I’m unable to use or build certain packages when using Atom’s REPL (Juno), but can use/build the packages when launching Julia from my terminal or when using the REPL from inside VSCode. For example,
issuing the following commands from inside the REPL of the Atom/Juno editor:
_
_ _ _(_)_ | A fresh approach to technical computing
(_) | (_) (_) | Documentation: https://docs.julialang.org
_ _ _| |_ __ _ | Type "?help" for help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 0.6.2 (2017-12-13 18:08 UTC)
_/ |\__'_|_|_|\__'_| | Official http://julialang.org/ release
|__/ | x86_64-pc-linux-gnu
julia> Pkg.build("HDF5")
INFO: Building Blosc
INFO: Building HDF5
==========================================[ ERROR: HDF5 ]===========================================
LoadError: could not spawn `apt-cache showpkg hdf5-tools`: no such file or directory(ENOENT)
while loading /home/zygmunt/.julia/v0.6/HDF5/deps/build.jl, in expression starting on line 40
====================================================================================================
==========================================[ BUILD ERRORS ]==========================================
WARNING: HDF5 had build errors.
- packages with build errors remain installed in /home/zygmunt/.julia/v0.6
- build the package(s) and all dependencies with `Pkg.build("HDF5")`
- build a single package by running its `deps/build.jl` script
====================================================================================================
whereas issuing the same command from the Julia REPL launched directly from my Linux terminal gives:
_
_ _ _(_)_ | A fresh approach to technical computing
(_) | (_) (_) | Documentation: https://docs.julialang.org
_ _ _| |_ __ _ | Type "?help" for help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 0.6.2 (2017-12-13 18:08 UTC)
_/ |\__'_|_|_|\__'_| | Official http://julialang.org/ release
|__/ | x86_64-pc-linux-gnu
julia> Pkg.build("HDF5")
INFO: Building Blosc
INFO: Building HDF5
julia>
julia> Pkg.test("HDF5")
INFO: Testing HDF5
Test Summary: | Pass Total
plain | 126 126
Test Summary: | Pass Total
readremote | 23 23
Test Summary: | Pass Total
extendtest | 15 15
Test Summary: | Pass Total
gc | 100 100
Test Summary: | Pass Total
external | 6 6
INFO: HDF5 tests passed
After building the package from the canonical REPL I still cannot use it inside Atom/Juno. I get the following
error:
Starting Julia...
_
_ _ _(_)_ | A fresh approach to technical computing
(_) | (_) (_) | Documentation: https://docs.julialang.org
_ _ _| |_ __ _ | Type "?help" for help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 0.6.2 (2017-12-13 18:08 UTC)
_/ |\__'_|_|_|\__'_| | Official http://julialang.org/ release
|__/ | x86_64-pc-linux-gnu
julia> Pkg.test("HDF5")
INFO: Testing HDF5
ERROR: LoadError: InitError: error compiling __init__: could not load library "/usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10"
/usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10: cannot open shared object file: No such file or directory
Stacktrace:
[1] _include_from_serialized(::String) at ./loading.jl:157
[2] _require_from_serialized(::Int64, ::Symbol, ::String, ::Bool) at ./loading.jl:200
[3] _require_search_from_serialized(::Int64, ::Symbol, ::String, ::Bool) at ./loading.jl:236
[4] _require(::Symbol) at ./loading.jl:441
[5] require(::Symbol) at ./loading.jl:405
[6] include_from_node1(::String) at ./loading.jl:576
[7] include(::String) at ./sysimg.jl:14
[8] process_options(::Base.JLOptions) at ./client.jl:305
[9] _start() at ./client.jl:371
during initialization of module HDF5
while loading /home/zygmunt/.julia/v0.6/HDF5/test/runtests.jl, in expression starting on line 1
==========================================[ ERROR: HDF5 ]===========================================
failed process: Process(`/media/zygmunt/big/Julia/bin/julia -Cx86-64 -J/media/zygmunt/big/Julia/lib/julia/sys.so --compile=yes --depwarn=yes --check-bounds=yes --code-coverage=none --color=yes --compilecache=yes /home/zygmunt/.julia/v0.6/HDF5/test/runtests.jl`, ProcessExited(1)) [1]
====================================================================================================
ERROR: HDF5 had test errors
There is a known issue with Atom 1.26.0 (and other versions) in that it does not load the PATH properly. I’ve been able to fix issues I’ve had with the usage of other packages by adding my path variables explicitly in the Edit--->Init Script file:
process.env.PATH = ['/home/zygmunt/bin:/home/zygmunt/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:', process.env.PATH].join(':')
However, this seems to be insufficient for resolving the HDF5 problem. Is there some other environment variable that I should be explicitly including?
I have tried push!(Libdl.DL_LOAD_PATH, "/usr/lib/x86_64-linux-gnu") as per the suggestion of the HDF5 installation instructions but this had no effect.
Following on from the installation instructions, I also cannot see the environment variable LD_LIBRARY_PATH defined when I do ; echo $ENV from either the canonical or Juno REPL. Hence, I am not sure what precisely Juno is blocking that is preventing the usage and compilation of this package. Many thanks for any suggestions you may have.