Errors with `GR_jll` loading `Libtiff_jll`: `tibtiff.so not found`

[MasonProtter]

I'm having trouble adding GR and some other packages and I've tracked it down (I think?) to GR_jll loading Libtiff_jll. Here's what I see in a fresh session after nuking my .julia/artifacts and .julia/compiled folders:

❯ julia --startup=no -q

(@v1.10) pkg> activate --temp
  Activating new project at `/tmp/jl_z6RYrd`

(jl_z6RYrd) pkg> add GR_jll
   Resolving package versions...
    Updating `/tmp/jl_z6RYrd/Project.toml`
  [d2c73de3] + GR_jll v0.73.3+0
    Updating `/tmp/jl_z6RYrd/Manifest.toml`
  [692b3bcd] + JLLWrappers v1.5.0
  [21216c6a] + Preferences v1.4.3
  [6e34b625] + Bzip2_jll v1.0.8+1
  [83423d85] + Cairo_jll v1.18.0+1
  [2702e6a9] + EpollShim_jll v0.0.20230411+0
  [2e619515] + Expat_jll v2.6.2+0
  [b22a6f82] + FFMPEG_jll v6.1.1+0
  [a3f928ae] + Fontconfig_jll v2.13.93+0
  [d7e528f0] + FreeType2_jll v2.13.1+0
  [559328eb] + FriBidi_jll v1.0.10+0
  [0656b61e] + GLFW_jll v3.3.9+0
  [d2c73de3] + GR_jll v0.73.3+0
  [78b55507] + Gettext_jll v0.21.0+0
  [7746bdde] + Glib_jll v2.80.0+0
  [3b182d85] + Graphite2_jll v1.3.14+0
  [2e76f6c2] + HarfBuzz_jll v2.8.1+1
  [aacddb02] + JpegTurbo_jll v3.0.2+0
  [c1c5ebd0] + LAME_jll v3.100.1+0
  [88015f11] + LERC_jll v4.0.0+0
  [1d63c593] + LLVMOpenMP_jll v15.0.7+0
  [dd4b983a] + LZO_jll v2.10.1+0
⌅ [e9f186c6] + Libffi_jll v3.2.2+1
  [d4300ac3] + Libgcrypt_jll v1.8.11+0
  [7e76a0d4] + Libglvnd_jll v1.6.0+0
  [7add5ba3] + Libgpg_error_jll v1.42.0+0
  [94ce4f54] + Libiconv_jll v1.17.0+0
  [4b2f31a3] + Libmount_jll v2.40.0+0
⌅ [89763e89] + Libtiff_jll v4.5.1+1
  [38a345b3] + Libuuid_jll v2.40.0+0
  [e7412a2a] + Ogg_jll v1.3.5+1
  [458c3c95] + OpenSSL_jll v3.0.13+1
  [91d4177d] + Opus_jll v1.3.2+0
  [30392449] + Pixman_jll v0.42.2+0
  [c0090381] + Qt6Base_jll v6.5.3+1
  [a44049a8] + Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] + Wayland_jll v1.21.0+1
  [2381bf8a] + Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] + XML2_jll v2.12.6+0
  [aed1982a] + XSLT_jll v1.1.34+0
  [ffd25f8a] + XZ_jll v5.4.6+0
  [f67eecfb] + Xorg_libICE_jll v1.0.10+1
  [c834827a] + Xorg_libSM_jll v1.2.3+0
  [4f6342f7] + Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] + Xorg_libXau_jll v1.0.11+0
  [935fb764] + Xorg_libXcursor_jll v1.2.0+4
  [a3789734] + Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] + Xorg_libXext_jll v1.3.4+4
  [d091e8ba] + Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] + Xorg_libXi_jll v1.7.10+4
  [d1454406] + Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] + Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] + Xorg_libXrender_jll v0.9.10+4
  [14d82f49] + Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] + Xorg_libxcb_jll v1.15.0+0
  [cc61e674] + Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] + Xorg_xcb_util_cursor_jll v0.1.4+0
  [12413925] + Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] + Xorg_xcb_util_jll v0.4.0+1
  [975044d2] + Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] + Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] + Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] + Xorg_xkbcomp_jll v1.4.6+0
  [33bec58e] + Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] + Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] + Zstd_jll v1.5.6+0
  [35ca27e7] + eudev_jll v3.2.9+0
  [1a1c6b14] + gperf_jll v3.1.1+0
  [a4ae2306] + libaom_jll v3.4.0+0
  [0ac62f75] + libass_jll v0.15.1+0
  [2db6ffa8] + libevdev_jll v1.11.0+0
  [f638f0a6] + libfdk_aac_jll v2.0.2+0
  [36db933b] + libinput_jll v1.18.0+0
  [b53b4c65] + libpng_jll v1.6.43+1
  [f27f6e37] + libvorbis_jll v1.3.7+1
  [009596ad] + mtdev_jll v1.1.6+0
  [1270edf5] + x264_jll v2021.5.5+0
  [dfaa095f] + x265_jll v3.5.0+0
  [d8fb68d0] + xkbcommon_jll v1.4.1+1
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [b77e0a4c] + InteractiveUtils
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [efcefdf7] + PCRE2_jll v10.42.0+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
Precompiling project...
  ✗ GR_jll
  0 dependencies successfully precompiled in 2 seconds. 80 already precompiled.
  1 dependency errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

and then

julia> err
PkgPrecompileError: The following 1 direct dependency failed to precompile:

GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9]

