Package: src:rpy2
Version: 3.5.16-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
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[...]
debian/rules build
dh build --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.12 setup.py config
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
running config
I: pybuild base:311: python3.11 setup.py config
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3.12 setup.py build
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
running build
cffi mode: CFFI_MODE.ANY
running build_py
file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
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copying rpy2/tests/robjects/lib/test_grid.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_tidyr.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_dplyr.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_dbplyr.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/robjects/lib
running egg_info
writing rpy2.egg-info/PKG-INFO
writing dependency_links to rpy2.egg-info/dependency_links.txt
writing requirements to rpy2.egg-info/requires.txt
writing top-level names to rpy2.egg-info/top_level.txt
reading manifest file 'rpy2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README' anywhere in distribution
warning: no previously-included files matching '*patch*' found anywhere in
distribution
warning: no previously-included files matching '*diff*' found anywhere in
distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
warning: no files found matching 'MANIFEST'
warning: no files found matching '_rinterface_cffi_build'
warning: no files found matching 'rpy/__init__.py'
warning: no files found matching 'rpy/situation.py'
warning: no files found matching '*.py' under directory 'rpy/robjects'
warning: no files found matching '*.py' under directory 'rpy/ipython'
warning: no files found matching '*.py' under directory 'rpy/interactive'
warning: no files found matching '*.py' under directory 'rpy/rlike'
no previously-included directories found matching 'dist'
warning: no files found matching 'doc/source/rpy2_logo.png'
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'rpy2.egg-info/SOURCES.txt'
copying rpy2/rinterface_lib/R_API.h ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/R_API_eventloop.h ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/R_API_eventloop.c ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/RPY2.h ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/_bufferprotocol.c ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface_lib
file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
generating cffi module
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/_rinterface_cffi_abi.py'
running build_ext
generating cffi module
'build/temp.linux-x86_64-cpython-312/_rinterface_cffi_api.c'
creating build
creating build/temp.linux-x86_64-cpython-312
building 'rpy2.rinterface_lib._bufferprotocol' extension
creating build/temp.linux-x86_64-cpython-312/rpy2
creating build/temp.linux-x86_64-cpython-312/rpy2/rinterface_lib
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security
-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c
rpy2/rinterface_lib/_bufferprotocol.c -o
build/temp.linux-x86_64-cpython-312/rpy2/rinterface_lib/_bufferprotocol.o
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro
-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-312/rpy2/rinterface_lib/_bufferprotocol.o -L/usr/lib/x86_64-linux-gnu
-o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface_lib/_bufferprotocol.cpython-312-x86_64-linux-gnu.so
building '_rinterface_cffi_api' extension
creating build/temp.linux-x86_64-cpython-312/build
creating build/temp.linux-x86_64-cpython-312/build/temp.linux-x86_64-cpython-312
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security
-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DRPY2_RLEN_LONG=True
-DR_INTERFACE_PTRS=True -Irpy2/rinterface_lib/ -I/usr/include/python3.12 -c
build/temp.linux-x86_64-cpython-312/_rinterface_cffi_api.c -o
build/temp.linux-x86_64-cpython-312/build/temp.linux-x86_64-cpython-312/_rinterface_cffi_api.o
-std=c99
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro
-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-312/build/temp.linux-x86_64-cpython-312/_rinterface_cffi_api.o
-L/usr/lib/R/lib -L/usr/lib/x86_64-linux-gnu -lR -lpcre2-8 -ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl
-lm -licuuc -licui18n -lblas -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/_rinterface_cffi_api.abi3.so
-Wl,--export-dynamic -fopenmp -Wl,-z,relro -Wl,-rpath,/usr/lib/R/lib
---
CFFI_MODE.ANY
ABI mode interface built.
API mode interface built.
To change the API/ABI build mode, set or modify the environment variable
RPY2_CFFI_MODE.
