Comments (13)
papamarkou
commented on June 10, 2024
Thanks for your feedback @scheidan. I am aware that the model parsing of the MCMC package is unfortunately broken with version 0.3.0 of Julia. I am not intervening as we agreed with @fredo-dedup to let him deal with the issue, particularly in relation to the graph model-based parsing.
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fredo-dedup
commented on June 10, 2024
I think the problem is related to changes in the AST for the ~ symbol in the new version of julia ( #4882 ? ) . @scheidan would it be practical for you to revert to Julia 0.2.0 ?
I'll correct this once 0.3.0 is officially out.
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scheidan
commented on June 10, 2024
Thanks @fredo-dedup and @scidom, I appreciate your effort very much!
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fredo-dedup
commented on June 10, 2024
Last commit solves this issue.
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papamarkou
commented on June 10, 2024
@fredo-dedup, this hasn't been resolved (this is why I am reopening the issue). This is the error I get, which seems to be a bug in the ReverseDiffSource package:
ERROR: no method start(Symbol)
in union! at set.jl:23
in getSymbols at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:40
in mr_pairwise at reduce.jl:534
in mapreduce at reduce.jl:546
in getSymbols at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:44
in getSymbols at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:42
in explore at /home/theodore/.julia/v0.3/ReverseDiffSource/src/pass1.jl:104
in explore at /home/theodore/.julia/v0.3/ReverseDiffSource/src/pass1.jl:83
in map_to! at abstractarray.jl:1234
in map at abstractarray.jl:1243
in varGraph at /home/theodore/.julia/v0.3/ReverseDiffSource/src/pass1.jl:131
in reversediff at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:136
in generateModelFunction at /home/theodore/.julia/v0.3/MCMC/src/parsers/modelparser.jl:73
in MCMCLikelihoodModel at /home/theodore/.julia/v0.3/MCMC/src/modellers/MCMCLikModel.jl:93
in model at /home/theodore/.julia/v0.3/MCMC/src/modellers/models.jl:28
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fredo-dedup
commented on June 10, 2024
Sorry about that @scidom. Can you tell me how it happened so that I can reproduce it ?
Thanks.
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papamarkou
commented on June 10, 2024
Thanks for looking into it @fredo-dedup. I am not in front of my laptop to copy-paste the relevant code, it's simply the first example in readme (mymodel3).
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fredo-dedup
commented on June 10, 2024
I can't reproduce your error message. I have tried both master and 0.0.5 - tagged versions of MCMC and all the tests pass.
Here is the output of Pkg.status() :
Pkg.status()
3 required packages:
- Gadfly 0.2.5
- IJulia 0.1.4
- PyPlot 1.2.2
28 additional packages:
- ArrayViews 0.4.1
- BinDeps 0.2.12
- Blocks 0.0.2
- Codecs 0.1.0
- Color 0.2.8
- Compose 0.1.27
- DataArrays 0.1.3
- DataFrames 0.5.3
- Datetime 0.1.2
- Distance 0.3.1
- Distributions 0.4.2
- GZip 0.2.12
- Hexagons 0.0.1
- Iterators 0.1.2
- JSON 0.3.5
- Loess 0.0.2
- MCMC 0.0.5+ master
- Nettle 0.1.3
- NumericExtensions 0.6.0
- NumericFuns 0.2.1
- PDMats 0.1.1
- PyCall 0.4.2
- REPLCompletions 0.0.0
- ReverseDiffSource 0.0.2
- SortingAlgorithms 0.0.1
- StatsBase 0.3.9
- URIParser 0.0.1
- ZMQ 0.1.9
and versioninfo() :
Julia Version 0.3.0-prerelease
Platform Info:
System: Linux (x86_64-linux-gnu)
CPU: Intel(R) Core(TM) i7 CPU 920 @ 2.67GHz
WORD_SIZE: 64
BLAS: libopenblas (NO_LAPACK NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY)
LAPACK: liblapack.so.3
LIBM: libopenlibm
Do you have the correct version of ReverseDiffSource (0.0.2) ?
