[BUG] Issues with installing and using Plots due to GR. Possibly related to #5047

[ajinkya-k]

Details

when installing Plots I got a wall of text, the main issue being the folliwing error (which may be related to #5047 )

│  ┌ Error: import GR_jll failed.
│  │ Consider using `GR.GRPreferences.use_jll_binary()` or
│  │ `GR.GRPreferences.use_upstream_binary()` to repair.
│  │ Importing GR a second time will allow use of these functions.
│  └ @ GR.GRPreferences ~/.julia/packages/GR/WSEqS/src/preferences.jl:8

full output

Info Given Plots was explicitly requested, output will be shown live
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
  ✓ Requires
  ✓ FFMPEG_jll
  ? FFMPEG
  ? GR_jll
  ? GR
  ? Plots
  ? Plots → UnitfulExt
  5 dependencies successfully precompiled in 9 seconds. 177 already precompiled.
  2 dependencies precompiled but different versions are currently loaded. Restart julia to access the new versions. Otherwise, loading dependents of these packages may trigger further precompilation to work with the unexpected versions.
  5 dependencies failed but may be precompilable after restarting julia
  5 dependencies had output during precompilation:
┌ FFMPEG
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ Plots
│  [Output was shown above]
└
┌ GR
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
│  ┌ Error: import GR_jll failed.
│  │ Consider using `GR.GRPreferences.use_jll_binary()` or
│  │ `GR.GRPreferences.use_upstream_binary()` to repair.
│  │ Importing GR a second time will allow use of these functions.
│  └ @ GR.GRPreferences ~/.julia/packages/GR/WSEqS/src/preferences.jl:8
└
┌ Plots → UnitfulExt
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ GR_jll
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
[ Info: Precompiling Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Info: Skipping precompilation due to precompilable error. Importing Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Precompiling TimeZonesRecipesBaseExt...
  1 dependency successfully precompiled in 1 seconds. 27 already precompiled.
Precompiling FFMPEG...
Info Given FFMPEG was explicitly requested, output will be shown live
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
  ? FFMPEG
[ Info: Precompiling FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Info: Skipping precompilation due to precompilable error. Importing FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Precompiling GR...
Info Given GR was explicitly requested, output will be shown live
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Error: import GR_jll failed.
│ Consider using `GR.GRPreferences.use_jll_binary()` or
│ `GR.GRPreferences.use_upstream_binary()` to repair.
│ Importing GR a second time will allow use of these functions.
└ @ GR.GRPreferences ~/.julia/packages/GR/WSEqS/src/preferences.jl:8
  ? GR_jll
  ? GR
[ Info: Precompiling GR [28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Error: import GR_jll failed.
│ Consider using `GR.GRPreferences.use_jll_binary()` or
│ `GR.GRPreferences.use_upstream_binary()` to repair.
│ Importing GR a second time will allow use of these functions.
└ @ GR.GRPreferences ~/.julia/packages/GR/WSEqS/src/preferences.jl:8
┌ Info: Skipping precompilation due to precompilable error. Importing GR [28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Precompiling GR_jll...
Info Given GR_jll was explicitly requested, output will be shown live
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
  ? GR_jll
[ Info: Precompiling GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Info: Skipping precompilation due to precompilable error. Importing GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Precompiling FileIOExt...
Info Given FileIOExt was explicitly requested, output will be shown live
└ @ Base loading.jl:2541
│ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
  ? FFMPEG
  ? GR_jll
  ? GR
  ? Plots
  ? Plots → UnitfulExt
  ? Plots → FileIOExt
  1 dependency successfully precompiled in 4 seconds. 183 already precompiled.
  4 dependencies precompiled but different versions are currently loaded. Restart julia to access the new versions. Otherwise, loading dependents of these packages may trigger further precompilation to work with the unexpected versions.
  6 dependencies failed but may be precompilable after restarting julia
  6 dependencies had output during precompilation:
┌ FFMPEG
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ Plots → FileIOExt
│  [Output was shown above]
└
┌ Plots
│  ┌ Warning: Module FFMPEG with build ID ffffffff-ffff-ffff-0003-11306eff3ca8 is missing from the cache.
│  │ This may mean FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ GR
│  ┌ Warning: Module GR_jll with build ID ffffffff-ffff-ffff-0003-11316c241a14 is missing from the cache.
│  │ This may mean GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
│  ┌ Error: import GR_jll failed.
│  │ Consider using `GR.GRPreferences.use_jll_binary()` or
│  │ `GR.GRPreferences.use_upstream_binary()` to repair.
│  │ Importing GR a second time will allow use of these functions.
│  └ @ GR.GRPreferences ~/.julia/packages/GR/WSEqS/src/preferences.jl:8
└
┌ Plots → UnitfulExt
│  ┌ Warning: Module Plots with build ID ffffffff-ffff-ffff-0003-112f880fcdc7 is missing from the cache.
│  │ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ GR_jll
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
[ Info: Precompiling FileIOExt [f5f51d8f-5827-5d2e-939b-192fcd6ec70c] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module Plots with build ID ffffffff-ffff-ffff-0003-112f880fcdc7 is missing from the cache.
│ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Info: Skipping precompilation due to precompilable error. Importing FileIOExt [f5f51d8f-5827-5d2e-939b-192fcd6ec70c].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Precompiling UnitfulExt...
Info Given UnitfulExt was explicitly requested, output will be shown live
┌ Warning: Module Plots with build ID ffffffff-ffff-ffff-0003-112f880fcdc7 is missing from the cache.
│ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
  ✓ StaticArrays
  ? FFMPEG
  ? GR_jll
  ? GR
  ? Plots
  ✓ StaticArrays → StaticArraysStatisticsExt
  ? Plots → UnitfulExt
  2 dependencies successfully precompiled in 4 seconds. 187 already precompiled.
  6 dependencies precompiled but different versions are currently loaded. Restart julia to access the new versions. Otherwise, loading dependents of these packages may trigger further precompilation to work with the unexpected versions.
  5 dependencies failed but may be precompilable after restarting julia
  5 dependencies had output during precompilation:
┌ FFMPEG
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ Plots
│  ┌ Warning: Module FFMPEG with build ID ffffffff-ffff-ffff-0003-11306eff3ca8 is missing from the cache.
│  │ This may mean FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
┌ GR
│  ┌ Warning: Module GR_jll with build ID ffffffff-ffff-ffff-0003-11316c241a14 is missing from the cache.
│  │ This may mean GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
│  ┌ Error: import GR_jll failed.
│  │ Consider using `GR.GRPreferences.use_jll_binary()` or
│  │ `GR.GRPreferences.use_upstream_binary()` to repair.
│  │ Importing GR a second time will allow use of these functions.
│  └ @ GR.GRPreferences ~/.julia/packages/GR/WSEqS/src/preferences.jl:8
└
┌ Plots → UnitfulExt
│  [Output was shown above]
└
┌ GR_jll
│  ┌ Warning: Module FFMPEG_jll with build ID fafbfcfd-f69b-fa55-0003-0eab47c5c27f is missing from the cache.
│  │ This may mean FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:2541
└
[ Info: Precompiling UnitfulExt [0e51ec96-f580-5f12-a625-1297083d7970] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module Plots with build ID ffffffff-ffff-ffff-0003-112f880fcdc7 is missing from the cache.
│ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Info: Skipping precompilation due to precompilable error. Importing UnitfulExt [0e51ec96-f580-5f12-a625-1297083d7970].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
Precompiling DataFramesExt...
  1 dependency successfully precompiled in 1 seconds. 37 already precompiled.
Precompiling GeometryBasicsExt...
Info Given GeometryBasicsExt was explicitly requested, output will be shown live
┌ Warning: Module Plots with build ID ffffffff-ffff-ffff-0003-112f880fcdc7 is missing from the cache.
│ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
  ? FFMPEG
  ? GR_jll
  ? GR
  ? Plots
  ? Plots → UnitfulExt
  ? Plots → GeometryBasicsExt
[ Info: Precompiling GeometryBasicsExt [b238bd29-021f-5edc-8b0e-16b9cda5f63a] (cache misses: wrong dep version loaded (4), incompatible header (4))
┌ Warning: Module Plots with build ID ffffffff-ffff-ffff-0003-112f880fcdc7 is missing from the cache.
│ This may mean Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2541
┌ Info: Skipping precompilation due to precompilable error. Importing GeometryBasicsExt [b238bd29-021f-5edc-8b0e-16b9cda5f63a].
└   exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
WARNING: using Plots.spy in module Main conflicts with an existing identifier.