I: pybuild base:311: /usr/bin/python3 setup.py build
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
cffi mode is CFFI_MODE.ANY
Looking for R home with: R RHOME
R home found: /usr/lib/R
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --ldflags
['-Wl,--export-dynamic -fopenmp -Wl,-z,relro -L/usr/lib/R/lib -lR -lpcre2-8
-ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl -lm -licuuc -licui18n', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config BLAS_LIBS
['-lblas', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config --cppflags
['-I/usr/share/R/include', '']
R exec path: /usr/lib/R/bin/R
Looking for R CONFIG with: /usr/lib/R/bin/R CMD config LIBnn
['lib', '']
running build
cffi mode: CFFI_MODE.ANY
running build_py
file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2
copying rpy2/situation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2
copying rpy2/rinterface.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2
copying rpy2/_rinterface_cffi_build.py ->
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rlike
copying rpy2/rlike/functional.py ->
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copying rpy2/rlike/indexing.py ->
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copying rpy2/rinterface_lib/memorymanagement.py ->
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copying rpy2/rinterface_lib/openrlib.py ->
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copying rpy2/rinterface_lib/na_values.py ->
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copying rpy2/rinterface_lib/_rinterface_capi.py ->
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copying rpy2/rinterface_lib/ffi_proxy.py ->
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copying rpy2/rinterface_lib/sexp.py ->
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copying rpy2/rinterface_lib/bufferprotocol.py ->
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copying rpy2/rinterface_lib/callbacks.py ->
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copying rpy2/rinterface_lib/embedded.py ->
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copying rpy2/rinterface_lib/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/robjects
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copying rpy2/robjects/environments.py ->
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copying rpy2/robjects/packages_utils.py ->
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copying rpy2/robjects/lib/grdevices.py ->
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copying rpy2/robjects/lib/dbplyr.py ->
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copying rpy2/robjects/lib/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/robjects/lib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/interactive
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/interactive
copying rpy2/interactive/packages.py ->
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copying rpy2/interactive/__init__.py ->
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/ipython
copying rpy2/ipython/ggplot.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/ipython
copying rpy2/ipython/rmagic.py ->
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copying rpy2/ipython/__init__.py ->
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copying rpy2/ipython/html.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/ipython
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests
copying rpy2/tests/utils.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests
copying rpy2/tests/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/rinterface
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copying rpy2/tests/rinterface/test_na.py ->
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copying rpy2/tests/rinterface/test_conversion.py ->
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copying rpy2/tests/rinterface/test_externalptr.py ->
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copying rpy2/tests/rinterface/test_embedded_r.py ->
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copying rpy2/tests/rinterface/test_environment.py ->
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copying rpy2/tests/rinterface/test_memorymanagement.py ->
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copying rpy2/tests/rinterface/test_vector_complex.py ->
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copying rpy2/tests/rinterface/test_vector_byte.py ->
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copying rpy2/tests/rinterface/test_symbol.py ->
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copying rpy2/tests/rinterface/test_vector_bool.py ->
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copying rpy2/tests/rinterface/__init__.py ->
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copying rpy2/tests/rinterface/test_threading.py ->
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/rlike
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copying rpy2/tests/rlike/test_indexing.py ->
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copying rpy2/tests/rlike/test_container.py ->
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creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
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copying rpy2/tests/robjects/test_vector.py ->
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copying rpy2/tests/robjects/test_serialization.py ->