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papamarkou
commented on June 10, 2024
Hi @fredo-dedup, thanks for looking into this. I have the latest Julia (based on its latest commit on Github), and the packages updated to their latest version (ReverseDiffSource is indeed v0.0.2). Trying the example
using MCMC
modelexpr = quote
v ~ Normal(0, 1)
end
mcmodel = model(modelexpr, v=ones(3))
I get the error
ERROR: no method start(Symbol)
in union! at set.jl:23
in getSymbols at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:40
in mr_pairwise at reduce.jl:534
in mapreduce at reduce.jl:546
in getSymbols at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:44
in getSymbols at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:42
in explore at /home/theodore/.julia/v0.3/ReverseDiffSource/src/pass1.jl:104
in explore at /home/theodore/.julia/v0.3/ReverseDiffSource/src/pass1.jl:83
in map_to! at abstractarray.jl:1234
in map at abstractarray.jl:1243
in varGraph at /home/theodore/.julia/v0.3/ReverseDiffSource/src/pass1.jl:131
in reversediff at /home/theodore/.julia/v0.3/ReverseDiffSource/src/reversediff.jl:136
in generateModelFunction at /home/theodore/.julia/v0.3/MCMC/src/parsers/modelparser.jl:73
in MCMCLikelihoodModel at /home/theodore/.julia/v0.3/MCMC/src/modellers/MCMCLikModel.jl:93
in model at /home/theodore/.julia/v0.3/MCMC/src/modellers/models.jl:28
Here is what I get via Pkg.versioninfo():
Julia Version 0.3.0-prerelease+2118
Commit 6ea7022* (2014-03-19 21:35 UTC)
Platform Info:
System: Linux (x86_64-linux-gnu)
CPU: Intel(R) Core(TM) i3 CPU M 370 @ 2.40GHz
WORD_SIZE: 64
BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY)
LAPACK: libopenblas
LIBM: libopenlibm
and here is what Pkg.status() gives me:
12 required packages:
- DualNumbers 0.0.1
- GLM 0.3.0
- Gadfly 0.2.5
- IJulia 0.1.4
- MAT 0.2.3
- NLopt 0.0.3
- Optim 0.2.0
- ProgressMeter 0.0.1
- ReverseDiffSource 0.0.2
- TimeSeries 0.3.7
- Vega 0.0.0
- Winston 0.9.0
33 additional packages:
- ArrayViews 0.4.1
- BinDeps 0.2.12
- Blocks 0.0.2
- Cairo 0.2.12
- Calculus 0.1.3
- Codecs 0.1.0
- Color 0.2.8
- Compose 0.1.27
- DataArrays 0.1.4
- DataFrames 0.5.3
- Datetime 0.1.2
- Distance 0.3.1
- Distributions 0.4.2
- GZip 0.2.12
- HDF5 0.2.20
- Hexagons 0.0.1
- IniFile 0.2.2
- Iterators 0.1.2
- JSON 0.3.5
- Loess 0.0.2
- MCMC 0.0.3+ master
- Nettle 0.1.3
- NumericExtensions 0.6.0
- NumericFuns 0.2.1
- Options 0.2.2
- PDMats 0.1.1
- REPLCompletions 0.0.0
- SortingAlgorithms 0.0.1
- StatsBase 0.3.9
- Tk 0.2.11
- URIParser 0.0.1
- ZMQ 0.1.9
- Zlib 0.1.5
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fredo-dedup
commented on June 10, 2024
Sorry for the delay @scidom, I am still looking into it but can't reproduce at this moment. I am trying to see if it is related to a specific julia version.
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papamarkou
commented on June 10, 2024
No worries @fredo-dedup, I think you are right, it has to do with the version of Julia. To double check whether this is true, I will try later to use an older version of Julia in order to see if the error vanishes.
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fredo-dedup
commented on June 10, 2024
I finally found it ( you can no longer create sets with Set(a,b,c,d) ).
I upgraded ReverseDiffSource to 0.0.3 (the pull request in METADATA is pending), updated the REQUIRE of MCMC, and removed commented out tests in runtests.jl.
Let me know if it works for you (tested on my side with the latest julia ), I won't close this issue until then. Thanks.
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papamarkou
commented on June 10, 2024
Yes, this works now, I don't get the above error anymore. Thanks @fredo-dedup, I will now close this issue.
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