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CI checks fail on macOS due to conda installation error #28

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milanmlft opened this issue May 10, 2024 · 0 comments
Open

CI checks fail on macOS due to conda installation error #28

milanmlft opened this issue May 10, 2024 · 0 comments

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@milanmlft
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The current GHA checks are failing with the following error:

> test_check("jupytextR")
PREFIX=/Users/runner/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0
Unpacking payload ...
dyld[6803]: Library not loaded: @rpath/libz.1.dylib
  Referenced from: <E7AE95EE-B2D0-362A-A48A-6164032BED64> /Users/runner/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0/conda.exe
  Reason: tried: '/Users/runner/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0/../../../../../libz.1.dylib' (no such file), '/Users/runner/Library/Caches/org.R-project.R/R/basilisk/1.16.0/0/../../../../../libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.3-9.0/arm64/Contents/Home//lib/server/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.3-9.0/arm64/Contents/Home//lib/server/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.3-9.0/arm64/Contents/Home//lib/server/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.3-9.0/arm64/Contents/Home//lib/server/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.3-9.0/arm64/Contents/Home//lib/server/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.3-9.0/arm64/Contents/Home//lib/server/libz.1.dylib' (no such file)
/Users/runner/Library/Caches/org.R-project.R/R/basilisk/Miniconda3-py39_4.12.0-MacOSX-arm64.sh: line 410:  6802 Exit 141                { dd if="$THIS_PATH" bs=1 skip=12215086 count=7378 2> /dev/null; dd if="$THIS_PATH" bs=16384 skip=746 count=2592 2> /dev/null; dd if="$THIS_PATH" bs=1 skip=54689792 count=8120 2> /dev/null; }

This does not happen locally though. Possibly related to ContinuumIO/anaconda-issues#11184
Bioconductor/basilisk#16 might also be related

Will disable the workflow for macOS for now in #17, but should probably dig further into this to find a proper fix.

milanmlft added a commit that referenced this issue May 10, 2024
milanmlft added a commit that referenced this issue May 10, 2024
* Another attempt to fix macos CI

* Need basilisk as well

* Is this problem Arm specific?

* Try setting the `BASILISK_USE_SYSTEM_DIR` envvar

* Only run actions on most recent push

* Set `BASILISK_USE_SYSTEM_DIR` envvar for all steps

* Install basilisk from source

* Does this work?

See conda/conda#7113

* Install basilisk after other R depencencies

* Only do this on macOS

* Update roxygen version

* Fix typo

* Build ignore more files

* Manually trigger basilisk env configuration

* Don't use system dir for basilisk?

* Invalidate dependencies cache and move basilisk installation up a step

* Revert non-working fixes

* Disable macOS workflow

See #28
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