Cannot open shared object: libproj.so.25

[nataliemyers12]

Hi,

I have successfully run Julia Setup in R, but when I go to actually use Julia in R, I receive this error. I've tried a variety of steps to fix this, but have not been successful. Could anyone provide insight? I am using R 4.3.0 and Julia 1.8.5

Error: Error happens in Julia.
InitError: could not load library "/home/thomsonlab/.julia/artifacts/e4afa6442d82c9e3819067808b91aa8308d90db6/lib/libgeotiff.so"
libproj.so.25: cannot open shared object file: No such file or directory

version info:
Julia Version 1.8.5
Commit 17cfb8e (2023-01-08 06:45 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 40 × Intel(R) Xeon(R) CPU E5-2660 v2 @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, ivybridge)
Threads: 1 on 40 virtual cores
Environment:
LD_LIBRARY_PATH = /usr/local/lib/R/lib:/home/thomsonlab/Desktop/revbayes/projects/cmake/boost_1_74_0/stage/lib:

Full:

jl.inputs<- jl.prep(n.Pops=NROW(plhon),CS_Point.File=plhonsp,response=lower(as.matrix(gen.dist)),cholmod = TRUE, JULIA_HOME = JULIA_HOME)
Error: Error happens in Julia.
InitError: could not load library "/home/thomsonlab/.julia/artifacts/e4afa6442d82c9e3819067808b91aa8308d90db6/lib/libgeotiff.so"
libproj.so.25: 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/QpMQW/src/products/library_generators.jl:54 [inlined]
[4] init()
@ libgeotiff_jll ~/.julia/packages/libgeotiff_jll/EG4x2/src/wrappers/x86_64-linux-gnu.jl:15
[5] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
@ Base ./loading.jl:831
[6] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, sourcepath::String, depmods::Vector{Any})
@ Base ./loading.jl:938
[7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64)
@ Base ./loa

[KristofferC]

Try remove LD_LIBRARY_PATH env variable.

[nataliemyers12]

Hi,

How would I do that? And in Julia or R, or just in terminal before I begin either program?

Apologies, I am not very experienced with either program.

[KristofferC]

LD_LIBRARY_PATH="" julia or remove it where ever it is getting set. And you should probably not use that env variable at all (ref http://xahlee.info/UnixResource_dir/_/ldpath.html).

[nataliemyers12]

I see. Thank you for sharing that! This is a lab shared computer so I unfortunately don't have control over who accesses it or sets things, as I haven't set the variable. I removed the variable, but now am getting this error:

Error: Error happens in Julia.
InitError: could not load library "/home/thomsonlab/.julia/artifacts/2d4a566ad73ee204aaae3ef08cfc954f2674e5f1/lib/libnetcdf.so"
/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_4' not found (required by /home/thomsonlab/.julia/artifacts/2d4a566ad73ee204aaae3ef08cfc954f2674e5f1/lib/libnetcdf.so)
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/QpMQW/src/products/library_generators.jl:54 [inlined]
[4] init()
@ NetCDF_jll ~/.julia/packages/NetCDF_jll/VOWKB/src/wrappers/x86_64-linux-gnu.jl:12
[5] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any})
@ Base ./loading.jl:831
[6] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, sourcepath::String, depmods::Vector{Any})
@ Base ./loading.jl:938
[7] require_search