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Latest Conda-forge version of ncvis-climate not linking on MacOS (Mac CPU) #15

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czender opened this issue Feb 15, 2025 · 14 comments
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bug Something isn't working

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@czender
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czender commented Feb 15, 2025

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

Hi @xylar and @mahf708. This issue appears to be due to a slight mismatch between the desired and actual versions (3.2.0.2.3 vs 3.2.0.2.0) of libwx_osx_cocoau_xrc that are installed. My understanding is that Conda-Forge feedstock are supposed to take care of library synchronization across any given Conda installation.

NB: The same behavior occurs from an environment that only includes ncvis-climate, so I'm in a pickle. My reproducer script is

conda --version
conda update --all
conda remove ncvis-climate 
conda install ncvis-climate
which ncvis
ncvis /Users/zender/data/bm/elmv3_r05l15.nc
ls -l /Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc*

the results of which follow:

zender@spectral:~/anaconda/bin$ conda --version
conda 25.1.1
zender@spectral:~/anaconda/bin$ conda update --all
Channels:
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

# All requested packages already installed.

zender@spectral:~/anaconda/bin$ conda remove ncvis-climate 

PackagesNotFoundError: The following packages are missing from the target environment:
  - ncvis-climate

zender@spectral:~/anaconda/bin$ conda install ncvis-climate
Channels:
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/zender/anaconda

  added / updated specs:
    - ncvis-climate

The following NEW packages will be INSTALLED:

  lerc               conda-forge/osx-arm64::lerc-4.0.0-h9a09cb3_0 
  libdeflate         conda-forge/osx-arm64::libdeflate-1.23-hec38601_0 
  libpng             conda-forge/osx-arm64::libpng-1.6.46-h3783ad8_0 
  libtiff            conda-forge/osx-arm64::libtiff-4.7.0-h551f018_3 
  libwebp-base       conda-forge/osx-arm64::libwebp-base-1.5.0-h2471fea_0 
  ncvis-climate      conda-forge/osx-arm64::ncvis-climate-2024.01.26-h0468993_0 
  pcre2              conda-forge/osx-arm64::pcre2-10.44-h297a79d_2 
  wxwidgets          conda-forge/osx-arm64::wxwidgets-3.2.6-h6a86719_1 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
zender@spectral:~/anaconda/bin$ which ncvis
.//ncvis
zender@spectral:~/anaconda/bin$ ncvis /Users/zender/data/bm/elmv3_r05l15.nc
dyld[14285]: Library not loaded: @rpath/libwx_osx_cocoau_xrc-3.2.0.2.3.dylib
  Referenced from: <76C4EB57-0906-3946-AD85-6F87A61B37FA> /Users/zender/anaconda/bin/ncvis
  Reason: tried: '/Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc-3.2.0.2.3.dylib' (no such file), '/Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc-3.2.0.2.3.dylib' (no such file), '/usr/local/lib/libwx_osx_cocoau_xrc-3.2.0.2.3.dylib' (no such file), '/usr/lib/libwx_osx_cocoau_xrc-3.2.0.2.3.dylib' (no such file, not in dyld cache)
Abort trap: 6
zender@spectral:~/anaconda/bin$ ls -l /Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc*
-rwxr-xr-x 2 zender staff 903648 Dec 13 10:24 /Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc-3.2.0.3.0.dylib*
lrwxr-xr-x 1 zender staff     36 Feb  8 15:47 /Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc-3.2.0.dylib -> libwx_osx_cocoau_xrc-3.2.0.3.0.dylib*
lrwxr-xr-x 1 zender staff     36 Feb  8 15:47 /Users/zender/anaconda/bin/../lib/libwx_osx_cocoau_xrc-3.2.dylib -> libwx_osx_cocoau_xrc-3.2.0.3.0.dylib*
zender@spectral:~/anaconda/bin$ 

