scipy: BUG: Build fails on latest commit

Describe your issue.

I am trying to build SciPy, it worked well, now it throws the following error when I try to build.

Reproducing Code Example

git clone https://github.com/scipy/scipy
cd scipy
git checkout 41c61b2de9a2dbef6705f961fe6836f1b5916d31
mamba env create -f environment.yml --force
conda activate scipy-dev
git submodule update --init
python dev.py build

Error message

% python dev.py build
💻  meson setup /Users/pranavchiku/repos/scipy/build --prefix /Users/pranavchiku/repos/scipy/build-install
The Meson build system
Version: 1.2.1
Source dir: /Users/pranavchiku/repos/scipy
Build dir: /Users/pranavchiku/repos/scipy/build
Build type: native build
Project name: SciPy
Project version: 1.12.0.dev0
C compiler for the host machine: arm64-apple-darwin20.0.0-clang (clang 15.0.7 "clang version 15.0.7")
C linker for the host machine: arm64-apple-darwin20.0.0-clang ld64 609
C++ compiler for the host machine: arm64-apple-darwin20.0.0-clang++ (clang 15.0.7 "clang version 15.0.7")
C++ linker for the host machine: arm64-apple-darwin20.0.0-clang++ ld64 609
Cython compiler for the host machine: cython (cython 3.0.1)
Host machine cpu family: aarch64
Host machine cpu: aarch64
Program python3 found: YES (/Users/pranavchiku/mambaforge/envs/scipy-dev/bin/python3.11)
Found pkg-config: /Users/pranavchiku/mambaforge/envs/scipy-dev/bin/pkg-config (0.29.2)
Run-time dependency python found: YES 3.11
Program cython found: YES (/Users/pranavchiku/mambaforge/envs/scipy-dev/bin/cython)
Compiler for C supports arguments -Wno-unused-but-set-variable: YES 
Compiler for C supports arguments -Wno-unused-function: YES 
Compiler for C supports arguments -Wno-conversion: YES 
Compiler for C supports arguments -Wno-misleading-indentation: YES 
Library m found: YES
Fortran compiler for the host machine: /Users/pranavchiku/mambaforge/envs/scipy-dev/bin/arm64-apple-darwin20.0.0-gfortran (gcc 12.3.0 "GNU Fortran (GCC) 12.3.0")
Fortran linker for the host machine: /Users/pranavchiku/mambaforge/envs/scipy-dev/bin/arm64-apple-darwin20.0.0-gfortran ld64 609
Compiler for Fortran supports arguments -Wno-conversion: YES 
Checking if "-Wl,--version-script" : links: NO 
Program pythran found: YES (/Users/pranavchiku/mambaforge/envs/scipy-dev/bin/pythran)
Did not find CMake 'cmake'
Found CMake: NO
Run-time dependency xsimd found: NO (tried pkgconfig, framework and cmake)
Run-time dependency threads found: YES
Library npymath found: YES
Library npyrandom found: YES
Run-time dependency pybind11 found: YES 2.11.1
Run-time dependency openblas found: YES 0.3.23
Dependency openblas found: YES 0.3.23 (cached)
Compiler for C supports arguments -Wno-maybe-uninitialized: NO 
Compiler for C supports arguments -Wno-discarded-qualifiers: NO 
Compiler for C supports arguments -Wno-empty-body: YES 
Compiler for C supports arguments -Wno-implicit-function-declaration: YES 
