sglyon
commented
8 years ago sometimes Blosc has given people issues on ubuntu.
Can you try Pkg.build("Blosc"); using Blosc in a fresh Julia session and post the output?
Closed jstac closed 8 years ago
sglyon
commented
8 years ago sometimes Blosc has given people issues on ubuntu.
Can you try Pkg.build("Blosc"); using Blosc in a fresh Julia session and post the output?
sglyon
commented
8 years ago On second thought. I actually think we should publish another release of QuantEcon.jl as I believe Blosc is no longer a dependency
sglyon
commented
8 years ago Ok so I was wrong, the latest released version does not have HDF5 or Blosc as a dependency. So these error shouldn't be coming up.
If you cd into the repo ~/.julia/v0.4/QuantEcon, does git status say the repo is clean or has changes? If it has changes you probably aren't getting the most recent QuantEcon.jl. We should clean out your local copy of the repo so you can be on the latest release.
jstac
commented
8 years ago Running git status gives
HEAD detached at fe2be6b
nothing to commit, working directory cleanI've tried removing and reinstalling. I'll try again.
jstac
commented
8 years ago Blosc:
julia> Pkg.build("Blosc")
INFO: Building Blosc
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations:
CAfile: /etc/pki/tls/certs/ca-bundle.crt
CApath: none
================================[ ERROR: Blosc ]================================
LoadError: failed process: Process(`curl -f -o c-blosc-1.7.0.tar.gz -L https://github.com/Blosc/c-blosc/archive/v1.7.0.tar.gz`, ProcessExited(77)) [77]
while loading /home/john/.julia/v0.4/Blosc/deps/build.jl, in expression starting on line 18
================================================================================
==========================================[ BUILD ERRORS ]===========================================
WARNING: Blosc had build errors.
- packages with build errors remain installed in /home/john/.julia/v0.4
- build the package(s) and all dependencies with `Pkg.build("Blosc")`
- build a single package by running its `deps/build.jl` script
=====================================================================================================
Excellent. I've seen this one.
@cc7768 might know a magic trick to get around this one...
cc7768
commented
8 years ago Blosc problem probably has to do with BinDeps. My typical fix to this is to go into the BinDeps/src/BinDeps.jl and change downloadcmd = nothing to downloadcmd = :wget. Try this and let me know whether it works.
albop
commented
8 years ago This last one is probably related to bug: https://github.com/JuliaWeb/MbedTLS.jl/issues/10 . It is apparently related to where the distribution (Ubuntu I guess) stores its certificates. Another fix, without touching julia sources is:
echo "cacert=/etc/ssl/certs/ca-certificates.crt" > ~/.curlrc
sglyon
commented
8 years ago Thanks @cc7768
And yes, thank you @albop. That's the fix I had in mind.
jstac
commented
8 years ago @spencerlyon2 @cc7768 @albop Thanks guys. I used @albop 's fix. Blosc builds and QuantEcon loads, albeit with a bunch of warnings.
Anything we can do for other users? Do we need a message here:
http://quant-econ.net/jl/getting_started.html#the-quantecon-library
or here:
sglyon
commented
8 years ago I don't see any warnings when build/load quantecon. Can you post what you're seeing?
Some instructions might be helpful.
We really need to do an overhaul of the qe.jl docs. They are really out of date and should probably have a users' guide component in addition to the docstring generated API docs we have right now.
jstac
commented
8 years ago Very happy to devote resources to such things over summer, assuming our coffers are replenished. (We'll know the outcome of the application in mid June but I would say the probability is above 80%.) Even better if you can recruit suitable people and run that show.
Here's my output:
julia> using QuantEcon
WARNING: Method definition levicivita(AbstractArray{#T<:Integer, 1}) in module Base at combinatorics.jl:611 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/permutations.jl:188.
WARNING: Method definition nthperm(AbstractArray{#T<:Integer, 1}) in module Base at combinatorics.jl:92 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/permutations.jl:161.
WARNING: Method definition nthperm(AbstractArray{T<:Any, 1}, Integer) in module Base at combinatorics.jl:89 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/permutations.jl:157.
WARNING: Method definition partitions(Integer) in module Base at combinatorics.jl:252 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/partitions.jl:26.
WARNING: Method definition partitions(Integer, Integer) in module Base at combinatorics.jl:318 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/partitions.jl:93.
WARNING: Method definition partitions(AbstractArray{T<:Any, 1}) in module Base at combinatorics.jl:380 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/partitions.jl:158.
WARNING: Method definition partitions(AbstractArray{T<:Any, 1}, Int64) in module Base at combinatorics.jl:447 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/partitions.jl:228.
WARNING: Method definition combinations(Any, Integer) in module Base at combinatorics.jl:182 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/combinations.jl:42.
WARNING: Method definition nthperm!(AbstractArray{T<:Any, 1}, Integer) in module Base at combinatorics.jl:70 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/permutations.jl:136.
WARNING: Method definition permutations(Any) in module Base at combinatorics.jl:219 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/permutations.jl:24.
WARNING: Method definition factorial(#T<:Integer, #T<:Integer) in module Base at combinatorics.jl:56 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/factorials.jl:18.
