为 R 中的文本包构建奇点容器未找到 python 个库
Building a singularity container for the text-package in R does not find python libraries
我想为 R 中的 text
包构建一个奇点容器(使用网状结构访问 python)。构建奇点容器,安装文本包,并且可以 运行 textEmbed("hello") 作为安装过程的一部分。
但是当我启动奇点容器然后 运行:Rscript -e 'text::textEmbed("hello")'
。我收到一个错误读数:
Error: Python shared library not found, Python bindings not loaded.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
但我已确认它已安装并且 textEmbed("hello")
在安装过程的最后有效。下面是我用来构建奇点容器的文件。
Bootstrap: docker
From: ubuntu:20.04
%environment
export LANG=C.UTF-8 LC_ALL=C.UTF-8
export XDG_RUNTIME_DIR=/tmp/.run_$(uuidgen)
%post
# Install
apt-get -y update
export R_VERSION=4.1.3
echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
# Install R
apt-get update
apt-get install -y --no-install-recommends software-properties-common dirmngr wget uuid-runtime
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository \
"deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt-get install -y --no-install-recommends \
r-base=${R_VERSION}* \
r-base-core=${R_VERSION}* \
r-base-dev=${R_VERSION}* \
r-recommended=${R_VERSION}* \
r-base-html=${R_VERSION}* \
r-doc-html=${R_VERSION}* \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libcairo2-dev \
libxt-dev \
libopenblas-dev
# Add a default CRAN mirror
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
# Fix R package libpaths (helps RStudio Server find the right directories)
mkdir -p /usr/lib64/R/etc
echo "R_LIBS_USER='/usr/lib64/R/library'" >> /usr/lib64/R/etc/Renviron
echo "R_LIBS_SITE='${R_PACKAGE_DIR}'" >> /usr/lib64/R/etc/Renviron
# Clean up
rm -rf /var/lib/apt/lists/*
# Install python3
apt-get -y install python3 wget
apt-get -y clean
/bin/bash <<EOF
# Install reticulate and text
Rscript -e 'install.packages("reticulate")'
Rscript -e 'install.packages("devtools")'
Rscript -e 'install.packages("glmnet")'
Rscript -e 'devtools::install_github("oscarkjell/text")'
# Create the Conda environment at a system folder
Rscript -e 'text::textrpp_install(prompt = FALSE)'
Rscript -e 'text::textrpp_initialize(save_profile = TRUE, prompt = FALSE, textEmbed_test = TRUE)'
EOF
我设法通过在安装 text-package 之前安装 Miniconda 使其工作(请参阅下面的安装 Miniconda 部分)。
Bootstrap: docker
From: ubuntu:20.04
%environment
export LANG=C.UTF-8 LC_ALL=C.UTF-8
export XDG_RUNTIME_DIR=/tmp/.run_$(uuidgen)
%post
# Install
apt-get -y update
export R_VERSION=4.1.3
echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
# Install R
apt-get update
apt-get install -y --no-install-recommends software-properties-common dirmngr wget uuid-runtime
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository \
"deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt-get install -y --no-install-recommends \
r-base=${R_VERSION}* \
r-base-core=${R_VERSION}* \
r-base-dev=${R_VERSION}* \
r-recommended=${R_VERSION}* \
r-base-html=${R_VERSION}* \
r-doc-html=${R_VERSION}* \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libcairo2-dev \
libxt-dev \
libopenblas-dev
# Add a default CRAN mirror
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
# Fix R package libpaths (helps RStudio Server find the right directories)
mkdir -p /usr/lib64/R/etc
echo "R_LIBS_USER='/usr/lib64/R/library'" >> /usr/lib64/R/etc/Renviron
echo "R_LIBS_SITE='${R_PACKAGE_DIR}'" >> /usr/lib64/R/etc/Renviron
# Clean up
rm -rf /var/lib/apt/lists/*
# Install python3
apt-get -y install python3 wget
apt-get -y clean
# Install Miniconda
cd /
wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda
/bin/bash <<EOF
rm Miniconda3-latest-Linux-x86_64.sh
source /miniconda/etc/profile.d/conda.sh
conda update -y conda
# Install reticulate and text
Rscript -e 'install.packages("reticulate")'
Rscript -e 'install.packages("devtools")'
Rscript -e 'install.packages("glmnet")'
Rscript -e 'devtools::install_github("oscarkjell/text")'
# Create the Conda environment at a system folder
Rscript -e 'text::textrpp_install(prompt = FALSE)'
Rscript -e 'text::textrpp_initialize(save_profile = TRUE, prompt = FALSE, textEmbed_test = TRUE)'
EOF
我想为 R 中的 text
包构建一个奇点容器(使用网状结构访问 python)。构建奇点容器,安装文本包,并且可以 运行 textEmbed("hello") 作为安装过程的一部分。
但是当我启动奇点容器然后 运行:Rscript -e 'text::textEmbed("hello")'
。我收到一个错误读数:
Error: Python shared library not found, Python bindings not loaded.
