From nobody Sun Apr 05 04:29:53 2026 X-Original-To: python@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4fpKHk3b1Rz6YClM for ; Sun, 05 Apr 2026 04:29:54 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R12" (not verified)) by mx1.freebsd.org (Postfix) with ESMTPS id 4fpKHk2BnYz3YSG for ; Sun, 05 Apr 2026 04:29:54 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1775363394; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=jRRGKZ/9n+PnFQhGxomQDxIq0RX5Nb4RILpM+cgPmpA=; b=gb5ltKjEBTF7w+8BKrLBlC4WQX9Y/jKZNTEp6WuMZmtNIZj1ogMn6eh0qmD4l1Jzx1/qDu jXnjqI/y8sW37XJE2X72trgXgefKK0BJA8SnyD2R/xqifv8hWTIzjWpQpJ9JYaFhMCGnR5 bLvaWfEw3itO6FVdtxdzAE0E9KfzS0kxsRubGd1pCFYiRWOBRiJqLXkHH0ht0X1WZv1BS6 O8H0oFjiy2R4iwucX8BoFMXiI+tBSrAiEsM6bDcHWcOCpkRq5lotnK7hrmfs6Yt/Xq5jKz 7VMbmGeNGgzszo0J9DgsFBgnEiCvSClK2dblP16vj79wO0CUxE/2X4bZQUQHyA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1775363394; a=rsa-sha256; cv=none; b=Uov3KyPzXCFL044X2o3Zkf++154AaEBRO+tqKzIGKZpVeECX2sbVKl0wAH55xyWRt1KFDN jAj1IdgUNq5lwW4g4+cgmtk1+3PYMR/shVIj6onrqVf9hXN5SU84QMKZRgtHML2UaBRu0W a+NSi53/1AlYp8lVGpns1404acOJyqjF6ultuGdq6DEmvVgdf1aOa2tts7MwvHw3dmgoFb bMAk/GtAt6Ko5TJjid8rYq8+q+tTTeBtVIGz0Qs0fKAjf4nGA39Ytxmj3eYAeWP7OIrkFv lgcBfif1YXqJk4yQTWRdae2K9xPJNe0pZ7pVtJoDYkPpZoKan2S8TteFN3TDeQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1775363394; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=jRRGKZ/9n+PnFQhGxomQDxIq0RX5Nb4RILpM+cgPmpA=; b=rXBaxjl+slLeUlg1R0/Q5HuTmVSyz7DdX0Qzbov9JAWthWMJMn5TOe1dKrhehbxWdbh4sN rTl4Ykc8FO721uCObcZK4Tkfi54s0nLpNx9QrbcwnTBr1MFQ7BvBLDxiITm7XbFQRrc7Is wTstKR4uWmbV0vG6zK8bfGZ0JFY4RKxzU3V6GKUI3ep69IeQDG9uk90ym5XZXM1hiLw20Z WPnNYIHqBMQdlBzLnY17iblTwFIF1kyJH/6UCpJk3MRjUnpG87wjkUVAPyZlsuniX16Wpp Lfi2yJqWxy/0l8SUgz9dQSTgUIHmMJIcqWHlqd72HSTOZc3kKfE3ZaiB7KIEOg== Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2610:1c1:1:606c::50:1d]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4fpKHk1n8Kzqt1 for ; Sun, 05 Apr 2026 04:29:54 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org ([127.0.1.5]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id 6354TsUv028776 for ; Sun, 5 Apr 2026 04:29:54 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id 6354Tsfx028775 for python@FreeBSD.org; Sun, 5 Apr 2026 04:29:54 GMT (envelope-from bugzilla-noreply@freebsd.org) X-Authentication-Warning: kenobi.freebsd.org: www set sender to bugzilla-noreply@freebsd.org using -f From: bugzilla-noreply@freebsd.org To: python@FreeBSD.org Subject: [Bug 294255] science/py-scipy fails to build after update to 1.17.1 Date: Sun, 05 Apr 2026 04:29:53 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Only Me X-Bugzilla-Who: russo@bogodyn.org X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: python@FreeBSD.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter flagtypes.name Message-ID: Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="UTF-8" X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated List-Id: FreeBSD-specific Python issues List-Archive: https://lists.freebsd.org/archives/freebsd-python List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: freebsd-python@freebsd.org Sender: owner-freebsd-python@FreeBSD.org MIME-Version: 1.0 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D294255 Bug ID: 294255 Summary: science/py-scipy fails to build after update to 1.17.1 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: python@FreeBSD.org Reporter: russo@bogodyn.org Flags: maintainer-feedback?