vtjnash
commented
1 year ago Setting LD_LIBRARY_PATH is likely to be the mistake here, since that is an environment variable you can set to override and ignore the program settings that it was built with.
Aside, maybe we should inject a comment into this error message informing users of
export DYLD_PRINT_SEARCHING=1 (man dyld) and export LD_DEBUG=libs (LD_DEBUG=help env) as appropriate to their system?
Hi,
I am trying to use Circuitscape to optimize resistance layers in R, via julia. I have successfully install Circuitscape to Julia, and successfully loaded it there. I have also successfully called JuliaCall, and am able to use julia to perform other functions inside R.
I have 2 errors occuring. When I am in julia, and test Circuitscape, I get this warning, although it passes all of the tests:
WARNING: could not import Circuitscape.compute_mklpardiso into Main.
Then, when I try to call and test circuitscape within Julia in R, I get this error: 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/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
I believe this is an issue with Circuitscape integrating with Julia because I can use Julia within R to do other functions, just not use Circuitscape. I would love any advice.
R info: R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.2 LTS
Matrix products: default BLAS: /usr/local/lib/R/lib/libRblas.so LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.10.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Pacific/Honolulu tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] compiler_4.3.0
Julia info:
Julia Version 1.8.5 Commit 17cfb8e65ea (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