Failed to precompile GR_jll [d2c73de3-f751-5644-a686-071e5b155ba9] to "/home/mason/.julia/compiled/v1.10/GR_jll/jl_DAeVcu".
ERROR: LoadError: InitError: could not load library "/home/mason/.julia/artifacts/e18a60e84fd8aefa967cb9f1d11dc6cbd9cac88b/lib/libtiff.so"
libLerc.so: cannot open shared object file: No such file or directory
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:116
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ Libtiff_jll ~/.julia/packages/Libtiff_jll/H65IB/src/wrappers/x86_64-linux-gnu.jl:13
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1134
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1122
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1067
  [8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1581
  [9] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1938
 [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [11] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [12] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [14] macro expansion
    @ ./loading.jl:1790 [inlined]
 [15] macro expansion
    @ ./lock.jl:267 [inlined]
 [16] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [17] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [18] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [19] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:495
 [21] top-level scope
    @ ~/.julia/packages/JLLWrappers/pG9bm/src/toplevel_generators.jl:192
 [22] include
    @ ./Base.jl:495 [inlined]
 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2222
 [24] top-level scope
    @ stdin:3
during initialization of module Libtiff_jll
in expression starting at /home/mason/.julia/packages/GR_jll/JpW5O/src/wrappers/x86_64-linux-gnu-cxx11.jl:12
in expression starting at /home/mason/.julia/packages/GR_jll/JpW5O/src/GR_jll.jl:2
in expression starting at stdin:

Here's my version info:

julia> versioninfo()
Julia Version 1.10.3
Commit 0b4590a5507 (2024-04-30 10:59 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 12 × AMD Ryzen 5 5600X 6-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 6 default, 0 interactive, 3 GC (on 12 virtual cores)
Environment:
  JULIA_NUM_THREADS = 6

This is especially weird because I checked, and there definitely is a file at /home/mason/.julia/artifacts/e18a60e84fd8aefa967cb9f1d11dc6cbd9cac88b/lib/libtiff.so.

[giordano]

CC @eschnett #8570 sounds suspiciously relevant.

[giordano]

The soname changed: JuliaBinaryWrappers/LERC_jll.jl@61d4fe8#diff-3cc11de0be9ee7ec4418b927ad1ef4843580f91a71e40885c887d7a6fd7e4229. Downgrading lerc_jll to v3 should fix the issue. Someone (not me because I'm on the phone) should fix this in the registry. I'm here once again asking folks to use compat bounds, we can't go on in this way.

[MasonProtter]

Adding LERC_jll@v3 and re-nuking my .julia/compiled/v10 (because GR does bad things that cause code to be cached incorrectly) fixes this issue for me temporarily until something can be upstreamed.

[bvdmitri]

Same here

[giordano]

Someone (not me because I'm on the phone) should fix this in the registry.

That's still valid 🙂 you basically need to tell the registry that all packages requiring LERC_jll are only compatible with the major version 3

[mkitti]

Here's the fix including forced recompilation.

using Pkg
Pkg.activate(; temp=true) # skip this if you are trying to fix your environment
Pkg.add([
    PackageSpec(name="GR"),
    PackageSpec(name="LERC_jll", version="3")
])
Base.compilecache(Base.PkgId(Base.UUID("28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"), "GR")) # Force GR to precompile

Note that if you already tried to used a package, you may need to restart Julia.

Here's a session in action.

(@v1.10) pkg> activate --temp
  Activating new project at `/tmp/jl_rHVccF`

(jl_rHVccF) pkg> add GR
   Resolving package versions...
    Updating `/tmp/jl_rHVccF/Project.toml`
  [28b8d3ca] + GR v0.73.3
    Updating `/tmp/jl_rHVccF/Manifest.toml`
...
  [28b8d3ca] + GR v0.73.3
...
  [88015f11] + LERC_jll v4.0.0+0
...
Precompiling project...
  ✗ GR_jll
  3 dependencies successfully precompiled in 11 seconds. 95 already precompiled.
  1 dependency had output during precompilation:
┌ GR
│  ERROR: LoadError: InitError: could not load library "/home/mkitti/.julia/artifacts/e18a60e84fd8aefa967cb9f1d11dc6cbd9cac88b/lib/libtiff.so"
│  libLerc.so: cannot open shared object file: No such file or directory

(jl_rHVccF) pkg> add LERC_jll@3
   Resolving package versions...
    Updating `/tmp/jl_rHVccF/Project.toml`
⌃ [88015f11] + LERC_jll v3.0.0+1
    Updating `/tmp/jl_rHVccF/Manifest.toml`
⌃ [88015f11] ↓ LERC_jll v4.0.0+0 ⇒ v3.0.0+1
        Info Packages marked with ⌃ have new versions available and may be upgradable.

julia> Base.compilecache(Base.PkgId(Base.UUID("28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"), "GR"))
[ Info: Precompiling GR [28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71]
("/home/mkitti/.julia/compiled/v1.10/GR/NDU5Y_3YAIL.ji", "/home/mkitti/.julia/compiled/v1.10/GR/NDU5Y_3YAIL.so")

julia> Base.compilecache(Base.PkgId(Base.UUID("28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"), "GR"))
[ Info: Precompiling GR [28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71]
("/home/mkitti/.julia/compiled/v1.10/GR/NDU5Y_3YAIL.ji", "/home/mkitti/.julia/compiled/v1.10/GR/NDU5Y_3YAIL.so")

julia> using GR

julia> plot(rand(5))

[mkitti]

because GR does bad things that cause code to be cached incorrectly

I'll own it. I think this should resolve that particular issue.

jheinen/GR.jl#543

[imciner2]

The soname changed

It would be good to have an auditor pass that can flag the SONAME/SOVERSION changing, either that or we can start requiring the libraries to be listed with their soname in the product description, then I think if the name changes we will get an auditor error about a missing product (this is what some Linux distributions recommend).