Can't build the "examples/MyLib" project on Arch Linux due to provilege errors

[andrea993]

I use Arch Linux with Julia 1.9.3 and PackageCompiler v2.1.7. I'm trying to build the example "MyLib" from PackageCompiler source.

I installed PackageCompiler with Pkg.Add('PackageCompiler')

I copied the "examples" directory and I tried to run make in the "MyLib" subdirectory I get the error:

ERROR: LoadError: ArgumentError: Package PackageCompiler [9b87118b-4619-50d2-8e1e-99f35a4d4d9d] is required but does not seem to be installed:
 - Run `Pkg.instantiate()` to install all recorded dependencies.

To avoid this problem I have deleted build\Manifest.toml I then tried again with make.

I get the error:

ERROR: LoadError: IOError: open("/usr/lib/dbus-1.0/dbus-daemon-launch-helper", 0, 0): permission denied (EACCES)
Stacktrace:
  [1] uv_error
    @ ./libuv.jl:100 [inlined]
  [2] open(path::String, flags::UInt8, mode::Int64)
    @ Base.Filesystem ./filesystem.jl:121
  [3] open
    @ ./filesystem.jl:113 [inlined]
  [4] sendfile(src::String, dst::String)
    @ Base.Filesystem ./file.jl:992
  [5] cptree(src::String, dst::String; force::Bool, follow_symlinks::Bool)
    @ Base.Filesystem ./file.jl:351
  [6] cptree(src::String, dst::String; force::Bool, follow_symlinks::Bool)
    @ Base.Filesystem ./file.jl:348
  [7] cptree
    @ ./file.jl:338 [inlined]
  [8] cp(src::String, dst::String; force::Bool, follow_symlinks::Bool)
    @ Base.Filesystem ./file.jl:382
  [9] cp
    @ ./file.jl:376 [inlined]
 [10] bundle_julia_libraries(dest_dir::String)
    @ PackageCompiler ~/.julia/packages/PackageCompiler/b2smD/src/PackageCompiler.jl:1118
 [11] create_library(package_dir::String, dest_dir::String; lib_name::String, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, incremental::Bool, filter_stdlibs::Bool, force::Bool, header_files::Vector{String}, julia_init_c_file::String, version::Nothing, compat_level::String, cpu_target::String, include_lazy_artifacts::Bool, sysimage_build_args::Cmd, include_transitive_dependencies::Bool, script::Nothing)
    @ PackageCompiler ~/.julia/packages/PackageCompiler/b2smD/src/PackageCompiler.jl:980
 [12] top-level scope

The program is trying to run /usr/lib/dbus-1.0/dbus-daemon-launch-helper that is not executable by a normal user

ls -l /usr/lib/dbus-1.0/dbus-daemon-launch-helper
-rwsr-x--- 1 root dbus 30680 Sep  2 15:42 /usr/lib/dbus-1.0/dbus-daemon-launch-helper*

So I tried again for test with sudo -g dbus make

I get a new error

ERROR: LoadError: IOError: open("/usr/lib/ssh/ssh-keysign", 0, 0): permission denied (EACCES)

My user can run this file in theory

ls -l "/usr/lib/ssh/ssh-keysign"
-rws--x--x 1 root root 334072 Sep  9 10:08 /usr/lib/ssh/ssh-keysign

/usr/lib/ssh/ssh-keysign
ssh-keysign not enabled in /etc/ssh/ssh_config

Definitely as root the make command works but not as user.

[DilumAluthge]

How did you install Julia?

[andrea993]

I'm using the package Julia-bin from AUR https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=julia-bin That should download the official release

[MachSilva]

@andrea993 , I think the problem is in the file examples/MyLib/build/Manifest.toml, in this section:

[[PackageCompiler]]
deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs"]
path = "../../.."
uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
version = "2.1.7"

I got this problem too. If you copy the examples/MyLib outside the PackageCompiler repo, this relative path ../../.. breaks. So I deleted this line and then it worked.

Begin edit

I forgot to say that after deleting the line, I started the Julia REPL and reinstalled the PackageCompiler:

julia> ]
(@v1.10) pkg> activate build/
  Activating project at `~/Sources/MyLib/build`

(build) pkg> st
Status `~/Sources/MyLib/build/Project.toml`
ERROR: Could not locate the source code for the PackageCompiler package. Are you trying to use a manifest generated by a different version of Julia?

