creating build/lib.netbsd-9.0-i386-3.9/rpy2/ipython
copying ./rpy/ipython/html.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/ipython
copying ./rpy/ipython/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/ipython
copying ./rpy/ipython/ggplot.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/ipython
copying ./rpy/ipython/rmagic.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/ipython
creating build/lib.netbsd-9.0-i386-3.9/rpy2/ipython/tests
copying ./rpy/ipython/tests/__init__.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/ipython/tests
copying ./rpy/ipython/tests/test_rmagic.py -> build/lib.netbsd-9.0-i386-3.9/rpy2/ipython/tests
running build_clib
building 'r_utils' library
creating build/temp.netbsd-9.0-i386-3.9
creating build/temp.netbsd-9.0-i386-3.9/rpy
creating build/temp.netbsd-9.0-i386-3.9/rpy/rinterface
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -fPIC -I./rpy/rinterface -I/usr/pkg/lib/R/include -c ./rpy/rinterface/r_utils.c -o build/temp.netbsd-9.0-i386-3.9/./rpy/rinterface/r_utils.o
ar rcs build/temp.netbsd-9.0-i386-3.9/libr_utils.a build/temp.netbsd-9.0-i386-3.9/./rpy/rinterface/r_utils.o
running build_ext
R version 4.1.1 (2021-08-10) -- "Kick Things"
building 'rpy2.rinterface._rinterface' extension
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/usr/pkg/lib/R/include -I/usr/pkg/include/python3.9 -c ./rpy/rinterface/_rinterface.c -o build/temp.netbsd-9.0-i386-3.9/./rpy/rinterface/_rinterface.o
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_WriteConsoleEx':
./rpy/rinterface/_rinterface.c:349:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:369:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
result = PyEval_CallObject(consolecallback, arglist);
^~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ShowMessage':
./rpy/rinterface/_rinterface.c:420:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:440:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
result = PyEval_CallObject(showMessageCallback, arglist);
^~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ReadConsole':
./rpy/rinterface/_rinterface.c:489:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:513:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
result = PyEval_CallObject(readConsoleCallback, arglist);
^~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_FlushConsole':
./rpy/rinterface/_rinterface.c:626:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:631:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
PyEval_CallObject(flushConsoleCallback, NULL);
^~~~~~~~~~~~~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ResetConsole':
./rpy/rinterface/_rinterface.c:660:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:666:5: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
PyEval_CallObject(resetConsoleCallback, NULL);
^~~~~~~~~~~~~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ChooseFile':
./rpy/rinterface/_rinterface.c:710:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:725:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
result = PyEval_CallObject(chooseFileCallback, arglist);
^~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_ShowFiles':
./rpy/rinterface/_rinterface.c:800:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./rpy/rinterface/_rinterface.c:52:0:
./rpy/rinterface/_rinterface.h:58:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (rbool == NA_LOGICAL) { \
^
./rpy/rinterface/_rinterface.c:819:3: note: in expansion of macro 'RPY_PY_FROM_RBOOL'
RPY_PY_FROM_RBOOL(py_del, del);
^~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:859:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
result = PyEval_CallObject(showFilesCallback, arglist);
^~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'EmbeddedR_CleanUp':
./rpy/rinterface/_rinterface.c:933:3: warning: 'PyEval_ThreadsInitialized' is deprecated [-Wdeprecated-declarations]
const int is_threaded = PyEval_ThreadsInitialized();
^~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:129:36: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(int) PyEval_ThreadsInitialized(void);
^~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c:943:3: warning: 'PyEval_CallObjectWithKeywords' is deprecated [-Wdeprecated-declarations]
PyObject *result = PyEval_CallObject(cleanUpCallback, arglist);
^~~~~~~~
In file included from /scratch/work/math/py-rpy/work/.buildlink/include/python3.9/Python.h:154:0,
from ./rpy/rinterface/_rinterface.c:49:
/scratch/work/math/py-rpy/work/.buildlink/include/python3.9/ceval.h:17:43: note: declared here
Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./rpy/rinterface/_rinterface.c: In function 'Sexp_rcall':
./rpy/rinterface/_rinterface.c:1719:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
argNameString = Rf_mkCharCE(PyBytes_AsString(pybytes), CE_UTF8);
^
./rpy/rinterface/_rinterface.c:1720:32: warning: passing argument 1 of 'Rf_installTrChar' from incompatible pointer type [-Wincompatible-pointer-types]
SET_TAG(c_R, installChar(argNameString));
^~~~~~~~~~~~~
In file included from ./rpy/rinterface/_rinterface.h:9:0,
from ./rpy/rinterface/_rinterface.c:52:
/scratch/work/math/py-rpy/work/.buildlink/lib/R/include/Rinternals.h:1162:6: note: expected 'SEXP {aka struct SEXPREC *}' but argument is of type 'const char *'
SEXP Rf_installTrChar(SEXP);
^~~~~~~~~~~~~~~~
gcc -pthread -shared -L. -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline build/temp.netbsd-9.0-i386-3.9/./rpy/rinterface/_rinterface.o -L/usr/pkg/lib -L/usr/lib -L/usr/X11R7/lib -L/usr/pkg/lib/R/lib -L/usr/pkg/lib -L/usr/pkg/lib -Lbuild/temp.netbsd-9.0-i386-3.9 -Wl,-R/usr/pkg/lib -Wl,-R/usr/lib -Wl,-R/usr/X11R7/lib -Wl,-R/usr/pkg/lib/R/lib -Wl,-R/usr/pkg/lib -lR -lpcre2-8 -llzma -lbz2 -lz -lrt -lm -liconv -lr_utils -o build/lib.netbsd-9.0-i386-3.9/rpy2/rinterface/_rinterface.so -Wl,--export-dynamic -fopenmp -Wl,-R/usr/lib -Wl,-R/usr/pkg/lib -pthread -Wl,-R/usr/X11R7/lib -Wl,-R/usr/pkg/lib/R/lib -Wl,-R/usr/pkg/lib
ld: warning: libgomp.so.1, needed by /scratch/work/math/py-rpy/work/.buildlink/lib/R/lib/libR.so, may conflict with libgomp.so.2
building 'rpy2.rinterface._rpy_device' extension
gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -O2 -D_FORTIFY_SOURCE=2 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.9 -I/usr/include/readline -fPIC -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I/usr/pkg/lib/R/include -Irpy/rinterface -I/usr/pkg/include/python3.9 -c ./rpy/rinterface/_rpy_device.c -o build/temp.netbsd-9.0-i386-3.9/./rpy/rinterface/_rpy_device.o
./rpy/rinterface/_rpy_device.c: In function '_GrDev_close':
./rpy/rinterface/_rpy_device.c:175:7: error: '_Py_DEC_REFTOTAL' undeclared (first use in this function); did you mean '_Py_DECREF'?
_Py_DEC_REFTOTAL;
^~~~~~~~~~~~~~~~
_Py_DECREF
./rpy/rinterface/_rpy_device.c:175:7: note: each undeclared identifier is reported only once for each function it appears in
error: command '/scratch/work/math/py-rpy/work/.cwrapper/bin/gcc' failed with exit code 1
*** Error code 1
Stop.
make[1]: stopped in /tree/pkgsrc/math/py-rpy
*** Error code 1
Stop.
make: stopped in /tree/pkgsrc/math/py-rpy