Use reticulate::install_miniconda() if you'd like to install a Miniconda Python environment.
但我已确认它已安装并且 textEmbed("hello")
在安装过程的最后有效。下面是我用来构建奇点容器的文件。
Bootstrap: docker
From: ubuntu:20.04
%environment
export LANG=C.UTF-8 LC_ALL=C.UTF-8
export XDG_RUNTIME_DIR=/tmp/.run_$(uuidgen)
%post
# Install
apt-get -y update
export R_VERSION=4.1.3
echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
# Install R
apt-get update
apt-get install -y --no-install-recommends software-properties-common dirmngr wget uuid-runtime
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository \
"deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt-get install -y --no-install-recommends \
r-base=${R_VERSION}* \
r-base-core=${R_VERSION}* \
r-base-dev=${R_VERSION}* \
r-recommended=${R_VERSION}* \
r-base-html=${R_VERSION}* \
r-doc-html=${R_VERSION}* \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libcairo2-dev \
libxt-dev \
libopenblas-dev
# Add a default CRAN mirror
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
# Fix R package libpaths (helps RStudio Server find the right directories)
mkdir -p /usr/lib64/R/etc
echo "R_LIBS_USER='/usr/lib64/R/library'" >> /usr/lib64/R/etc/Renviron
echo "R_LIBS_SITE='${R_PACKAGE_DIR}'" >> /usr/lib64/R/etc/Renviron
# Clean up
rm -rf /var/lib/apt/lists/*
# Install python3
apt-get -y install python3 wget
apt-get -y clean
/bin/bash <<EOF
# Install reticulate and text
Rscript -e 'install.packages("reticulate")'
Rscript -e 'install.packages("devtools")'
Rscript -e 'install.packages("glmnet")'
Rscript -e 'devtools::install_github("oscarkjell/text")'
# Create the Conda environment at a system folder
Rscript -e 'text::textrpp_install(prompt = FALSE)'
Rscript -e 'text::textrpp_initialize(save_profile = TRUE, prompt = FALSE, textEmbed_test = TRUE)'
EOF
我设法通过在安装 text-package 之前安装 Miniconda 使其工作(请参阅下面的安装 Miniconda 部分)。
Bootstrap: docker
From: ubuntu:20.04
%environment
export LANG=C.UTF-8 LC_ALL=C.UTF-8
export XDG_RUNTIME_DIR=/tmp/.run_$(uuidgen)
%post
# Install
apt-get -y update
export R_VERSION=4.1.3
echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
# Install R
apt-get update
apt-get install -y --no-install-recommends software-properties-common dirmngr wget uuid-runtime
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository \
"deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
apt-get install -y --no-install-recommends \
r-base=${R_VERSION}* \
r-base-core=${R_VERSION}* \
r-base-dev=${R_VERSION}* \
r-recommended=${R_VERSION}* \
r-base-html=${R_VERSION}* \
r-doc-html=${R_VERSION}* \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libcairo2-dev \
libxt-dev \
libopenblas-dev
# Add a default CRAN mirror
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
# Fix R package libpaths (helps RStudio Server find the right directories)
mkdir -p /usr/lib64/R/etc
echo "R_LIBS_USER='/usr/lib64/R/library'" >> /usr/lib64/R/etc/Renviron
echo "R_LIBS_SITE='${R_PACKAGE_DIR}'" >> /usr/lib64/R/etc/Renviron
# Clean up
rm -rf /var/lib/apt/lists/*
# Install python3
apt-get -y install python3 wget
apt-get -y clean
# Install Miniconda
cd /
wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda
/bin/bash <<EOF
rm Miniconda3-latest-Linux-x86_64.sh
source /miniconda/etc/profile.d/conda.sh
conda update -y conda
# Install reticulate and text
Rscript -e 'install.packages("reticulate")'
Rscript -e 'install.packages("devtools")'
Rscript -e 'install.packages("glmnet")'
Rscript -e 'devtools::install_github("oscarkjell/text")'
# Create the Conda environment at a system folder
Rscript -e 'text::textrpp_install(prompt = FALSE)'
Rscript -e 'text::textrpp_initialize(save_profile = TRUE, prompt = FALSE, textEmbed_test = TRUE)'
EOF