(python@FreeBSD.org) Assignee: python@FreeBSD.org Not actually sure if this is caused when scipy was updated in ports ef9180aa84690bd5181cd60be75c891ee7bdb74e or if it's due to the numpy/numpy1 shakeup, but I am unable to build science/py-scipy [see below for the workaround I found while writing this report].=20=20 As an aside, I was forced to "pkg delete -f py311-numpy" because it wanted = to upgrade to numpy 2, and py-scipy now has an explicit BUILD_DEPENDS on math/py-numpy1 --- which it refused to install after py311-numpy was updated because they conflict. The vast majority of the ports I have that depend on scipy *also* depend on numpy1 this way anyway, so that's fine. But that on= ly helped a little. Now I get a compilation failure. The build error is: [853/1238] Compiling C++ object scipy/...1.so.p/src__fmm_core_write_coo_64.= cpp. FAILED: [code=3D1] scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write= _coo_64.cpp.o=20 c++ -Iscipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p -Iscipy/io/_fast_matrix_market -I../scipy/io/_fast_matrix_market -I../scipy/io/_fast_matrix_market/fast_matrix_market/include -I../../../../../../local/lib/python3.11/site-packages/numpy/core/include -I../scipy/io/_fast_matrix_market/fast_matrix_market/dependencies/fast_floa= t/include -Iscipy/io/_fast_matrix_market/fast_matrix_market/dependencies/ryu -I../scipy/io/_fast_matrix_market/fast_matrix_market/dependencies/ryu -I/include -I/usr/local/include/python3.11 -fvisibility=3Dhidden -fvisibility-inlines-hidden -fdiagnostics-color=3Dalways -DNDEBUG -D_FILE_OFFSET_BITS=3D64 -Wall -Winvalid-pch -std=3Dc++17 -O3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -DNPY_NO_DEPRECATED_API=3DNPY_1_9_API_VERSION -DFMM_SCIPY_PRUNE -DFMM_USE_FAST_FLOAT -DFMM_USE_RYU -DFMM_FROM_CHARS_INT_SUPPORTED -DFMM_TO_CHARS_INT_SUPPORTED -MD -MQ scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write= _coo_64.cpp.o -MF scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write= _coo_64.cpp.o.d -o scipy/io/_fast_matrix_market/_fmm_core.cpython-311.so.p/src__fmm_core_write= _coo_64.cpp.o -c ../scipy/io/_fast_matrix_market/src/_fmm_core_write_coo_64.cpp In file included from ../scipy/io/_fast_matrix_market/src/_fmm_core_write_coo_64.cpp:5: ../scipy/io/_fast_matrix_market/src/_fmm_core.hpp:14:10: fatal error: 'pybind11/pybind11.h' file not found 14 | #include | ^~~~~~~~~~~~~~~~~~~~~ 1 error generated. (the same problem is reported in several files if I build without setting MAKE_JOBS_UNSAFE) Yet my system has pybind11 installed, and /usr/local/include/pybind11/pybind11.h exists. from pkg info: py311-pybind11-3.0.1 Seamless interoperability between C++11 and Python pybind11-3.0.1 Seamless interoperability between C++11 and Python (cmake part) and ls -l /usr/local/include/pybind11/pybind11.h shows: -rw-r--r-- 1 root wheel 160679 Aug 22 2025 /usr/local/include/pybind11/pybind11.h Uname: FreeBSD xxxx.xx 14.3-STABLE FreeBSD 14.3-STABLE stable/14-n273238-c95f96dea= 30a GENERIC amd64 In /usr/ports, git describe shows: git describe 14.2-eol-19692-gcc704ef2c80e UPDATE: After reading a comment in 281470 about CMake maybe being a problem= , I removed the "cmake part" of pybind11, which *removed* pybind11/pybind11.h.= =20=20 After that the py-scipy port compiled and installed without throwing this e= rror about not being able to find the file. So this is an oddity introduced entirely by the presence of the pybind11 package. py-pybind11 is still needed. There's still something fishy about this port, but that's the workaround. --=20 You are receiving this mail because: You are the assignee for the bug.=