I tried to compute a small example with the library SimpleHypergraphs. I followed the install instructions however, I have this error :
ERROR: "HyperNetX is not installed in Python used by this Julia. Install HyperNetX and reload SimpleHypergraphs.jl"
Here's my code:
using PyCall
using Conda
Conda.runconda(`install matplotlib --yes`)
Conda.runconda(`install networkx --yes`)
run(`$(PyCall.python) -m pip install hypernetx`)
using SimpleHypergraphs
h = Hypergraph{Float64}(5,4)
h[1:3,1] .= 1.5
h[3,4] = 2.5
h[2,3] = 3.5
h[4,3:4] .= 4.5
h[5,4] = 5.5
h[5,2] = 6.5
draw(h, HyperNetX; width=5, height=5)
I don't understand why this error occurs since hypernetx is well installed.
It seems that pandas has been added to the dependencies of hypernetx and now it will not load unless pandas is available.
Restart your Julia session and run
using Conda
Conda.runconda(`install pandas --yes`)
Now it will work as expected:
draw(h, HyperNetX; width=5, height=5)
Thanks for posting that out! - I will add it to the README of SimpleHypergraphs.
Finally, note that SimpleHypergraphs uses the Python only for the last step - plotting. All processing/computations always take part in Julia so do not worry about all those Python libraries.
Related
I keep receiving this error when trying to derive using sympy.
I have updated sympy using Anaconda Prompt and "conda update sympy" but it made no change when trying to use the derive_by_array function in jupyter-notebook. Perhaps the update isn't registering in jupyter?
What can I do to fix this issue?
Here is a general example of the code where I receive the error:
import sympy as sp
x= sp.symbols('x')
f = x**2
sp.derive_by_array(f,x)
After removing using Anaconda Prompt then installing a newer version of Anaconda, sympy started working.
I'm having issues with Azure Machine Learning SDK for R: "module 'azureml' has no attribute 'core'"...
For reasons that aren't my own, I have to use azureml to apply machine learning (my own stuff, written in R) to data from our data warehouse that is put in the blob storage. The modelled output should be put back into the blob storage so it can be accessed from the data warehouse.
I've written the code in R on my local machine (stored in a git repo). Preferably, I'd find some method to pull my code from git into a pipeline in the azureml environment so that it can be directly run whenever new data is available in the blob storage.
I've embarked on a tutorial-spree and found this seemingly relevant walkthrough: Train and deploy your first model with Azure ML (and this one).
But... after trying all I could think of, I'm stuck on the first steps. After installing all (or at least.. that's what I think) packages, modules, apps etc, and running the following code in RStudio:
library(azuremlsdk)
existing_ws <- get_workspace(name = name,
subscription_id = subscription_id,
resource_group)
I run into an error that I haven't been able to fix:
AttributeError: module 'azureml' has no attribute 'core'
It seems that the azuerml is supposed to have an attribute "core", but when looking at it more closely, there is indeed no such attribute.
The function "get_workspace()" is trying to access: "azureml$core$Workspace$get".
I found that "azuerML$Workspace" does exist, but then I can't figure out how to make that work.
Can anyone explain to me why I'm encountering this error?
Does anyone know of a better tutorial on how to connect my R code the azureml's cloud service?
Any pointers in the right direction are much appreciated!
EDITS - still not solved:
After advice from others, I double, triple and quadruple checked the installation.
I updated R and I'm now running:
R.version
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 6.2
year 2019
month 12
day 12
svn rev 77560
language R
version.string R version 3.6.2 (2019-12-12)
nickname Dark and Stormy Night
I installed Conda with Python 3.6.10.
I installed the azuremlsdk R package (I tried both provided options).
I then realized that there are some inconsistencies with the versions of the azure-modules, so I also tried installing it with the keyword 'multi-arch':
remotes::install_cran('azuremlsdk', repos = 'http://cran.us.r-project.org', INSTALL_opts=c("--no-multiarch"))
Then, I installed the azureml python sdk.
