I’ve had this problem on a couple of HPC clusters (where the system libraries are relatively old). When trying to install/precompile Plots.jl, there’s an error because the system-provided libz.so is not version 1.2.9 (see error message below). Jullia’s packages include a version of libz.so (which I assume would be compatible) - why is this one not being used?
I’m not familiar with how Julia links shared libraries like this, so hints on fixing/debugging or even which package I should raise an issue with (if that is what needs doing) would be appreciated.
Error message (with user-name and system-specific info edited out):
$ julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _ | |
| | |_| | | | (_| | | Version 1.6.2 (2021-07-14)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(@v1.6) pkg> add Plots
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
Updating `~/.julia/environments/v1.6/Project.toml`
[91a5bcdd] + Plots v1.23.5
Updating `~/.julia/environments/v1.6/Manifest.toml`
[d360d2e6] + ChainRulesCore v1.11.1
[35d6a980] + ColorSchemes v3.15.0
[3da002f7] + ColorTypes v0.11.0
[5ae59095] + Colors v0.12.8
[34da2185] + Compat v3.40.0
[d38c429a] + Contour v0.5.7
[9a962f9c] + DataAPI v1.9.0
[864edb3b] + DataStructures v0.18.10
[e2d170a0] + DataValueInterfaces v1.0.0
[c87230d0] + FFMPEG v0.4.1
[53c48c17] + FixedPointNumbers v0.8.4
[59287772] + Formatting v0.4.2
[28b8d3ca] + GR v0.62.1
[5c1252a2] + GeometryBasics v0.4.1
[42e2da0e] + Grisu v1.0.2
[cd3eb016] + HTTP v0.9.16
[83e8ac13] + IniFile v0.5.0
[3587e190] + InverseFunctions v0.1.1
[92d709cd] + IrrationalConstants v0.1.1
[c8e1da08] + IterTools v1.3.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[b964fa9f] + LaTeXStrings v1.3.0
[23fbe1c1] + Latexify v0.15.9
[2ab3a3ac] + LogExpFunctions v0.3.4
[1914dd2f] + MacroTools v0.5.9
[739be429] + MbedTLS v1.0.3
[442fdcdd] + Measures v0.3.1
[e1d29d7a] + Missings v1.0.2
[77ba4419] + NaNMath v0.3.5
[ccf2f8ad] + PlotThemes v2.0.1
[995b91a9] + PlotUtils v1.0.15
[91a5bcdd] + Plots v1.23.5
[3cdcf5f2] + RecipesBase v1.1.2
[01d81517] + RecipesPipeline v0.4.1
[189a3867] + Reexport v1.2.2
[6c6a2e73] + Scratch v1.1.0
[992d4aef] + Showoff v1.0.3
[a2af1166] + SortingAlgorithms v1.0.1
[90137ffa] + StaticArrays v1.2.13
[82ae8749] + StatsAPI v1.0.0
[2913bbd2] + StatsBase v0.33.12
[09ab397b] + StructArrays v0.6.3
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.6.0
[5c2747f8] + URIs v1.3.0
[1cfade01] + UnicodeFun v0.4.1