(build) pkg> remove PackageCompiler
[...]

(build) pkg> add PackageCompiler
[...]

And then it worked.

End edit

However, I ended with another problem:

gcc my_application.c -o my_application.out -I"MyLibCompiled"/include -L"MyLibCompiled"/lib -ljulia -lmylib
/usr/bin/ld: /tmp/cc0RSZVq.o: in function `main':
my_application.c:(.text+0x26): undefined reference to `increment32'
collect2: error: ld returned 1 exit status
make: *** [Makefile:20: build-executable] Error 1

When inspecting the generated library, I noticed that increment32 is marked as a LOCAL symbol:

~/S/P/e/MyLib (master)> readelf MyLibCompiled/lib/libmylib.so -s | grep -i increment32
 21758: 0000000000167b10   281 FUNC    LOCAL  DEFAULT   11 increment32
~/S/P/e/MyLib (master)> readelf MyLibCompiled/lib/libmylib.so -s | grep -i _julia
   110: 0000000000568390     5 FUNC    GLOBAL DEFAULT   11 shutdown_julia
   118: 0000000000568330    93 FUNC    GLOBAL DEFAULT   11 init_julia
  1391: 0000000000320170    70 FUNC    LOCAL  DEFAULT   11 jfptr_load_julia[...]
  5157: 00000000001bc830   576 FUNC    LOCAL  DEFAULT   11 julia_load_julia[...]
 24793: 0000000000568390     5 FUNC    GLOBAL DEFAULT   11 shutdown_julia
 24878: 0000000000568330    93 FUNC    GLOBAL DEFAULT   11 init_julia

Does anyone have an idea on how I can mark the symbol increment32 as global?

Edit 2:

Nevermind. Actually, this symbol problem happens only in Julia 1.10-beta2. It worked in Julia 1.9.3.

[andrea993]

I already solved the .toml error directly deleting the file (as I wrote) but the real problem of this topic is about the error

ERROR: LoadError: IOError: open("/usr/lib/ssh/ssh-keysign", 0, 0): permission denied (EACCES)

I have the same error also if I try to build package written by myself without root

[MachSilva]

Ok. I was able to reproduce your problem and I think I found the cause:

 [10] bundle_julia_libraries(dest_dir::String)
    @ PackageCompiler ~/.julia/packages/PackageCompiler/b2smD/src/PackageCompiler.jl:1118

In PackageCompiler.jl:1118:

cp(julia_libdir(), app_libdir; force=true)

For distribuition packages / system installations like julia-binin AUR, the package compiler will try to copy the entire /usr/bin directory to MyLibCompiled folder, since julia_libdir() evaluates to "/usr/lib" (at least on my computer).

julia> isdebugbuild() = ccall(:jl_is_debugbuild, Cint, ()) != 0 
isdebugbuild (generic function with 1 method)

julia> using Libdl

julia> function julia_libdir()
           libname = isdebugbuild() ? "libjulia-debug" : 
                                      "libjulia"
           return dirname(abspath(Libdl.dlpath(libname)))
       end
julia_libdir (generic function with 1 method)

julia> julia_libdir()
"/usr/lib"

Although it is not the problem cause itself, copying the entire "/usr/lib" directory seems as an undesirable behavior.

[andrea993]

Thanks this sound like an issue imho. In other kinds of installation which is the output of julia_libdir()?

In any case the aur package is only a script that download Julia from the official release and copy it to the system directories so I think that it's should not be a package problem. You can look at the package source that I linked

[MachSilva]

Manjaro (julia installed by sudo pacman -S julia): "/usr/lib" Juliaup: "/home/me/.julia/juliaup/julia-1.9.3+0.x64.linux.gnu/lib" Julia docker image (docker run -it julia:1.9 bash): "/usr/local/julia/lib"

PackageCompiler doesn't need dbus or cups libraries, which read permissions are denied, but it tries to copy the files anyway if they are in same directory as libjulia.so.

[KristofferC]

I think this should be fixed now. Would be good if someone can confirm.