I had a look at all the versions again (using python -m pip freeze):
azure-common==1.1.24
azure-graphrbac==0.61.1
azure-mgmt-authorization==0.60.0
azure-mgmt-containerregistry==2.8.0
azure-mgmt-keyvault==2.0.0
azure-mgmt-resource==7.0.0
azure-mgmt-storage==7.1.0
azureml==0.2.7
azureml-automl-core==1.0.83.1
azureml-core==1.0.69
azureml-dataprep==1.1.36
azureml-dataprep-native==13.2.0
azureml-pipeline==1.0.69
azureml-pipeline-core==1.0.69
azureml-pipeline-steps==1.0.69
azureml-sdk==1.0.69
azureml-telemetry==1.0.69
azureml-train==1.0.69
azureml-train-automl-client==1.0.83
azureml-train-core==1.0.69
azureml-train-restclients-hyperdrive==1.0.69
As I was surprised to see all the 1.0.69 versions, instead of the 1.0.83 versions, I re-installed the azureml python sdk using:
azuremlsdk::install_azureml(version = "1.0.83")
This worked, in the sense that indeed all versions are now 1.0.83:
azure-common==1.1.24
azure-graphrbac==0.61.1
azure-mgmt-authorization==0.60.0
azure-mgmt-containerregistry==2.8.0
azure-mgmt-keyvault==2.0.0
azure-mgmt-resource==7.0.0
azure-mgmt-storage==7.1.0
azureml==0.2.7
azureml-automl-core==1.0.83.1
azureml-core==1.0.83
azureml-dataprep==1.1.36
azureml-dataprep-native==13.2.0
azureml-pipeline==1.0.83
azureml-pipeline-core==1.0.83
azureml-pipeline-steps==1.0.83
azureml-sdk==1.0.83
azureml-telemetry==1.0.83
azureml-train==1.0.83
azureml-train-automl-client==1.0.83
azureml-train-core==1.0.83
azureml-train-restclients-hyperdrive==1.0.83
But still... I get the error with the missing core. I get it both when running:
library(azuremlsdk)
get_current_run()
and also when running:
library(azuremlsdk)
existing_ws <- get_workspace(name = name,
subscription_id = subscription_id,
resource_group)
Note that the first time running this code after starting up RStudio, I get the error:
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'azureml' has no attribute '_base_sdk_common'
And every time after that I get this error:
Error in py_get_attr_impl(x, name, silent) :
AttributeError: module 'azureml' has no attribute 'core'
Any help would be much appreciated!
This issue was introduced by the latest reticulate 1.14 release, in which reticulate would create a default r-reticulate conda environment. Since Azure ML was installing the python SDK in an environment named r-azureml, the r-reticulate environment used by reticulate was missing the python SDK. A fix for this issue was addressed in a PR and has been merged into master. Please install from GitHub for now if you have reticulate version 1.14 and are running into this issue. We will be releasing an update to CRAN shortly.
I seemed to have fixed the issue by specifically installing the python package azureml AND azureml.core:
python -m pip install azureml
and then...
python -m pip install azureml.core
I did this for the Conda version that was called by R (r-reticulate). It's a bit odd to not be able to use the Conda environment 'r-azureml' without R switching back to 'r-reticulate', but ah well... at least I don't get my 'azureml' has no attribute 'core' anymore.