Any help appreciated,
Charlie

Installed packages

conda list
# packages in environment at /Users/zender/anaconda:
#
# Name                    Version                   Build  Channel
archspec                  0.2.5              pyhd8ed1ab_0    conda-forge
blosc                     1.21.6               h7dd00d9_1    conda-forge
boltons                   24.0.0             pyhd8ed1ab_1    conda-forge
brotli-python             1.1.0           py310hb4ad77e_2    conda-forge
bzip2                     1.0.8                h99b78c6_7    conda-forge
c-ares                    1.34.4               h5505292_0    conda-forge
ca-certificates           2025.1.31            hf0a4a13_0    conda-forge
certifi                   2025.1.31          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py310h497396d_0    conda-forge
charset-normalizer        3.4.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
conda                     25.1.1          py310hbe9552e_0    conda-forge
conda-content-trust       0.2.0              pyhd8ed1ab_0    conda-forge
conda-libmamba-solver     25.1.1             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.4.0              pyh7900ff3_2    conda-forge
conda-package-streaming   0.11.0             pyhd8ed1ab_0    conda-forge
cpp-expected              1.1.0                hffc8910_0    conda-forge
cryptography              44.0.0          py310h69cbf43_1    conda-forge
distro                    1.9.0              pyhd8ed1ab_1    conda-forge
esmf                      8.8.0           mpi_mpich_h5625ee3_100    conda-forge
fmt                       11.0.2               h420ef59_0    conda-forge
frozendict                2.4.6           py310hf9df320_0    conda-forge
gsl                       2.8                  h8d0574d_1    conda-forge
h2                        4.2.0              pyhd8ed1ab_0    conda-forge
hdf4                      4.2.15               h2ee6834_7    conda-forge
hdf5                      1.14.3          mpi_mpich_h13a04de_9    conda-forge
hpack                     4.1.0              pyhd8ed1ab_0    conda-forge
hyperframe                6.1.0              pyhd8ed1ab_0    conda-forge
icu                       75.1                 hfee45f7_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_1    conda-forge
jsonpointer               3.0.0           py310hbe9552e_1    conda-forge
krb5                      1.21.3               h237132a_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libaec                    1.1.3                hebf3989_0    conda-forge
libarchive                3.7.7                h3b16cec_3    conda-forge
libblas                   3.9.0           28_h10e41b3_openblas    conda-forge
libcblas                  3.9.0           28_hb3479ef_openblas    conda-forge
libcurl                   8.11.1               h73640d1_0    conda-forge
libcxx                    19.1.7               ha82da77_0    conda-forge
libdeflate                1.23                 hec38601_0    conda-forge
libedit                   3.1.20250104    pl5321hafb1f1b_0    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libexpat                  2.6.4                h286801f_0    conda-forge
libfabric                 2.0.0                hce30654_1    conda-forge
libfabric1                2.0.0                h5505292_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
libhwloc                  2.11.2          default_hbce5d74_1001    conda-forge
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
liblapack                 3.9.0           28_hc9a63f6_openblas    conda-forge
liblzma                   5.6.4                h39f12f2_0    conda-forge
liblzma-devel             5.6.4                h39f12f2_0    conda-forge
libmamba                  2.0.5                hdf44a08_1    conda-forge
libmambapy                2.0.5           py310h4090bb8_1    conda-forge
libnetcdf                 4.9.2           mpi_mpich_hf75f9b5_14    conda-forge
libnghttp2                1.64.0               h6d7220d_0    conda-forge
libopenblas               0.3.28          openmp_hf332438_1    conda-forge
libpnetcdf                1.13.0          mpi_mpich_h16bb634_101    conda-forge
libpng                    1.6.46               h3783ad8_0    conda-forge
libsolv                   0.7.30               h6c9b7f8_0    conda-forge
libsqlite                 3.48.0               h3f77e49_1    conda-forge
libssh2                   1.11.1               h9cc3647_0    conda-forge
libtiff                   4.7.0                h551f018_3    conda-forge
libudunits2               2.2.28               h5f3f34b_3    conda-forge
libwebp-base              1.5.0                h2471fea_0    conda-forge
libxml2                   2.13.5               h178c5d8_1    conda-forge
libzip                    1.11.2               h1336266_0    conda-forge
libzlib                   1.3.1                h8359307_2    conda-forge
llvm-openmp               19.1.7               hdb05f8b_0    conda-forge
lz4-c                     1.10.0               h286801f_1    conda-forge
lzo                       2.10              h93a5062_1001    conda-forge
menuinst                  2.2.0           py310hbe9552e_0    conda-forge
mpi                       1.0.1                     mpich    conda-forge
mpich                     4.3.0              h9d9a6ae_100    conda-forge
ncurses                   6.5                  h5e97a16_3    conda-forge
ncvis                     1.5.13          py310h3343dac_2    conda-forge
ncvis-climate             2024.01.26           h0468993_0    conda-forge
netcdf-fortran            4.6.1           mpi_mpich_he94a790_8    conda-forge
nlohmann_json             3.11.3               h00cdb27_1    conda-forge
numpy                     1.26.4          py310hd45542a_0    conda-forge
openssl                   3.4.1                h81ee809_0    conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
parallelio                2.6.3           mpi_mpich_h24e929f_100    conda-forge
pcre2                     10.44                h297a79d_2    conda-forge
pip                       25.0               pyh8b19718_0    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_1    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_1    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h078409c_2    conda-forge
pycparser                 2.22               pyh29332c3_1    conda-forge
pysocks                   1.7.1              pyha55dd90_7    conda-forge
python                    3.10.14         h2469fbe_0_cpython    conda-forge
python.app                1.4             py310hb845c5c_4    conda-forge
python_abi                3.10                    5_cp310    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
reproc                    14.2.5.post0         h5505292_0    conda-forge
reproc-cpp                14.2.5.post0         h286801f_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_1    conda-forge
ruamel.yaml               0.18.10         py310h078409c_0    conda-forge
ruamel.yaml.clib          0.2.8           py310hf9df320_1    conda-forge
scipy                     1.15.1          py310hd50a768_0    conda-forge
setuptools                75.8.0             pyhff2d567_0    conda-forge
simdjson                  3.11.6               ha393de7_0    conda-forge
snappy                    1.2.1                h98b9ce2_1    conda-forge
spdlog                    1.15.1               hed1c2b2_0    conda-forge
tempest-remap             2.2.0                hf3c615f_5    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tqdm                      4.67.1             pyhd8ed1ab_1    conda-forge
truststore                0.10.1             pyh29332c3_0    conda-forge
tzdata                    2025a                h78e105d_0    conda-forge
urllib3                   2.3.0              pyhd8ed1ab_0    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
wxwidgets                 3.2.6                h6a86719_1    conda-forge
xz                        5.6.4                h9a6d368_0    conda-forge
xz-gpl-tools              5.6.4                h9a6d368_0    conda-forge
xz-tools                  5.6.4                h39f12f2_0    conda-forge
yaml-cpp                  0.8.0                h13dd4ca_0    conda-forge
zlib                      1.3.1                h8359307_2    conda-forge
zstandard                 0.23.0          py310h2665a74_1    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