Compiler for C supports arguments -Wno-parentheses: YES 
Compiler for C supports arguments -Wno-switch: YES 
Compiler for C supports arguments -Wno-unused-label: YES 
Compiler for C supports arguments -Wno-unused-variable: YES 
Compiler for C supports arguments -Wno-incompatible-pointer-types: YES 
Compiler for C++ supports arguments -Wno-cpp: YES 
Compiler for C++ supports arguments -Wno-deprecated-declarations: YES 
Compiler for C++ supports arguments -Wno-class-memaccess: NO 
Compiler for C++ supports arguments -Wno-format-truncation: NO 
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES 
Compiler for C++ supports arguments -Wno-sign-compare: YES 
Compiler for C++ supports arguments -Wno-switch: YES 
Compiler for C++ supports arguments -Wno-terminate: NO 
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES 
Compiler for C++ supports arguments -Wno-unused-function: YES 
Compiler for C++ supports arguments -Wno-unused-local-typedefs: YES 
Compiler for C++ supports arguments -Wno-unused-variable: YES 
Compiler for C++ supports arguments -Wno-int-in-bool-context: YES 
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES 
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-intrinsic-shadow: YES 
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES 
Compiler for Fortran supports arguments -Wno-surprising: YES 
Compiler for Fortran supports arguments -Wno-uninitialized: YES 
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES 
Compiler for Fortran supports arguments -Wno-unused-label: YES 
Compiler for Fortran supports arguments -Wno-unused-variable: YES 
Compiler for Fortran supports arguments -Wno-tabs: YES 
Compiler for Fortran supports arguments -Wno-argument-mismatch: YES (cached)
Compiler for Fortran supports arguments -Wno-conversion: YES (cached)
Compiler for Fortran supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-dummy-argument: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-label: YES (cached)
Compiler for Fortran supports arguments -Wno-unused-variable: YES (cached)
Compiler for Fortran supports arguments -Wno-tabs: YES (cached)
Checking if "Check atomic builtins without -latomic" : links: YES 
Configuring __config__.py using configuration
Checking for function "open_memstream" : YES 
Configuring messagestream_config.h using configuration
Compiler for Fortran supports arguments -w: YES 
Checking for size of "void*" : 8 
Compiler for C supports arguments -Wno-unused-variable: YES (cached)
Compiler for C supports arguments -Wno-parentheses: YES (cached)
Compiler for C supports arguments -Wno-unused-label: YES (cached)
Compiler for C supports arguments -Wno-implicit-function-declaration: YES (cached)
Compiler for C supports arguments -Wno-switch: YES (cached)
Compiler for Fortran supports arguments -w: YES (cached)
Checking for size of "void*" : 8 (cached)
Build targets in project: 244