[6e34b625] + Bzip2_jll v1.0.8+0
[83423d85] + Cairo_jll v1.16.1+0
[5ae413db] + EarCut_jll v2.2.3+0
[2e619515] + Expat_jll v2.2.10+0
[b22a6f82] + FFMPEG_jll v4.4.0+0
[a3f928ae] + Fontconfig_jll v2.13.93+0
[d7e528f0] + FreeType2_jll v2.10.4+0
[559328eb] + FriBidi_jll v1.0.10+0
[0656b61e] + GLFW_jll v3.3.5+1
[d2c73de3] + GR_jll v0.62.0+0
[78b55507] + Gettext_jll v0.21.0+0
[7746bdde] + Glib_jll v2.68.3+0
[3b182d85] + Graphite2_jll v1.3.14+0
[2e76f6c2] + HarfBuzz_jll v2.8.1+0
[aacddb02] + JpegTurbo_jll v2.1.0+0
[c1c5ebd0] + LAME_jll v3.100.1+0
[dd4b983a] + LZO_jll v2.10.1+0
[e9f186c6] + Libffi_jll v3.2.2+0
[d4300ac3] + Libgcrypt_jll v1.8.7+0
[7e76a0d4] + Libglvnd_jll v1.3.0+3
[7add5ba3] + Libgpg_error_jll v1.42.0+0
[94ce4f54] + Libiconv_jll v1.16.1+1
[4b2f31a3] + Libmount_jll v2.35.0+0
[89763e89] + Libtiff_jll v4.3.0+0
[38a345b3] + Libuuid_jll v2.36.0+0
[e7412a2a] + Ogg_jll v1.3.5+0
[458c3c95] + OpenSSL_jll v1.1.10+0
[91d4177d] + Opus_jll v1.3.2+0
[2f80f16e] + PCRE_jll v8.44.0+0
[30392449] + Pixman_jll v0.40.1+0
[ea2cea3b] + Qt5Base_jll v5.15.3+0
[a2964d1f] + Wayland_jll v1.19.0+0
[2381bf8a] + Wayland_protocols_jll v1.18.0+4
[02c8fc9c] + XML2_jll v2.9.12+0
[aed1982a] + XSLT_jll v1.1.34+0
[4f6342f7] + Xorg_libX11_jll v1.6.9+4
[0c0b7dd1] + Xorg_libXau_jll v1.0.9+4
[935fb764] + Xorg_libXcursor_jll v1.2.0+4
[a3789734] + Xorg_libXdmcp_jll v1.1.3+4
[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 v0.1.0+3
[c7cfdc94] + Xorg_libxcb_jll v1.13.0+3
[cc61e674] + Xorg_libxkbfile_jll v1.1.0+4
[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 v1.4.2+4
[33bec58e] + Xorg_xkeyboard_config_jll v2.27.0+4
[c5fb5394] + Xorg_xtrans_jll v1.4.0+3
[3161d3a3] + Zstd_jll v1.5.0+0
[0ac62f75] + libass_jll v0.15.1+0
[f638f0a6] + libfdk_aac_jll v2.0.2+0
[b53b4c65] + libpng_jll v1.6.38+0
[f27f6e37] + libvorbis_jll v1.3.7+0
[1270edf5] + x264_jll v2021.5.5+0
[dfaa095f] + x265_jll v3.5.0+0
[d8fb68d0] + xkbcommon_jll v0.9.1+5
[8bb1440f] + DelimitedFiles
[1a1011a3] + SharedArrays
[8dfed614] + Test
(@v1.6) pkg> precompile
Precompiling project...
✗ Cairo_jll
✗ HarfBuzz_jll
✗ libass_jll
✗ FFMPEG_jll
✗ GR_jll
✗ Plots
0 dependencies successfully precompiled in 38 seconds (147 already precompiled)
ERROR: The following 1 direct dependency failed to precompile:
Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80]
Failed to precompile Plots [91a5bcdd-55d7-5caf-9e0b-520d859cae80] to <home-directory>/.julia/compiled/v1.6/Plots/jl_RerNQU.