Environment info

active environment : None
            shell level : 0
       user config file : /Users/zender/.condarc
 populated config files : /Users/zender/.condarc
          conda version : 25.1.1
    conda-build version : not installed
         python version : 3.10.14.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=m1
                          __conda=25.1.1=0
                          __osx=15.3=0
                          __unix=0=0
       base environment : /Users/zender/anaconda  (writable)
      conda av data dir : /Users/zender/anaconda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/zender/anaconda/pkgs
                          /Users/zender/.conda/pkgs
       envs directories : /Users/zender/anaconda/envs
                          /Users/zender/.conda/envs
               platform : osx-arm64
             user-agent : conda/25.1.1 requests/2.32.3 CPython/3.10.14 Darwin/24.3.0 OSX/15.3 solver/libmamba conda-libmamba-solver/25.1.1 libmambapy/2.0.5
                UID:GID : 501:20
             netrc file : /Users/zender/.netrc
           offline mode : False
@czender czender added the bug Something isn't working label Feb 15, 2025
@xylar
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xylar commented Feb 15, 2025

@czender and @mahf708, I would suspect this is a problem with wxwidgets dependency and not with ncvis-climate itself. I have no experience with that package so I'm not sure how much help I'll be here.

@xylar
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xylar commented Feb 15, 2025

@mahf708, is this something you have the bandwidth to look into? It seems like maybe the run_exports are just too loose on this package:
https://github.com/conda-forge/wxwidgets-feedstock/blob/main/recipe/meta.yaml#L21

@mahf708
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mahf708 commented Feb 16, 2025

@czender install anything before wxwidgets 3.2.6 resolves the issues (so try conda install 'wxwidgets<3.2.6')

@xylar that's a good suggestion; it's clearly the issue at play, though I would need to defer to the wxwidgets feestock maintainers

@hmaarrfk: any thoughts on this appreciated; if not objections, I will be happy to issue a PR and get this sorted.