WARNING: Method definition factorial(Integer, Integer) in module Base at combinatorics.jl:66 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/factorials.jl:28.
WARNING: Method definition parity(AbstractArray{#T<:Integer, 1}) in module Base at combinatorics.jl:642 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/permutations.jl:221.
WARNING: Method definition prevprod(Array{Int64, 1}, Any) in module Base at combinatorics.jl:565 overwritten in module Combinatorics at /home/john/.julia/v0.4/Combinatorics/src/partitions.jl:354.That'd be great! Let's be on the lookout for people to work on that.
That's really strange that you are seeing those warnings as Combinatorics.jl is a new julia 0.5 only package. It simply contains the combinatorics pieces that are in the julia 0.4 standard library that were split out into their own package. According to the REQUIRE file in Combinatorics.jl you shouldn't even be allowed to install it under and julia 0.4.x
oyamad
commented
8 years ago I got similar warnings on OS X:
julia> using QuantEcon
...
WARNING: Method definition factorial(#T<:Integer, #T<:Integer) in module Base at combinatorics.jl:56 overwritten in module Combinatorics at /Volumes/HD1/Users/oyama/.julia/v0.4/Combinatorics/src/factorials.jl:18.
...
WARNING: Method definition partitions(AbstractArray{T<:Any, 1}, Int64) in module Base at combinatorics.jl:447 overwritten in module Combinatorics at /Volumes/HD1/Users/oyama/.julia/v0.4/Combinatorics/src/partitions.jl:228.julia> versioninfo()
Julia Version 0.4.5
Commit 2ac304d (2016-03-18 00:58 UTC)
Platform Info:
System: Darwin (x86_64-apple-darwin13.4.0)
CPU: Intel(R) Xeon(R) CPU W3580 @ 3.33GHz
WORD_SIZE: 64
BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Nehalem)
LAPACK: libopenblas64_
LIBM: libopenlibm
LLVM: libLLVM-3.3Are people still running into problems? I think @spencerlyon2 made the changes needed to remove errors and warnings.
jstac
commented
8 years ago I'm fine, although I used Pablo's fix earlier.
But in that case why don't we close and reopen if people report further problems?
jstac
commented
8 years ago Still having problems. Just did Pkg.update() and using QuantEcon produces
INFO: Precompiling module QuantEcon...
ERROR: LoadError: LoadError: HDF5 not properly installed. Please run Pkg.build("HDF5")
in error at ./error.jl:21
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
[inlined code] from none:2
in anonymous at no file:0
in process_options at ./client.jl:257
in _start at ./client.jl:378
while loading /home/john/.julia/v0.4/HDF5/src/plain.jl, in expression starting on line 23
while loading /home/john/.julia/v0.4/HDF5/src/HDF5.jl, in expression starting on line 3
ERROR: LoadError: Failed to precompile HDF5 to /home/john/.julia/lib/v0.4/HDF5.ji
in error at ./error.jl:21
in compilecache at loading.jl:400
in require at ./loading.jl:240
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
[inlined code] from none:2
in anonymous at no file:0
in process_options at ./client.jl:257
in _start at ./client.jl:378
while loading /home/john/.julia/v0.4/JLD/src/JLD.jl, in expression starting on line 8
ERROR: LoadError: LoadError: Failed to precompile JLD to /home/john/.julia/lib/v0.4/JLD.ji
in error at ./error.jl:21
in compilecache at loading.jl:400
in require at ./loading.jl:240
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
[inlined code] from none:2
in anonymous at no file:0
in process_options at ./client.jl:257
in _start at ./client.jl:378
while loading /home/john/.julia/v0.4/LightGraphs/src/persistence/jld.jl, in expression starting on line 1
while loading /home/john/.julia/v0.4/LightGraphs/src/LightGraphs.jl, in expression starting on line 159
ERROR: LoadError: LoadError: Failed to precompile LightGraphs to /home/john/.julia/lib/v0.4/LightGraphs.ji
in error at ./error.jl:21
in compilecache at loading.jl:400
in require at ./loading.jl:240
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:320
[inlined code] from none:2
in anonymous at no file:0
in process_options at ./client.jl:257
in _start at ./client.jl:378
while loading /home/john/.julia/v0.4/QuantEcon/src/markov/mc_tools.jl, in expression starting on line 13
while loading /home/john/.julia/v0.4/QuantEcon/src/QuantEcon.jl, in expression starting on line 120Here's version info
Julia Version 0.4.5
Commit 2ac304d (2016-03-18 00:58 UTC)
Platform Info:
System: Linux (x86_64-linux-gnu)
CPU: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
WORD_SIZE: 64
BLAS: libopenblas (NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Haswell)
LAPACK: liblapack.so.3
LIBM: libopenlibm
LLVM: libLLVM-3.3Regarding the warnings on my OS X, using QuantEcon no longer generates them after Pkg.update().
(Combinatorics disappeared from Pkg.status().)
This is what I'm getting. It's actually been failing for a few days, and since before I upgraded to LTS 16.04.
Julia is Version 0.4.5 (2016-03-18 00:58 UTC), downloaded as a PPA.