Comments (10)
I am also having this issue. Any help would be appreciated.
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This seems to be an issue with a specific R-python combination which I couldn't reproduce. Try this workaround:
When attaching the package, this line is normally executed: python.load(system.file("pysrc","init_data.py",package="scLVM“))
It seems this doesn’t happen for you which is why it doesn’t find the scLVM function. Execute this manually after loading the package, this normally solves the problem.
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This work around worked well for the init function, but I got a very similar error when trying to run Ycorr = getCorrectedExpression(sclvm)
Error in python.exec(paste("Ycorr = ", objName, ".getCorrectedExpression(rand_eff_ids)", :
name 'sclvm' is not defined
Is there a similar work around?
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I had a similar problem with this. My problem went away when I correctly installed rPython. First, make sure your ~/bash_To do this, download a new rPython package and open your terminal and type these commands
python --version
export RPYTHON_PYTHON_VERSION="whatever python anaconda version such as 2.7.12"
R CMD INSTALL /Users/egoossen/Downloads/rPython_0.0-6.tar.gz
Now go into R and type
library(rPython)
python.exec("import sys; print(sys.version)")
and verify that it is the same. When you load the scLVM package more than once, it doesn't give the same error about differing versions of python between the system and rPython versions.
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I have the same problem. I tried set "export RPYTHON_PYTHON_VERSION=2.7.13", and "R CMD INSTALL rPython_0.0-6.tar.gz", but when I check like this:
library(rPython)
python.exec("import sys;print(sys.version)")
I got something like:
"2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609]
"
I have several python version, and 2.7.13 is in the anaconda. Obviously, set "export" is invalid. Then, how should I do?
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I'm sure that my rPython was installed correctly now, but there was something wrong with scLVM like below:
library(scLVM)
[1] "It seems python package deprecated is not installed. Try to install it using 'pip install deprecated ' If the package is installed already, make sure rPyhton is using the correct python version. If you have several versions of python installed, have a look at our installation guide on github."
And when I tried to install deprecated like below:
pip install deprecated
Collecting deprecated
Could not find a version that satisfies the requirement deprecated (from versions: )
No matching distribution found for deprecated
I don't know why, and I'll appreciate if someone can give me a hand.
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Also having this problem with "deprecated". This is caused by the attempt to import limix.deprecated. From what I gather at some point they deprecated a whole version of LIMIX, they then deprecated that whole LIMIX package and made a new one with the same name. Now the new one does not have the deprecated version included and I assume this is the version installed by pip, so scLVM will not find limix.deprecated.
If the new version is backwards compatible then it may be possible to simply import limix rather than limix.deprecated, otherwise one would need to install the deprecated version of limix to get this software to work.
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@BinDuan unfortunately rPython does not work with Anaconda python (also check out the rPython docs), maybe try to use the one that came with your OS? I have fixed the "deprecated" problem though which occurred due to some changes in the latest release of limix.
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