Created attachment 220299 [details] numpy1194.patch The version of numpy currently in ports doesn't work with python 3.9, here's an update that does. --- notes --- The `${REINPLACE_CMD} -e '\|_examples/$$|d' ${_PYTHONPKGLIST}` line prevents the automatic plist from distutils from including a directory, which would crash pkg, see https://github.com/freebsd/pkg/issues/1911 / https://github.com/freebsd/pkg/pull/1912 The big chunk of files/patch-numpy-distutils-system_info.py that doesn't apply anymore has been removed — I don't think any change like that is necessary now? I have tried both openblas and atlas, make test does run tests with both.
Thanks Greg, AFAIK, NumPy >= 1.19.0 is python 3 only and you should add USES= python:3.6+ instead of USES= python
(In reply to Loïc Bartoletti from comment #1) And if it's the case, all ports depending on it have to be changed to python:3.6+ too
Created attachment 220988 [details] Numpy 1.9.0 and bump dependent ports
You're right, I updated all the ports. A note for math/plot, I tested this port with python:3.6+ and it compiles by adapting the plist. Can you run an exp-run, please? Thanks
More ports that need to be adjusted: [00:01:53] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package vera++-1.3.0_14 from devel/vera++ -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:01:55] Error: compute_deps_pkg failed to lookup pkgname for math/py-matplotlib2@py27 processing package vtk6-6.2.0_13 from math/vtk6 -- Is SUBDIR+=py-matplotlib2@py27 missing in math/Makefile and does the port provide the 'py27' FLAVOR? [00:01:56] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-kaa-base-0.6.0_12 from multimedia/py-kaa-base -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:01:56] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-kaa-base-0.6.0_12 [00:01:56] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package ceph12-12.2.12_2 from net/ceph12 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-tagpy-2013.1_21 from audio/py-tagpy@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:01] Error: compute_deps_pkg failed to lookup pkgname for math/py-pandas@py27 processing package py27-pandas-charm-0.3.0_1 from biology/py-pandas-charm@py27 -- Is SUBDIR+=py-pandas@py27 missing in math/Makefile and does the port provide the 'py27' FLAVOR? [00:02:01] Error: compute_deps_pkg failed to lookup existing pkgname for math/py-pandas@py27 processing package py27-pandas-charm-0.3.0_1 [00:02:01] Error: compute_deps_pkg failed to lookup pkgname for cad/py-gdspy@py27 processing package py27-phidl-1.0.1_1 from cad/py-phidl@py27 -- Is SUBDIR+=py-gdspy@py27 missing in cad/Makefile and does the port provide the 'py27' FLAVOR? [00:02:01] Error: compute_deps_pkg failed to lookup existing pkgname for cad/py-gdspy@py27 processing package py27-phidl-1.0.1_1 [00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-YouCompleteMe-g20191130_1 from devel/youcompleteme@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-hypatia_engine-0.3.1_4 from games/hypatia_engine@py27 -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:01] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-hypatia_engine-0.3.1_4 [00:02:01] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-pyspacewar-1.1.1_1 from games/pyspacewar@py27 -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-pyspacewar-1.1.1_1 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for graphics/py-gdal@py27 processing package py27-Fiona-1.8.18 from graphics/py-fiona@py27 -- Is SUBDIR+=py-gdal@py27 missing in graphics/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for graphics/py-gdal@py27 processing package py27-Fiona-1.8.18 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/py-game@py27 processing package py27-pyganim-0.9.2_3 from graphics/py-pyganim@py27 -- Is SUBDIR+=py-game@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-game@py27 processing package py27-pyganim-0.9.2_3 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-piranha-0.11_7 from math/py-piranha@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for math/py-pandas@py27 processing package py27-pandas-datareader-0.8.1 from math/py-pandas-datareader@py27 -- Is SUBDIR+=py-pandas@py27 missing in