ERROR: LoadError: LoadError: InitError: could not load library "<home-directory>/.julia/artifacts/ddfc455343aff48d27c1b39d7fcb07e0d9242b50/lib/libpng16.so"
<cluster-system-path>/libraries/zlib/1.2.8/gnu--6.1.0/lib/libz.so.1: version `ZLIB_1.2.9' not found (required by <home-directory>/.julia/artifacts/ddfc455343aff48d27c1b39d7fcb07e0d9242b50/lib/libpng16.so)
Stacktrace:
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:114
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl ./libdl.jl:114
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/bkwIo/src/products/library_generators.jl:54 [inlined]
[4] __init__()
@ libpng_jll ~/.julia/packages/libpng_jll/9vklf/src/wrappers/x86_64-linux-gnu.jl:9
[5] _include_from_serialized(path::String, depmods::Vector{Any})
@ Base ./loading.jl:696
[6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:782
[7] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1020
[8] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[9] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[10] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[11] top-level scope
@ ~/.julia/packages/JLLWrappers/bkwIo/src/toplevel_generators.jl:170
[12] include
@ ./Base.jl:386 [inlined]
[13] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[14] top-level scope
@ none:1
[15] eval
@ ./boot.jl:360 [inlined]
[16] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[17] top-level scope
@ none:1
during initialization of module libpng_jll
in expression starting at <home-directory>/.julia/packages/Cairo_jll/zRgOn/src/wrappers/x86_64-linux-gnu.jl:6
in expression starting at <home-directory>/.julia/packages/Cairo_jll/zRgOn/src/Cairo_jll.jl:2
ERROR: LoadError: LoadError: Failed to precompile Cairo_jll [83423d85-b0ee-5818-9007-b63ccbeb887a] to <home-directory>/.julia/compiled/v1.6/Cairo_jll/jl_dpoEzd.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[8] top-level scope
@ ~/.julia/packages/JLLWrappers/bkwIo/src/toplevel_generators.jl:170
[9] include
@ ./Base.jl:386 [inlined]
[10] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[11] top-level scope
@ none:1
[12] eval
@ ./boot.jl:360 [inlined]
[13] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[14] top-level scope
@ none:1
in expression starting at <home-directory>/.julia/packages/HarfBuzz_jll/eogPK/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at <home-directory>/.julia/packages/HarfBuzz_jll/eogPK/src/HarfBuzz_jll.jl:2
ERROR: LoadError: LoadError: Failed to precompile HarfBuzz_jll [2e76f6c2-a576-52d4-95c1-20adfe4de566] to <home-directory>/.julia/compiled/v1.6/HarfBuzz_jll/jl_KpjxsY.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[8] top-level scope
@ ~/.julia/packages/JLLWrappers/bkwIo/src/toplevel_generators.jl:170
[9] include
@ ./Base.jl:386 [inlined]
[10] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[11] top-level scope
@ none:1
[12] eval
@ ./boot.jl:360 [inlined]
[13] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[14] top-level scope
@ none:1
in expression starting at <home-directory>/.julia/packages/libass_jll/SaaQW/src/wrappers/x86_64-linux-gnu.jl:6
in expression starting at <home-directory>/.julia/packages/libass_jll/SaaQW/src/libass_jll.jl:2
ERROR: LoadError: LoadError: Failed to precompile libass_jll [0ac62f75-1d6f-5e53-bd7c-93b484bb37c0] to <home-directory>/.julia/compiled/v1.6/libass_jll/jl_TWRThR.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[8] top-level scope
@ ~/.julia/packages/JLLWrappers/bkwIo/src/toplevel_generators.jl:170
[9] include
@ ./Base.jl:386 [inlined]
[10] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[11] top-level scope
@ none:1
[12] eval
@ ./boot.jl:360 [inlined]
[13] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[14] top-level scope
@ none:1
in expression starting at <home-directory>/.julia/packages/FFMPEG_jll/ECokx/src/wrappers/x86_64-linux-gnu.jl:4
in expression starting at <home-directory>/.julia/packages/FFMPEG_jll/ECokx/src/FFMPEG_jll.jl:2
ERROR: LoadError: Failed to precompile FFMPEG_jll [b22a6f82-2f65-5046-a5b2-351ab43fb4e5] to <home-directory>/.julia/compiled/v1.6/FFMPEG_jll/jl_6VTcXq.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include
@ ./Base.jl:386 [inlined]
[8] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[9] top-level scope
@ none:1
[10] eval
@ ./boot.jl:360 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[12] top-level scope
@ none:1
in expression starting at <home-directory>/.julia/packages/FFMPEG/OUpap/src/FFMPEG.jl:1
ERROR: LoadError: Failed to precompile FFMPEG [c87230d0-a227-11e9-1b43-d7ebe4e7570a] to <home-directory>/.julia/compiled/v1.6/FFMPEG/jl_xNc0xN.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include
@ ./Base.jl:386 [inlined]
[8] 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, UInt64}}, source::Nothing)
@ Base ./loading.jl:1235
[9] top-level scope
@ none:1
[10] eval
@ ./boot.jl:360 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[12] top-level scope
@ none:1
in expression starting at <home-directory>/.julia/packages/Plots/1RWWg/src/Plots.jl:1
(@v1.6) pkg>