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copying rpy2/tests/robjects/test_robjects.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_vector_extractdelegator.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_packages.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_language.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_environment.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_conversion_numpy.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_translated_function.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_formula.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
copying rpy2/tests/robjects/test_vector_factor.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/ipython
copying rpy2/tests/ipython/test_ggplot.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/ipython
copying rpy2/tests/ipython/test_rmagic.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/ipython
copying rpy2/tests/ipython/test_html.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/ipython
copying rpy2/tests/ipython/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/ipython
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_grdevices.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_ggplot2.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_grid.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_tidyr.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_dplyr.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
copying rpy2/tests/robjects/lib/test_dbplyr.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/tests/robjects/lib
running egg_info
writing rpy2.egg-info/PKG-INFO
writing dependency_links to rpy2.egg-info/dependency_links.txt
writing requirements to rpy2.egg-info/requires.txt
writing top-level names to rpy2.egg-info/top_level.txt
reading manifest file 'rpy2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README' anywhere in distribution
warning: no previously-included files matching '*patch*' found anywhere in
distribution
warning: no previously-included files matching '*diff*' found anywhere in
distribution
warning: no previously-included files matching '.hg' found anywhere in
distribution
warning: no files found matching 'MANIFEST'
warning: no files found matching '_rinterface_cffi_build'
warning: no files found matching 'rpy/__init__.py'
warning: no files found matching 'rpy/situation.py'
warning: no files found matching '*.py' under directory 'rpy/robjects'
warning: no files found matching '*.py' under directory 'rpy/ipython'
warning: no files found matching '*.py' under directory 'rpy/interactive'
warning: no files found matching '*.py' under directory 'rpy/rlike'
no previously-included directories found matching 'dist'
warning: no files found matching 'doc/source/rpy2_logo.png'
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'rpy2.egg-info/SOURCES.txt'
copying rpy2/rinterface_lib/R_API.h ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/R_API_eventloop.h ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/R_API_eventloop.c ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/RPY2.h ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib
copying rpy2/rinterface_lib/_bufferprotocol.c ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib
file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found
generating cffi module
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/_rinterface_cffi_abi.py'
running build_ext
generating cffi module
'build/temp.linux-x86_64-cpython-311/_rinterface_cffi_api.c'
creating build/temp.linux-x86_64-cpython-311
building 'rpy2.rinterface_lib._bufferprotocol' extension
creating build/temp.linux-x86_64-cpython-311/rpy2
creating build/temp.linux-x86_64-cpython-311/rpy2/rinterface_lib
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g
-Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection
-Wformat -Werror=format-security -fcf-protection -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security
-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c
rpy2/rinterface_lib/_bufferprotocol.c -o
build/temp.linux-x86_64-cpython-311/rpy2/rinterface_lib/_bufferprotocol.o
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-311/rpy2/rinterface_lib/_bufferprotocol.o -L/usr/lib/x86_64-linux-gnu
-o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/rpy2/rinterface_lib/_bufferprotocol.cpython-311-x86_64-linux-gnu.so
building '_rinterface_cffi_api' extension
creating build/temp.linux-x86_64-cpython-311/build
creating build/temp.linux-x86_64-cpython-311/build/temp.linux-x86_64-cpython-311
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g
-Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection
-Wformat -Werror=format-security -fcf-protection -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security
-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DRPY2_RLEN_LONG=True
-DR_INTERFACE_PTRS=True -Irpy2/rinterface_lib/ -I/usr/include/python3.11 -c
build/temp.linux-x86_64-cpython-311/_rinterface_cffi_api.c -o
build/temp.linux-x86_64-cpython-311/build/temp.linux-x86_64-cpython-311/_rinterface_cffi_api.o
-std=c99
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-311/build/temp.linux-x86_64-cpython-311/_rinterface_cffi_api.o
-L/usr/lib/R/lib -L/usr/lib/x86_64-linux-gnu -lR -lpcre2-8 -ldeflate -llzma -lbz2 -lz -ltirpc -lrt -ldl
-lm -licuuc -licui18n -lblas -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/_rinterface_cffi_api.abi3.so
-Wl,--export-dynamic -fopenmp -Wl,-z,relro -Wl,-rpath,/usr/lib/R/lib
---
CFFI_MODE.ANY
ABI mode interface built.
API mode interface built.
To change the API/ABI build mode, set or modify the environment variable
RPY2_CFFI_MODE.
