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Cannot load dataset from sotu.jl #22

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williamjin1992 opened this issue Oct 7, 2021 · 5 comments
Open

Cannot load dataset from sotu.jl #22

williamjin1992 opened this issue Oct 7, 2021 · 5 comments

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@williamjin1992
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williamjin1992 commented Oct 7, 2021

Hi Professor Manela:
I'm running your tutorial of HurdleDMR for python in Jupyter Notebook, but in the data loading cell, an error pops out

---------------------------------------------------------------------------
JuliaError                                Traceback (most recent call last)
C:\Users\WILLIA~1\AppData\Local\Temp\15/ipykernel_4324/482917954.py in <module>
----> 1 covarsdf, counts, terms = jl.eval('include("D:/William/sotu.jl")')

C:\ProgramData\Anaconda3\lib\site-packages\julia\core.py in eval(self, src)
    603         if src is None:
    604             return None
--> 605         ans = self._call(src)
    606         if not ans:
    607             return None

C:\ProgramData\Anaconda3\lib\site-packages\julia\core.py in _call(self, src)
    536         # logger.debug("_call(%s)", src)
    537         ans = self.api.jl_eval_string(src.encode('utf-8'))
--> 538         self.check_exception(src)
    539 
    540         return ans

C:\ProgramData\Anaconda3\lib\site-packages\julia\core.py in check_exception(self, src)
    585         else:
    586             exception = sprint(showerror, self._as_pyobj(res))
--> 587         raise JuliaError(u'Exception \'{}\' occurred while calling julia code:\n{}'
    588                          .format(exception, src))
    589 

JuliaError: Exception 'LoadError: could not load library "libdSFMT"
The specified module could not be found. 
in expression starting at D:\William\sotu.jl:210' occurred while calling julia code:
include("D:/William/sotu.jl")

I think it maybe something wrong with the code in sotu.jl?

@williamjin1992
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A follow-up:
When a delete the argument in the last line in sotu.jl, use covarsdf, counts, terms = loadsoturet() instead of covarsdf, counts, terms = loadsoturet(cache=false), the code runs smoothly and no error returns.

@griff-rees
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Thanks @williamjin1992, this proved useful for my colleague and I. @AsafManela would you like a pull request?

@AsafManela
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Sure, a PR would be welcome!

griff-rees added a commit to griff-rees/HurdleDMR.jl that referenced this issue Mar 2, 2023
This is a first step in the pull request. Assuming this is amenable, then altering the notebooks to simply add that line in, easing customisation (ie skipping the cache option, which solves AsafManela#22 in `python`) would be the next step.
@griff-rees
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Hi @AsafManela: just thought I'd enquire if you're happy with that direction for developing a pull request. The next step would be to add the equivalent line removed there to all the notebook examples (which I think is more flexible and makes clearer what sotu.jl provides).

Line removed:

covarsdf, counts, terms = loadsoturet(cache=false)

@AsafManela
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This line cannot be removed entirely because then the jupyter notebooks that include sotu.jl won't get the variables they expect (covarsdf, counts, terms).
If you mean you want to move that line from sotu.jl to those notebooks, I'm fine with that. Just need to make sure it works in all 3 languages.

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