Problems to Install JLD, HDF5

[marcelord12]

Good Evening. I’m trying to install some packages on Julia 0.4.7 version to run an jl script originally coded on Julia 04.5 and I’m having troubles to install JLD, home-brew and MDF5. I don’t have a single clue about what I can do to solve this problem. I’m quite new in Julia,and I’m just trying to run these set of “old” scripts that I got from bitbucket.
julia> include(“Run.jl”)
INFO: Precompiling module JLD.
ERROR: LoadError: LoadError: HDF5 not properly installed. Please run Pkg.build(“HDF5”)
in error at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include_from_node1 at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include_from_node1 at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
[inlined code] from none:2
in anonymous at no file:0
in process_options at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in _start at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
while loading /Users/marcelord12/.julia/v0.4/HDF5/src/plain.jl, in expression starting on line 23
while loading /Users/marcelord12/.julia/v0.4/HDF5/src/HDF5.jl, in expression starting on line 3
ERROR: LoadError: Failed to precompile HDF5 to /Users/marcelord12/.julia/lib/v0.4/HDF5.ji
in error at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in compilecache at loading.jl:420
in require at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include_from_node1 at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
[inlined code] from none:2
in anonymous at no file:0
in process_options at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in _start at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
while loading /Users/marcelord12/.julia/v0.4/JLD/src/JLD.jl, in expression starting on line 4
ERROR: LoadError: Failed to precompile JLD to /Users/marcelord12/.julia/lib/v0.4/JLD.ji
in error at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in compilecache at loading.jl:420
in require at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
in include_from_node1 at /Users/marcelord12/Documents/phd2018/mppo/thesis2/MDP/Takeoff/Julia-0.4.7.app/Contents/Resources/julia/lib/julia/sys.dylib
while loading /Users/marcelord12/Run.jl, in expression starting on line 1

julia> Pkg.add(“JLD”)
INFO: Nothing to be done

julia> Pkg.add(“homebrew”)
INFO: Nothing to be done

julia> Pkg.build(“HDF5”)
INFO: Building Homebrew
fatal: Unable to find remote helper for ‘https’
fatal: Unable to find remote helper for ‘https’
Error: Fetching /Users/marcelord12/.julia/v0.4/Homebrew/deps/usr/Library/Taps/homebrew/homebrew-core failed!
Fetching /Users/marcelord12/.julia/v0.4/Homebrew/deps/usr failed!
git: ‘rebase’ is not a git command. See ‘git --help’.
git: ‘rebase’ is not a git command. See ‘git --help’.
Error: Failure while executing; git describe --tags --abbrev=0 8f3a80b562e911ec34cde3fcb8dcd8789c0affaf exited with 128. Here’s the output:
fatal: No names found, cannot describe anything.

==============================[ ERROR: Homebrew ]===============================

LoadError: failed process: Process(/Users/marcelord12/.julia/v0.4/Homebrew/deps/usr/bin/brew update --force, ProcessExited(1)) [1]
while loading /Users/marcelord12/.julia/v0.4/Homebrew/deps/build.jl, in expression starting on line 2

================================================================================
INFO: Building Blosc
INFO: Building HDF5
Warning: Use hdf5 instead of deprecated homebrew/science/hdf5
================================[ ERROR: HDF5 ]=================================

LoadError: SystemError: opening file /Users/marcelord12/.julia/v0.4/Homebrew/deps/usr/Library/Taps/homebrew/homebrew-science/hdf5.rb: No such file or directory
while loading /Users/marcelord12/.julia/v0.4/HDF5/deps/build.jl, in expression starting on line 27

================================================================================

==============================================================================================[ BUILD ERRORS ]==============================================================================================

WARNING: HDF5 and Homebrew had build errors.

• packages with build errors remain installed in /Users/marcelord12/.julia/v0.4
• build the package(s) and all dependencies with Pkg.build("HDF5", "Homebrew")
• build a single package by running its deps/build.jl script

============================================================================================================================================================================================================

julia> Pkg.build(“HDF5”, “Homebrew”)
INFO: Building Homebrew
fatal: Unable to find remote helper for ‘https’
fatal: Unable to find remote helper for ‘https’
Error: Fetching /Users/marcelord12/.julia/v0.4/Homebrew/deps/usr/Library/Taps/homebrew/homebrew-core failed!
Fetching /Users/marcelord12/.julia/v0.4/Homebrew/deps/usr failed!
git: ‘rebase’ is not a git command. See ‘git --help’.
git: ‘rebase’ is not a git command. See ‘git --help’.
Error: Failure while executing; git describe --tags --abbrev=0 8f3a80b562e911ec34cde3fcb8dcd8789c0affaf exited with 128. Here’s the output:
fatal: No names found, cannot describe anything.

==============================[ ERROR: Homebrew ]===============================

LoadError: failed process: Process(/Users/marcelord12/.julia/v0.4/Homebrew/deps/usr/bin/brew update --force, ProcessExited(1)) [1]
while loading /Users/marcelord12/.julia/v0.4/Homebrew/deps/build.jl, in expression starting on line 2

================================================================================
INFO: Building Blosc
INFO: Building HDF5
Warning: Use hdf5 instead of deprecated homebrew/science/hdf5
================================[ ERROR: HDF5 ]=================================

LoadError: SystemError: opening file /Users/marcelord12/.julia/v0.4/Homebrew/deps/usr/Library/Taps/homebrew/homebrew-science/hdf5.rb: No such file or directory
while loading /Users/marcelord12/.julia/v0.4/HDF5/deps/build.jl, in expression starting on line 27

================================================================================

==============================================================================================[ BUILD ERRORS ]==============================================================================================

WARNING: HDF5 and Homebrew had build errors.

• packages with build errors remain installed in /Users/marcelord12/.julia/v0.4
• build the package(s) and all dependencies with Pkg.build("HDF5", "Homebrew")
• build a single package by running its deps/build.jl script

[kevbonham]

I’d guess that the first step would be going back through all the dependencies and finding the versions that we’re around when Julia was still on version 0.4. This may be quite tedious. Happily, the new package manager will make it possible for future script/tutorial writers to give people the exact versions of all their packages, but that won’t help you in this situation.

That said, that version of Julia is no longer supported, I think you’d be much better off with an intro to the language that’s more current, or trying to update the script for a more current version (maybe target 0.6.4 because more of the older packages are likely to work).

Good luck!

[marcelord12]

I’m trying both ways. I have a Julia 0.6.4 installed and even so I"m debugging so many error for one week that sometimes seem better to try to come back to an older version.

[migarstka]

I had similar problems when I tried to install JLD, HDF5 in Julia 0.7

For me the following worked:

Anyone know status of HDF5 build problems?

Thank you @djsegal ! Success! To clarify @djsegal’s suggestion a little, I: Went to the Homebrew website, downloaded and installed Homebrew normally (i.e. not through Julia) ran brew install hdf5 in the terminal (not in julia) THEN did Pkg.build("HDF5") in julia (0.6.3). Success! More generally, though, this still seems like a big general problem for new users – being able to read data and save things seems pretty central to Julia. Surely we can make this install work better? (Sorry – I kn…