SciPy 1.12.0.dev0

  User defined options
    prefix: /Users/pranavchiku/repos/scipy/build-install

Found ninja-1.11.1 at /Users/pranavchiku/mambaforge/envs/scipy-dev/bin/ninja
Meson build setup OK
💻  ninja -C /Users/pranavchiku/repos/scipy/build -j8
ninja: Entering directory `/Users/pranavchiku/repos/scipy/build'
[12/1588] Linking target scipy/_lib/_fpumode.cpython-311-darwin.so
ld: warning: -pie being ignored. It is only used when linking a main executable
[13/1588] Linking target scipy/_lib/_test_ccallback.cpython-311-darwin.so
ld: warning: -pie being ignored. It is only used when linking a main executable
[52/1588] Compiling C object scipy/special/libcephes.a.p/cephes_airy.c.o
../scipy/special/cephes/airy.c:256:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int airy(x, ai, aip, bi, bip)
    ^
.....
WARNING: Overriding pythran description with argspec information for: numpy.random.standard_normal
WARNING: Overriding pythran description with argspec information for: numpy.random.uniform
WARNING: Overriding pythran description with argspec information for: numpy.random.weibull
[1202/1588] Compiling C object scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/meson-generated__upfirdn_apply.c.o
FAILED: scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/meson-generated__upfirdn_apply.c.o 
arm64-apple-darwin20.0.0-clang -Iscipy/signal/_upfirdn_apply.cpython-311-darwin.so.p -Iscipy/signal -I../scipy/signal -I../../../mambaforge/envs/scipy-dev/lib/python3.11/site-packages/numpy/core/include -I/Users/pranavchiku/mambaforge/envs/scipy-dev/include/python3.11 -fvisibility=hidden -fcolor-diagnostics -Wall -Winvalid-pch -std=c99 -O2 -g -Wno-unused-but-set-variable -Wno-unused-function -Wno-conversion -Wno-misleading-indentation -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/pranavchiku/mambaforge/envs/scipy-dev/include -D_FORTIFY_SOURCE=2 -isystem /Users/pranavchiku/mambaforge/envs/scipy-dev/include -DCYTHON_CCOMPLEX=0 -Wno-cpp -MD -MQ scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/meson-generated__upfirdn_apply.c.o -MF scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/meson-generated__upfirdn_apply.c.o.d -o scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/meson-generated__upfirdn_apply.c.o -c scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/_upfirdn_apply.c
scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/_upfirdn_apply.c:26466:25: error: initializing '__pyx_t_float_complex' with an expression of incompatible type 'int'
  __pyx_t_float_complex __pyx_v_cval = 0;
                        ^              ~
scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/_upfirdn_apply.c:26944:20: error: assigning to '__pyx_t_float_complex' from incompatible type 'int'
      __pyx_v_cval = 0;
                   ^ ~
scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/_upfirdn_apply.c:27598:26: error: initializing '__pyx_t_double_complex' with an expression of incompatible type 'int'
  __pyx_t_double_complex __pyx_v_cval = 0;
                         ^              ~
scipy/signal/_upfirdn_apply.cpython-311-darwin.so.p/_upfirdn_apply.c:28076:20: error: assigning to '__pyx_t_double_complex' from incompatible type 'int'
      __pyx_v_cval = 0;
                   ^ ~
4 errors generated.
[1209/1588] Compiling C object scipy/signal/_sosfilt.cpython-311-darwin.so.p/meson-generated__sosfilt.c.o
ninja: build stopped: subcommand failed.
Build failed!

SciPy/NumPy/Python version and system information

Apple mac m2 air

About this issue

Original URL
State: closed
Created 10 months ago
Comments: 19 (17 by maintainers)

Links to this issue

Commits related to this issue

MAINT: signal: Remove the cval parameter from the private function _pad_test. The parameter `cval` in the private helper function `_pad_test` is not used, so remove it. This change is inspired by a ... — committed to WarrenWeckesser/scipy by WarrenWeckesser 10 months ago
MAINT: signal: Remove the cval parameter from the private function _pad_test. The parameter `cval` in the private helper function `_pad_test` is not used, so remove it. This change is inspired by a ... — committed to tylerjereddy/scipy by WarrenWeckesser 10 months ago

Most upvoted comments

BTW Cython 3.0.2 was released with the issue fixed: https://github.com/cython/cython/releases/tag/3.0.2

matusvalo on Aug 27, 2023

I did a git bisect of Cython between tags 3.0.0 and 3.0.1, on the ability to build SciPy main:

6776c96f66fc799c62be4d6d4022903a5e36cbb2 is the first bad commit
commit 6776c96f66fc799c62be4d6d4022903a5e36cbb2
Author: da-woods <dw-git@d-woods.co.uk>
Date:   Fri Aug 4 10:48:50 2023 +0100

    Fix using NULL as pointer default value for fused function arguments (#5578)
    
    In general, there is no need to go through a temp if the node is literal.
    
    Fixes https://github.com/cython/cython/issues/5554

 Cython/Compiler/FusedNode.py | 12 +++++++++---
 tests/run/fused_types.pyx    | 29 +++++++++++++++++++++++++++++
 2 files changed, 38 insertions(+), 3 deletions(-)

tylerjereddy on Aug 25, 2023

I mean, a man can only dream I guess

ilayn on Aug 25, 2023

cc @matusvalo perhaps

tylerjereddy on Aug 25, 2023

Cython 3.0.1 was released 7 hours ago, but not yet on PyPI it seems, but you are using it above.

I confirmed locally that we build with 3.0.0 but not 3.0.1 in standard Ubuntu Linux venv. We’ve had Cython folks helping us out recently so I imagine we can ping someone.

tylerjereddy on Aug 25, 2023