Relative linkage path prevents run script from any directory except "core"

[VPetukhov]

Hi,

I'm trying to build an app, which depends on RMath package. Building script is the following:

using ApplicationBuilder
using Rmath
import SpecialFunctions

lib_deps = [Rmath.libRmath, SpecialFunctions.openspecfun, SpecialFunctions.openspecfun * ".1.3",
            "/lib64/libgfortran.so.4", "/lib64/libgfortran.so.4.0.0"];

build_app_bundle("segment_data.jl", appname="Segmentation", libraries=lib_deps);

Is creates "builddir/Segmentation/" folder, which contains "core", "res" and "lib" folders. "lib" directory contains "libRmath-julia.so" library and several others.

When I run script from "core" folder, it works well. Though, if I change path (e.g. calling it from "builddir" with ./core/segment_data command), I get error:

fatal: error thrown and no exception handler available.
InitError(mod=:Rmath, error=ErrorException("could not load library "../lib/libRmath-julia.so"
../lib/libRmath-julia.so: cannot open shared object file: No such file or directory"))
rec_backtrace at /julia/src/stackwalk.c:94
record_backtrace at /julia/src/task.c:246
jl_throw at /julia/src/task.c:577
jl_errorf at /julia/src/rtutils.c:77
jl_dlerror at /julia/src/dlload.c:74 [inlined]
jl_load_dynamic_library_ at /julia/src/dlload.c:196
jl_get_library at /julia/src/runtime_ccall.cpp:48
jl_get_library at /julia/src/runtime_ccall.cpp:56 [inlined]
jl_load_and_lookup at /julia/src/runtime_ccall.cpp:59
__init__ at /home/vp/.julia/packages/Rmath/Py9gH/src/Rmath.jl:47
jfptr___init___27581 at /d0-mendel/home/viktor_petukhov/spatial/SpatialRNA/src/builddir/Segmentation/core/segment_data.so (unknown line)
jl_apply_generic at /julia/src/gf.c:2182
jl_apply at /julia/src/julia.h:1538 [inlined]
jl_module_run_initializer at /julia/src/toplevel.c:90
_julia_init at /julia/src/init.c:820
julia_init__threading at /julia/src/task.c:302
main at ./core/segment_data (unknown line)
__libc_start_main at /build/eglibc-SvCtMH/eglibc-2.19/csu/libc-start.c:287
_start at ./core/segment_data (unknown line)

[VPetukhov]

Found error in my "segment_data.jl" script. There I used code:

Core.eval(Rmath, :(libRmath = "../lib/libRmath-julia.so"))

But correct way was to use

Core.eval(Rmath, :(libRmath = "libRmath-julia.so"))

And to add "builddir/Segmentation/lib" to LD_LIBRARY_PATH (on both building machine and machine when I run the compiled package).

[NHDaly]

Thanks for sharing the solution!!

It looks like you're running on Linux, right? Has that solution worked for you? If so, we should add it to documentation somewhere.

[VPetukhov]

@NHDaly ,

Yes, it's linux (Centos 7), and it works well.