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build;
python3.12 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.12.3, pytest-8.1.2, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build
configfile: pyproject.toml
testpaths: rpy2/tests
collected 857 items
rpy2/tests/ipython/test_ggplot.py s [ 0%]
rpy2/tests/ipython/test_html.py ssssssss [ 1%]
rpy2/tests/ipython/test_rmagic.py ssssssssssssssssssssss [ 3%]
rpy2/tests/rinterface/test_bufferprotocol.py ... [ 3%]
rpy2/tests/rinterface/test_callbacks.py ...................s... [ 6%]
rpy2/tests/rinterface/test_conversion.py . [ 6%]
rpy2/tests/rinterface/test_embedded_r.py s.............................. [ 10%]
............. [ 11%]
rpy2/tests/rinterface/test_endr.py s [ 12%]
rpy2/tests/rinterface/test_environment.py ............................. [ 15%]
rpy2/tests/rinterface/test_externalptr.py ...ss [ 15%]
rpy2/tests/rinterface/test_functions.py ...................... [ 18%]
rpy2/tests/rinterface/test_memorymanagement.py ... [ 18%]
rpy2/tests/rinterface/test_na.py .....s...................... [ 22%]
rpy2/tests/rinterface/test_noinitialization.py ssss [ 22%]
rpy2/tests/rinterface/test_openrlib.py ......... [ 23%]
rpy2/tests/rinterface/test_sexp.py ..........................x..... [ 27%]
rpy2/tests/rinterface/test_symbol.py .... [ 27%]
rpy2/tests/rinterface/test_threading.py ss [ 28%]
rpy2/tests/rinterface/test_vector_bool.py .......... [ 29%]
rpy2/tests/rinterface/test_vector_byte.py ............ [ 30%]
rpy2/tests/rinterface/test_vector_complex.py ......... [ 31%]
rpy2/tests/rinterface/test_vector_float.py .......... [ 32%]
rpy2/tests/rinterface/test_vector_int.py ..s................... [ 35%]
rpy2/tests/rinterface/test_vector_lang.py ...... [ 36%]
rpy2/tests/rinterface/test_vector_list.py ....... [ 36%]
rpy2/tests/rinterface/test_vector_numpy.py ..s.. [ 37%]
rpy2/tests/rinterface/test_vector_pairlist.py ..... [ 38%]
rpy2/tests/rinterface/test_vector_str.py ........... [ 39%]
rpy2/tests/rinterface/test_vectors.py ................... [ 41%]
rpy2/tests/rlike/test_container.py .................................. [ 45%]
rpy2/tests/rlike/test_functional.py ... [ 45%]
rpy2/tests/rlike/test_indexing.py . [ 46%]
rpy2/tests/robjects/lib/test_dbplyr.py s [ 46%]
rpy2/tests/robjects/lib/test_dplyr.py sssssssssssssssssssss [ 48%]
rpy2/tests/robjects/lib/test_ggplot2.py ssssssssssssssssssssss [ 51%]
rpy2/tests/robjects/lib/test_grdevices.py ... [ 51%]
rpy2/tests/robjects/lib/test_grid.py ................ [ 53%]
rpy2/tests/robjects/lib/test_tidyr.py sss [ 53%]
rpy2/tests/robjects/test_array.py ................ [ 55%]
rpy2/tests/robjects/test_conversion.py ............................. [ 59%]
rpy2/tests/robjects/test_conversion_numpy.py ........................... [ 62%]
.......... [ 63%]
rpy2/tests/robjects/test_dataframe.py .................. [ 65%]
rpy2/tests/robjects/test_environment.py ........... [ 66%]
rpy2/tests/robjects/test_formula.py .... [ 67%]
rpy2/tests/robjects/test_function.py .............................. [ 70%]
rpy2/tests/robjects/test_help.py ........... [ 71%]
rpy2/tests/robjects/test_language.py ..... [ 72%]
rpy2/tests/robjects/test_methods.py ....... [ 73%]
rpy2/tests/robjects/test_packages.py .................... [ 75%]
rpy2/tests/robjects/test_packages_utils.py ....... [ 76%]
rpy2/tests/robjects/test_pandas_conversions.py sssssssssssssssssssssssss [ 79%]
ssssssssssssssssssssssssssssssssssssssssssssss [ 84%]
rpy2/tests/robjects/test_robjects.py ............. [ 86%]
rpy2/tests/robjects/test_rs4.py ... [ 86%]
rpy2/tests/robjects/test_serialization.py . [ 86%]
rpy2/tests/robjects/test_translated_function.py .... [ 87%]
rpy2/tests/robjects/test_vector.py ..................................... [ 91%]
..................X................... [ 96%]
rpy2/tests/robjects/test_vector_datetime.py ..x............... [ 98%]
rpy2/tests/robjects/test_vector_extractdelegator.py ....... [ 98%]
rpy2/tests/robjects/test_vector_factor.py ......... [100%]
=============================== warnings summary ===============================
rpy2/tests/ipython/test_html.py:10
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/ipython/test_html.py:10:
UserWarning: No module named 'IPython'
warnings.warn(str(no_ipython))
rpy2/tests/ipython/test_rmagic.py:29
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/ipython/test_rmagic.py:29:
UserWarning: No module named 'IPython'
warnings.warn(str(no_ipython))
rpy2/tests/ipython/test_rmagic.py:48
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/tests/ipython/test_rmagic.py:48:
PytestRemovedIn9Warning: Marks applied to fixtures have no effect
See docs:
https://docs.pytest.org/en/stable/deprecations.html#applying-a-mark-to-a-fixture-function
@pytest.mark.skipif(IPython is None,
rpy2/rinterface.py:1168
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[IntSexpVector-value0-INTEGER_ELT-_get_integer_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[BoolSexpVector-value1-LOGICAL_ELT-_get_logical_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[FloatSexpVector-value2-REAL_ELT-_get_real_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[IntSexpVector-value0-_set_integer_elt_fallback-_get_integer_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[BoolSexpVector-value1-_set_logical_elt_fallback-_get_logical_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[FloatSexpVector-value2-_set_real_elt_fallback-_get_real_elt_fallback]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface.py:1168: UserWarning:
Environment variable "LD_LIBRARY_PATH" redefined by R and overriding existing variable.
