[英]Installing rJava package with Docker
I am trying to install the 'rJava'
package in my RStudio docker image using my Dockerfile :我正在尝试使用我的Dockerfile在我的RStudio docker映像中安装'rJava'
包:
FROM rocker/tidyverse:3.6.1
RUN mkdir -p /rstudio
RUN mkdir -p /rscripts
RUN apt-get update && \
apt-get install -y openjdk-11-jdk && \
apt-get install -y liblzma-dev && \
apt-get install -y libbz2-dev
RUN R -e "install.packages(c('rJava','mailR'))"
Following this SO post I added the above part with the apt-get
commands but still I get the same error:在此SO 帖子之后,我使用apt-get
命令添加了上述部分,但仍然出现相同的错误:
java libs : '-L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm' checking whether Java run-time works... ./configure: line 3766: /usr/bin/java: No such file or directory no configure: error: Java interpreter '/usr/bin/java' does not work ERROR: configuration failed for package 'rJava' java libs:'-L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm'检查Java运行时是否有效......./configure:第3766行:/usr /bin/java:没有这样的文件或目录没有配置:错误:Java 解释器“/usr/bin/java”不起作用错误:包“rJava”的配置失败
So there is a missing file or directory but I don't know what changes I should make.所以有一个丢失的文件或目录,但我不知道我应该做哪些更改。
[EDIT 1]: [编辑 1]:
So, following Dirk's suggestion, I entered in the rstudio container and ran apt-get install r-cran-rjava
which seems to work.因此,按照 Dirk 的建议,我进入了 rstudio 容器并运行了apt-get install r-cran-rjava
这似乎有效。
But when I install rJava
package I get a new error:但是当我安装rJava
包时,我收到一个新错误:
error: Cannot compile a simple JNI program.错误:无法编译简单的 JNI 程序。 Make sure you have Java Development Kit installed and correctly registered in R. If in doubt, re-run "R CMD javareconf" as root.确保您已安装 Java Development Kit 并在 R 中正确注册。如果有疑问,请以 root 身份重新运行“R CMD javareconf”。
I tried to enter again in the container and run R CMD javareconf
but that did not change the error.我尝试再次进入容器并运行R CMD javareconf
但这并没有改变错误。 I also tried the following commands found on this article :我还尝试了本文中的以下命令:
sudo apt-get install default-jre
sudo apt-get install default-jdk
But I still get:但我仍然得到:
Cannot compile a simple JNI program.无法编译简单的 JNI 程序。
This is a duplicate of similar answers I have already given in the Debian / Ubuntu context.这是我在 Debian / Ubuntu 上下文中已经给出的类似答案的重复。 The fact that you are using Docker does not matter: you should still simply install the binary!您使用 Docker 的事实并不重要:您仍然应该简单地安装二进制文件!
edd@rob:~$ docker run --rm -ti r-base bash
root@ef4bb9726a21:/# apt update -qq
73 packages can be upgraded. Run 'apt list --upgradable' to see them.
root@ef4bb9726a21:/# apt install --no-install-recommends -y r-cran-rjava
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
ca-certificates-java default-jre default-jre-headless java-common libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libcups2 libdbus-1-3 libdrm-amdgpu1 libdrm-common
libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0 liblcms2-2 libllvm10 libnspr4 libnss3 libpciaccess0 libpcsclite1
libsensors-config libsensors5 libsqlite3-0 libvulkan1 libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-sync1 libxdamage1 libxfixes3 libxi6 libxshmfence1 libxtst6 libxxf86vm1 libz3-4
openjdk-11-jre openjdk-11-jre-headless
[.... many lines skipped ....]
Running hooks in /etc/ca-certificates/update.d...
done.
done.
root@ef4bb9726a21:/# R
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
[...some lines skipped...]
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(rJava)
>
I found a github repo suggesting to add these steps in the Dockerfile before installing R package rJava
and it worked:我发现一个 github repo 建议在安装 R 包rJava
之前在 Dockerfile 中添加这些步骤并且它起作用了:
RUN apt-get -y update && apt-get install -y \
default-jdk \
r-cran-rjava \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/
The reason why Dirk's answer doesn't work for you is because you're using rocker/tidyverse
as a base image instead of the r-base
that Dirk is using. Dirk 的答案对您不起作用的原因是因为您使用的是rocker/tidyverse
作为基础图像,而不是 Dirk 正在使用的r-base
。
In the rocker/tidyverse
documentation on Docker Hub they are discouraging the use of apt install --no-install-recommends -y r-cran-rjava
:在 Docker Hub 上的rocker/tidyverse
文档中,他们不鼓励使用apt install --no-install-recommends -y r-cran-rjava
:
do not use
apt-get install r-cran-*
to install R packages on this stack.不要使用apt-get install r-cran-*
在此堆栈上安装 R 包。 The requested R version and all R packages are installed from source in the version-stable stack.请求的 R 版本和所有 R 包都从版本稳定堆栈中的源代码安装。 Installing R packages from apt (eg the r-cran-* packages) will install the version of R and versions of the packages that were built for the stable debian release (eg debian:stretch), giving you a second version of R and different packages.从 apt 安装 R 包(例如 r-cran-* 包)将安装 R 的版本和为稳定的 debian 版本构建的包的版本(例如 debian:stretch),为您提供第二个 R 版本和不同的版本包。 Please install R packages from source using the install.packages() R function (or the install2.r script), and use apt only to install necessary system libraries (eg libxml2).请使用 install.packages() R 函数(或 install2.r 脚本)从源代码安装 R 包,并且仅使用 apt 安装必要的系统库(例如 libxml2)。 If you would prefer to install only the latest verions of packages from pre-built binaries using apt-get, consider using the r-base stack instead.如果您只想使用 apt-get 安装来自预先构建的二进制文件的最新版本的软件包,请考虑使用 r-base 堆栈。
Since rJava
is supposed to be installed with apt install r-cran-rjava
, but the rocker/...
base images explicitly tell you not to do that, it looks like you will not be able to use rJava
with any of the rocker/...
base images..由于rJava
应该与apt install r-cran-rjava
一起apt install r-cran-rjava
,但是apt install r-cran-rjava
rocker/...
基本图像明确告诉您不要这样做,看起来您将无法将rJava
与任何rJava
rocker/...
基本图像..
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