@mahf708
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mahf708 commented Feb 16, 2025

To be verbose, I think the solution would entail making wxwidgets a conda-forge-globally tracked pin on the patch version; this may have annoying consequence and may be undesirable, especially this could be a small bug that went undetected.

Either way, we will need to issue some patch in admin-requests to get things to fix things for current builds. I will take care of this second point once we get clarity about what we want to do.

@mahf708
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mahf708 commented Feb 16, 2025

@hmaarrfk
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@hmaarrfk: any thoughts on this appreciated; if not objections, I will be happy to issue a PR and get this sorted.

happy to get help with wxwidgets

However, they claim it is ABI compatible... https://www.wxwidgets.org/news/2024/09/wxwidgets-3.2.6-released/

maybe it is something I broke?

@mahf708
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mahf708 commented Feb 16, 2025

Interesting they claim that.

If you look at wxWidgets/wxWidgets@v3.2.5...v3.2.6 and find the Makefile.in file, do you think that keeps it ABI compatible? Quoted below for brevity:

From d7f6a7e8d2522e740af0899418c22af19fdb4aeb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Va=CC=81clav=20Slavi=CC=81k?= <vaclav@slavik.io>
Date: Sat, 10 Feb 2024 11:46:13 +0100
Subject: [PATCH 38/73] Fix AddAvailableCatalog() API

Knowing msgIdLanguage is necessary for correct evaluation of preferred
languages order; without it, it would be possible to load undesirable
translation file.

See 2af36e9560c694a750b6aa835d32d12a0393fb83 for details.
---
 Makefile.in                 |  6 +++---
 build/bakefiles/version.bkl |  6 +++---
 include/wx/translation.h    | 12 ++++++++++++
 interface/wx/translation.h  | 15 +++++++++++++--
 src/common/translation.cpp  | 31 ++++++++++++++++---------------
 version-script.in           |  7 +++++++
 6 files changed, 54 insertions(+), 23 deletions(-)