warnings.warn(
rpy2/rinterface.py:1168
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[IntSexpVector-value0-INTEGER_ELT-_get_integer_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[BoolSexpVector-value1-LOGICAL_ELT-_get_logical_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[FloatSexpVector-value2-REAL_ELT-_get_real_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[IntSexpVector-value0-_set_integer_elt_fallback-_get_integer_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[BoolSexpVector-value1-_set_logical_elt_fallback-_get_logical_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[FloatSexpVector-value2-_set_real_elt_fallback-_get_real_elt_fallback]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface.py:1168: UserWarning:
Environment variable "R_LIBS_SITE" redefined by R and overriding existing variable.
warnings.warn(
rpy2/rinterface.py:1168
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[IntSexpVector-value0-INTEGER_ELT-_get_integer_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[BoolSexpVector-value1-LOGICAL_ELT-_get_logical_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_get_vec_elt_fallback[FloatSexpVector-value2-REAL_ELT-_get_real_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[IntSexpVector-value0-_set_integer_elt_fallback-_get_integer_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[BoolSexpVector-value1-_set_logical_elt_fallback-_get_logical_elt_fallback]
rpy2/tests/rinterface/test_openrlib.py::test_set_vec_elt_fallback[FloatSexpVector-value2-_set_real_elt_fallback-_get_real_elt_fallback]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/rinterface.py:1168: UserWarning:
Environment variable "R_SESSION_TMPDIR" redefined by R and overriding existing variable.
warnings.warn(
rpy2/tests/robjects/test_dataframe.py: 6 warnings
rpy2/tests/robjects/test_language.py: 2 warnings
rpy2/tests/robjects/test_vector.py: 6 warnings
rpy2/tests/robjects/test_vector_factor.py: 5 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/robjects/conversion.py:28:
DeprecationWarning: The use of rpy2py in module rpy2.robjects.conversion is deprecated. Use
rpy2.robjects.conversion.get_conversion() instead of rpy2.robjects.conversion.converter.
warnings.warn(
rpy2/tests/robjects/test_language.py::test_eval
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12/build/rpy2/robjects/language.py:50:
DeprecationWarning: This function is deprecated. Use evaluation_context directly.
envir = ri.get_evaluation_context()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
===== 691 passed, 163 skipped, 2 xfailed, 1 xpassed, 44 warnings in 10.67s =====
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build;
python3.11 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.11.9, pytest-8.1.2, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build
configfile: pyproject.toml
testpaths: rpy2/tests
collected 857 items
rpy2/tests/ipython/test_ggplot.py s [ 0%]
rpy2/tests/ipython/test_html.py ssssssss [ 1%]
rpy2/tests/ipython/test_rmagic.py ssssssssssssssssssssss [ 3%]
rpy2/tests/rinterface/test_bufferprotocol.py ... [ 3%]
rpy2/tests/rinterface/test_callbacks.py ...................s... [ 6%]
rpy2/tests/rinterface/test_conversion.py . [ 6%]
rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error:
Segmentation fault
Current thread 0x00007f919e48e040 (most recent call first):
Segmentation fault
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=139: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12
3.11" returned exit code 13
make: *** [debian/rules:19: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large from AWS, using sbuild and a
reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