Firstly, I'm a newbie R, AWS and python guy. So I'm trying to get a python script with embedded R code running in AWS Lambda using rpy2. I created a Lambda package on an EC2 instance following the instructions here (modified for using python 3.4). It seems that there is something funky happening with loading the R libs using ctypes, as per the following error received in the console:
OSError: lib/libRrefblas.so: undefined symbol: xerbla_
The test file (py_test.py) looks like this:
import os
import ctypes
for file in os.listdir('lib'):
if os.path.isfile(os.path.join('lib', file)):
ctypes.cdll.LoadLibrary(os.path.join('lib', file))
os.environ["R_HOME"] = os.getcwd()
os.environ["R_USER"] = os.path.join(os.getcwd(), 'rpy2')
os.environ["R_LIBS"] = os.path.join(os.getcwd(), 'library')
os.environ["LD_LIBRARY_PATH"] = os.path.join(os.getcwd(), 'lib')
import sys
sys.path.append(os.path.join(os.getcwd(),'rpy2'))
import rpy2
from rpy2 import robjects
def test_handler(event, context):
robjects.r('''
f <- function(r, verbose=FALSE) {
if (verbose) {
cat("I am calling f().\n")
}
2 * pi * r
}
print(f(3))
''')
test_handler(None,None)
I have lib/libRrefblas.so in my virtual environment. I have scoured google looking for answers but have come up empty. Any suggestions would be greatly appreciated!
If you can get the traceback, that could help, but I suspect the problem is that it's looking for xerbla_ in the wrong place. Is xerbla_ defined in the path to RLIBS? Maybe in libR.so?
Turns out the BLAS that ships with R is corrupt. Your best bet is to make sure that BLAS and Lapack are installed on the machine you are building R on and see if you can get it to build with those libraries instead.
So steps would be to uninstall R, then run
yum -y install lapack-devel.x86_64 lapack.x86_64
yum -y install blas -devel
yum -y install R.x86_64
Check to see if it has still installed with libRrefblas.so. If it has - try deleting that file and see if it will default to the system BLAS. If you get a error because it is still looking for libRrefblas.so
rm lib/libRrefblas.so
cp /usr/lib64/libblas.so.3 lib/
mv lib/libblas.so.3 lib/libRrefblas.so
I just reported the following issue to the hadley/ggplot2-book repository:
When i press STRG+SHIFT+B in RStudio to build the book as described in the Readme I get this error:
mkdir -p book/tex
mkdir -p book/tex/_figures
mkdir -p book/tex/diagrams
cp book/ggplot2-book.tex book/tex/ggplot2-book.tex
Rscript book/render-tex.R data-manip.rmd
Error in rmarkdown::pandoc_options(to = "latex", from = "markdown_style", :
could not find function "pandoc_latex_engine_args"
Calls: <Anonymous> -> <Anonymous> -> structure -> <Anonymous>...
I have R 3.2.2, Rtools 3,2,x , pandoc 1.15.2 and installed all the dependencies as well as the inconsolata font. I have MikTeX 2.9 and also updated all packages that where updatable.
When I try ?pandoc_latex_engine_args (which presumably causes the error) the help page opens so this function should be available to R. I tried on 2 different computers (Windows 10 and Windows 7) and reran the complete installation process on each without any change. I also tried to manually build the book using the Cygwin terminal but this gives the same error.
Has anyone trying to build the book had the same problem or even better: does anyone know how to fix this?
I have used knitr for a long time, usually in the R Studio environment. Recently I installed Python (version 3.4.1) on my Windows machine, put it in the path, and tried out Yi Hui Xie's sample document for Python. But the Python code chunks won't run. From a chunk like this:
{r test-python, engine='python'}
x = 'hello, python world!'
print x
print x.split(' ')
I get an error message like this:
Warning: running command '"python" -c "print '**Write** _something_ in `Markdown` from `Python`!'"' had status 1
running: "python" -c "x = 'hello, python world!'
print x
print x.split(' ')"
File "<string>", line 2
print x
^
SyntaxError: invalid syntax
I'm in Windows 7, running R 3.1.0, with RStudio Version 0.98.847 (beta preview version). Interactive Python opens just fine from the command line.
Any ideas?
Your issue is that you've installed python3, but the syntax you're using is python2. The py2 -> py3 transition involved changes to the language itself -- in your example, print has changed from a syntax to a function. (So print(x) would work in your code above.)
The easiest option is to uninstall python3 and install the most recent Python 2.7 (currently Python 2.7.6). Alternately, onward and upward -- use py3, which just involves possibly tweaking any existing examples you run into in knitr.