julia> GR.GRPreferences.use_upstream_binary()
[ Info: Found existing GR run-time in /Users/ajinkya/.julia/artifacts/9ada70096e6dad3b5cfcb8d97f9aeaef17b5a941
┌ Info: grdir
└   grdir = "/Users/ajinkya/.julia/artifacts/9ada70096e6dad3b5cfcb8d97f9aeaef17b5a941"
[ Info: Please restart Julia to change the GR binary configuration.

Following a suggestion in the output I ran GR.GRPreferences.use_upstream_binary() and restarted. Then I tried to plot something, which triggered a macos error report and julia crashed with this:

julia> spy(sparse(diagm(rand(10))))
julia(33242,0x1f53e0840) malloc: *** error for object 0x100000001: pointer being realloc'd was not allocated
julia(33242,0x1f53e0840) malloc: *** set a breakpoint in malloc_error_break to debug

[33242] signal 6: Abort trap: 6
in expression starting at none:0
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 11737559 (Pool: 11736895; Big: 664); GC: 19

Backends

Backend	yes	no	untested
gr (default)	x
pythonplot			x
plotlyjs			x
pgfplotsx			x
unicodeplots			x
inspectdr			x
gaston			x

Versions

Plots.jl version: 1.40.9

(blk-chol-test) pkg> st Plots
Status `~/projects/julia_repos/blk-chol-test/Project.toml`
  [91a5bcdd] Plots v1.40.9

Backend version (]st -m <backend(s)>):

(blk-chol-test) pkg> st -m GR
Status `~/projects/julia_repos/blk-chol-test/Manifest.toml`
  [28b8d3ca] GR v0.73.13

Output of versioninfo():

Julia Version 1.11.3
Commit d63adeda50d (2025-01-21 19:42 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin24.0.0)
  CPU: 11 × Apple M3 Pro
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m2)
Threads: 1 default, 0 interactive, 1 GC (on 5 virtual cores)