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cma2015 / DeepGS

DeepGS is a R package for predicting phenotypes from genotypes using deep learning techniques.
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mxnet #4

Open ghost opened 5 years ago

ghost commented 5 years ago

Hey, Can you share the R package mxnet? I can't compile it.

zhaijj commented 5 years ago

@gulinlin @gulinlin Hi, the newest version of mxnet can be installed from official instructions (https://mxnet.incubator.apache.org/install/)

if you still can't compile it, you can try following steps: git clone --no-checkout https://github.com/apache/incubator-mxnet cd incubator-mxnet git remote -v git fetch origin git branch -avv git checkout #check out you version git submodule update --init --recursive comple for CPU version (optional) make -j $(nproc) USE_OPENCV=1 USE_BLAS=openblas USE_CUDA=0 compile for GPU version make -j $(nproc) USE_OPENCV=1 USE_BLAS=openblas USE_CUDA=1 USE_CUDA_PATH=/usr/local/cuda make rpkg R CMD INSTALLL mxnet_current_r.tar.gz

After these steps, mxnet will be installed successfully, and you can test by the following: library(mxnet) a <- mx.nd.ones(c(2,3), ctx=mx.gpu()) b <- a*2+1 b

Of note, for Linux operating system, some R packages have to be installed manually using "apt-get" when compiling

Anyway, we strongly recommend you to use our developed Docker image DeepGS, the detailed installation steps are available at: https://github.com/cma2015/DeepGS/blob/master/DeepGS_User_Manual.pdf

ghost commented 5 years ago

Hi, I tried to install it with your method. I get the following error message: I am using R 3.4.0 with centOS 6.2

1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version while accessing https://github.com/apache/incubator-mxnet/info/refs fatal: HTTP request failed

do you have any idea what the issue might be?

zhaijj commented 5 years ago

@gulinlin According to your description, the most possible reason is your network, for Chinese users, may be VPN is necessary when cloning some packages from github

ghost commented 5 years ago

Hi,I want to use your developed Docker image DeepGS. But I can't compile it. Can you help me to compile the R package mxnet? My email address is gulinlin_141006@163.com. Thank you very much.