diff --git a/Makefile.in b/Makefile.in
index d6c26128855e..86948bf57673 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -2215,7 +2215,7 @@ LOCALE_LINGUAS = ca cs da de el es fi fr hu id it ja nl pl ru sl sv tr uk zh zh_
 @COND_DEPS_TRACKING_1@CXXC = $(BK_DEPS) $(CXX)
 @COND_USE_PLUGINS_0@PLUGIN_ADV_EXTRALIBS = $(EXTRALIBS_SDL)
 @COND_PLATFORM_MACOSX_1@WXMACVERSION_CMD = \
-@COND_PLATFORM_MACOSX_1@	-compatibility_version 3.0 -current_version 3.4
+@COND_PLATFORM_MACOSX_1@	-compatibility_version 4.0 -current_version 4.0
 @COND_USE_GUI_0@PORTNAME = base
 @COND_USE_GUI_1@PORTNAME = $(TOOLKIT_LOWERCASE)$(TOOLKIT_VERSION)
 @COND_TOOLKIT_MAC@WXBASEPORT = _carbon
@@ -13977,9 +13977,9 @@ COND_MONOLITHIC_0_SHARED_1_USE_GUI_1_USE_HTML_1___htmldll_library_link_LIBR_0 \
 @COND_USE_SOVERSION_0@dll___targetsuf2 = .$(SO_SUFFIX)
 @COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@dll___targetsuf3 \
 @COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@	= \
-@COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@	.$(SO_SUFFIX).0.2.4
+@COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@	.$(SO_SUFFIX).0.3.0
 @COND_PLATFORM_MACOSX_1_USE_SOVERSION_1@dll___targetsuf3 \
-@COND_PLATFORM_MACOSX_1_USE_SOVERSION_1@	= .0.2.4.$(SO_SUFFIX)
+@COND_PLATFORM_MACOSX_1_USE_SOVERSION_1@	= .0.3.0.$(SO_SUFFIX)
 @COND_USE_SOVERCYGWIN_1_USE_SOVERSION_1@dll___targetsuf3 = -0.$(SO_SUFFIX)
 @COND_USE_SOVERSION_0@dll___targetsuf3 = .$(SO_SUFFIX)
 @COND_USE_SOVERSION_1_USE_SOVERSOLARIS_1@dll___targetsuf3 = .$(SO_SUFFIX).0
diff --git a/Makefile.in b/Makefile.in
index 93fbb2328d86..d6c26128855e 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -82,7 +82,7 @@ wxCFLAGS_C99 = @wxCFLAGS_C99@
 DESTDIR = 
 WX_RELEASE = 3.2
 WX_RELEASE_NODOT = 32
-WX_VERSION = $(WX_RELEASE).5
+WX_VERSION = $(WX_RELEASE).6
 LIBDIRNAME = $(wx_top_builddir)/lib
 WXREGEX_CFLAGS = $(WX_CPPFLAGS) -DNDEBUG \
 	-I$(wx_top_builddir)/3rdparty/pcre/src -D__WX__ -DHAVE_CONFIG_H \
@@ -2215,7 +2215,7 @@ LOCALE_LINGUAS = ca cs da de el es fi fr hu id it ja nl pl ru sl sv tr uk zh zh_
 @COND_DEPS_TRACKING_1@CXXC = $(BK_DEPS) $(CXX)
 @COND_USE_PLUGINS_0@PLUGIN_ADV_EXTRALIBS = $(EXTRALIBS_SDL)
 @COND_PLATFORM_MACOSX_1@WXMACVERSION_CMD = \
-@COND_PLATFORM_MACOSX_1@	-compatibility_version 3.0 -current_version 3.3
+@COND_PLATFORM_MACOSX_1@	-compatibility_version 3.0 -current_version 3.4
 @COND_USE_GUI_0@PORTNAME = base
 @COND_USE_GUI_1@PORTNAME = $(TOOLKIT_LOWERCASE)$(TOOLKIT_VERSION)
 @COND_TOOLKIT_MAC@WXBASEPORT = _carbon
@@ -13977,9 +13977,9 @@ COND_MONOLITHIC_0_SHARED_1_USE_GUI_1_USE_HTML_1___htmldll_library_link_LIBR_0 \
 @COND_USE_SOVERSION_0@dll___targetsuf2 = .$(SO_SUFFIX)
 @COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@dll___targetsuf3 \
 @COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@	= \
-@COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@	.$(SO_SUFFIX).0.2.3
+@COND_PLATFORM_MACOSX_0_USE_SOVERCYGWIN_0_USE_SOVERSION_1@	.$(SO_SUFFIX).0.2.4
 @COND_PLATFORM_MACOSX_1_USE_SOVERSION_1@dll___targetsuf3 \
-@COND_PLATFORM_MACOSX_1_USE_SOVERSION_1@	= .0.2.3.$(SO_SUFFIX)
+@COND_PLATFORM_MACOSX_1_USE_SOVERSION_1@	= .0.2.4.$(SO_SUFFIX)
 @COND_USE_SOVERCYGWIN_1_USE_SOVERSION_1@dll___targetsuf3 = -0.$(SO_SUFFIX)
 @COND_USE_SOVERSION_0@dll___targetsuf3 = .$(SO_SUFFIX)
 @COND_USE_SOVERSION_1_USE_SOVERSOLARIS_1@dll___targetsuf3 = .$(SO_SUFFIX).0

@hmaarrfk
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This is enough research for me to know the pr you would make is well thought out.

@czender
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czender commented Feb 16, 2025

Using conda install 'wxwidgets<3.2.6' works for me.

Thanks @xylar and @mahf708!

@mahf708
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mahf708 commented Feb 16, 2025

Using conda install 'wxwidgets<3.2.6' works for me.

Thanks @xylar and @mahf708!

happy to help, @czender; we will clean this up more systematically once we figure out a clean solution for the overall conda-forge ecosystem.

This is enough research for me to know the pr you would make is well thought out.

Let me investigate a little more; file an issue upstream; and then I will issue a PR with a reasonable solution. Thanks for your help and patience :)

@xylar
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xylar commented Feb 16, 2025

Thanks for jumping on this @mahf708, especially because I know you're not feeling great.

@mahf708
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mahf708 commented Feb 19, 2025

This is now resolved.

@mahf708 mahf708 closed this as completed Feb 19, 2025
@xylar
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xylar commented Feb 19, 2025

"now resolved", rather than "not resolved"?

@mahf708
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mahf708 commented Feb 19, 2025

Yes sorry. It is RESOLVED now. Resolution involved a few steps:

now hopefully everything should be fixed and no need for any workarounds.

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