math/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for math/py-pandas@py27 processing package py27-pandas-datareader-0.8.1 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for misc/py-onnx@py27 processing package py27-onnx-tf-1.6.0 from misc/py-onnx-tf@py27 -- Is SUBDIR+=py-onnx@py27 missing in misc/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for misc/py-onnx@py27 processing package py27-onnx-tf-1.6.0 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/py-flatbuffers@py27 processing package py27-tflite-2.3.0 from misc/py-tflite@py27 -- Is SUBDIR+=py-flatbuffers@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for devel/py-flatbuffers@py27 processing package py27-tflite-2.3.0 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-libtorrent-rasterbar-1.2.10 from net-p2p/py-libtorrent-rasterbar@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for science/py-netCDF4@py27 processing package py27-netcdf-flattener-1.2.0 from science/py-netcdf-flattener@py27 -- Is SUBDIR+=py-netCDF4@py27 missing in science/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for science/py-netCDF4@py27 processing package py27-netcdf-flattener-1.2.0 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for devel/boost-python-libs@py27 processing package py27-dlib-19.21 from science/py-dlib@py27 -- Is SUBDIR+=boost-python-libs@py27 missing in devel/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-dsl-6.4.0_1 from textproc/py-elasticsearch-dsl@py27 -- Is SUBDIR+=py-elasticsearch6@py27 missing in textproc/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-dsl-6.4.0_1 [00:02:02] Error: compute_deps_pkg failed to lookup pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-curator-5.6.0_1 from textproc/py-elasticsearch-curator@py27 -- Is SUBDIR+=py-elasticsearch6@py27 missing in textproc/Makefile and does the port provide the 'py27' FLAVOR? [00:02:02] Error: compute_deps_pkg failed to lookup existing pkgname for textproc/py-elasticsearch6@py27 processing package py27-elasticsearch-curator-5.6.0_1
Created attachment 221265 [details] numpy 1.9 and dependent ports v2 Here is the updated version which includes the latest python commits.
Some new failure logs: http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2021-01-04_17h31m54s/logs/py37-pandas-0.24.2_2,1.log http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2021-01-04_17h31m54s/logs/orange3-3.19.0_5.log
(In reply to Antoine Brodin from comment #7) Regarding the log file for py-pandas: There is a bug #251412 with an update for py-pandas from 0.24.2 to 1.15.0, ready to commit ;) Maybe the error with the undeclared identifier 'NUMPY_IMPORT_ARRAY_RETVAL' does not occur with this version of py-pandas (untested)?
(In reply to Rainer Hurling from comment #8) I tried your patch of py-pandas and it built fine with numpy 1.9, please commit it :)
Created attachment 223412 [details] py-numpy 1.19.4 v4 - update numpy to 1.19.4 - While here replace `${PYTHON_PKGNAMEPREFIX}numpy.*:math/py-numpy@${PY_FLAVOR}` by `${PYNUMPY}` - replace `USES=python:3.[4-5]` by `USES=python:3.6` - bump portrevision - replace range version in `Mk/Uses/python.mk` (workaround for https://github.com/freebsd/pkg/pull/1944)
Something is wrong, all ports depending on numpy are failing Installing py37-numpy-1.19.4... the most recent version of py37-numpy-1.19.4 is already installed ===> py37-metpy-1.0 depends on package: py37-numpy>=1.16.0,1 - not found
Created attachment 223519 [details] py-numpy 1.19.4 v5 antoine@ koobs@ The problem seems related to https://github.com/freebsd/pkg/pull/1944 I fix it removing portepoch (,1) in the version of numpy requirements. Tested against matplotlib on updated poudriere and cleaned packages.
You can remove PORTEPOCH=1 from math/py-numpy/Makefile , you have to add it back
Please consider updating to a newer release. openblas-0.3.13 does have a much larger memory footprint which causes numpy to segfault on import (virtual memory is limited per user in our environment) A more recent release of numpy fixes this by setting the BUFFERSIZE back to 20. Also see: https://github.com/numpy/numpy/pull/17924 https://github.com/xianyi/OpenBLAS/issues/3180 https://github.com/xianyi/OpenBLAS/issues/2970