Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
We are still having the open issue of rpy2 now segfaulting on the embedding tests which reproduces on my plain vanilla amd64 setup -- so I commented that test out too. Laurent: Any idea why R 4.4.0 and rpy2 do not get along on embedding? Cheers, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
On 25 May 2024 at 12:35, Bo YU wrote: | Hi, | On Sat, May 18, 2024 at 06:41:53AM -0500, Dirk Eddelbuettel wrote: | > | >On 17 May 2024 at 23:05, Santiago Vila wrote: | >| Dirk Eddelbuettel wrote: | >| > Is there a chance this could be spurious? | >| | >| Unlikely because it also happens here: | >| | >| https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rpy2.html | > | >Ok, I will get in touch with Laurent. | | hmm, the failure will not happen on riscv64 real hardware when I am | trying to get below diff file. Thanks for working through this, and a good idea to piggy-back on the existing test skipping for mips64! The only thing that is a little troubling the overall skip of the 'datetime from timestamp' test but we probably added that one for a reason too... I think I will apply this. Many thanks! Dirk | -- | Regards, | -- |Bo YU | | x[DELETED ATTACHMENT rpy2_fix_ftbfs_riscv64.debdiff, plain text] | x[DELETED ATTACHMENT signature.asc, application/pgp-signature] -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
Hi,
On Sat, May 18, 2024 at 06:41:53AM -0500, Dirk Eddelbuettel wrote:
On 17 May 2024 at 23:05, Santiago Vila wrote:
| Dirk Eddelbuettel wrote:
| > Is there a chance this could be spurious?
|
| Unlikely because it also happens here:
|
| https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rpy2.html
Ok, I will get in touch with Laurent.
hmm, the failure will not happen on riscv64 real hardware when I am
trying to get below diff file.
--
Regards,
--
Bo YU
diff -Nru rpy2-3.5.16/debian/changelog rpy2-3.5.16/debian/changelog
--- rpy2-3.5.16/debian/changelog2024-04-05 04:42:35.0 +0800
+++ rpy2-3.5.16/debian/changelog2024-05-19 22:32:19.0 +0800
@@ -1,3 +1,10 @@
+rpy2 (3.5.16-1.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Skip some tests on riscv64. (Closes: #-1)
+
+ -- BO YU Sun, 19 May 2024 22:32:19 +0800
+
rpy2 (3.5.16-1) unstable; urgency=medium
* New upstream release
diff -Nru rpy2-3.5.16/debian/patches/series rpy2-3.5.16/debian/patches/series
--- rpy2-3.5.16/debian/patches/series 2023-08-27 00:04:33.0 +0800
+++ rpy2-3.5.16/debian/patches/series 2024-05-19 22:30:46.0 +0800
@@ -1,3 +1,3 @@
#relax_cffi_version_requirement
#comment_out_one_test
-skip_complex_tests_on_mips64el
+skip_complex_tests_on_mips64el_and_riscv64
diff -Nru rpy2-3.5.16/debian/patches/skip_complex_tests_on_mips64el
rpy2-3.5.16/debian/patches/skip_complex_tests_on_mips64el
--- rpy2-3.5.16/debian/patches/skip_complex_tests_on_mips64el 2023-08-27
00:59:57.0 +0800
+++ rpy2-3.5.16/debian/patches/skip_complex_tests_on_mips64el 1970-01-01
08:00:00.0 +0800
@@ -1,148 +0,0 @@
-Description: Skip complex-valued tests on mips64el
-Bug-Debian: https://bugs.debian.org/1050432
-Reviewed-By: Dirk Eddelbuettel
-Last-Update: 2023-08-26
-
rpy2-3.5.13.orig/rpy2/tests/rinterface/test_na.py
-+++ rpy2-3.5.13/rpy2/tests/rinterface/test_na.py
-@@ -1,6 +1,8 @@
- import pytest
- import math
- import rpy2.rinterface as ri
-+import sys
-+import platform
-
- ri.initr()
-
-@@ -147,7 +149,8 @@ def test_NACharacter_in_vector():
- assert x.get_charsxp(1).rid == na_str.rid
- assert x[2] == 'cd'
-
--
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_R_to_NAComplex():
- r_na_complex = ri.evalr('NA_complex_')[0]
- assert math.isnan(r_na_complex.real)
rpy2-3.5.13.orig/rpy2/tests/rinterface/test_vector_complex.py
-+++ rpy2-3.5.13/rpy2/tests/rinterface/test_vector_complex.py
-@@ -1,9 +1,13 @@
- import pytest
- import rpy2.rinterface as ri
-+import sys
-+import platform
-
- ri.initr()
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_init_from_seqr():
- seq = [1+2j, 5+7j, 0+1j]
- v = ri.ComplexSexpVector(seq)
-@@ -18,17 +22,23 @@ def test_init_from_seq_invalid_item():
- ri.ComplexSexpVector(seq)
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_getitem():
- vec = ri.ComplexSexpVector([1+2j, 5+7j, 0+1j])
- assert vec[1] == 5+7j
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_setitem():
- vec = ri.ComplexSexpVector([1+2j, 5+7j, 0+1j])
- vec[1] = 100+3j
- assert vec[1] == 100+3j
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_getslice():
- vec = ri.ComplexSexpVector([1+2j, 5+7j, 0+1j])
- vec_s = vec[0:2]
-@@ -37,6 +47,8 @@ def test_getslice():
- assert vec_s[1] == 5+7j
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_getslice_negative():
- vec = ri.ComplexSexpVector([1+2j, 5+7j, 0+1j])
- vec_s = vec[-2:-1]
-@@ -44,6 +56,8 @@ def test_getslice_negative():
- assert vec_s[0] == 5+7j
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_setslice():
- vec = ri.ComplexSexpVector([1+2j, 5+7j, 0+1j])
- vec[0:2] = ri.ComplexSexpVector([100+3j, 5-5j])
-@@ -52,6 +66,8 @@ def test_setslice():
- assert vec[1] == 5-5j
-
-
-+@pytest.mark.skipif(platform.machine() == 'mips64' and sys.byteorder ==
'little',
-+reason="Complex tests fail for 'mips64el'.")
- def test_setslice_negative():
- vec = ri.ComplexSexpVector([1+2j, 5+7j, 0+1j])
- vec[-2:-1] = ri.ComplexSexpVector([100+3j, ])
-@@ -59,6 +75,8 @@ def test_setslice_negative():
-
Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
On 17 May 2024 at 23:05, Santiago Vila wrote: | Dirk Eddelbuettel wrote: | > Is there a chance this could be spurious? | | Unlikely because it also happens here: | | https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rpy2.html Ok, I will get in touch with Laurent. Dirk | Thanks. -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
Dirk Eddelbuettel wrote: Is there a chance this could be spurious? Unlikely because it also happens here: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/rpy2.html Thanks.
Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
Is there a chance this could be spurious? The R API is reasonably stable, including the part for embedding R (and I am upstream for a small project doing that from C++). rpy2 is also mature and stable. So could this be a one-off? Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1071362: rpy2: FTBFS: rpy2/tests/rinterface/test_embedded_r.py s.......Fatal Python error: Segmentation fault
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: [...] 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 creating /<>/.pybuild/cpython3_3.12/build/rpy2 copying rpy2/situation.py -> /<>/.pybuild/cpython3_3.12/build/rpy2 copying rpy2/rinterface.py ->
