Dockerfile配置R环境-无法加载某些包

Question

Dockerfile配置R环境-无法加载某些包

4

我在尝试通过dockerfile将R加载到我的Docker容器中。某些R包无法成功安装，例如rvest。我同时也在安装NiFi和Python。以下是我的dockerfile：

FROM apache/nifi

ADD run.sh .
COPY nifi-extracttext-nar-1.5.nar /opt/nifi/nifi-1.8.0/lib
USER root
RUN apt-get update
RUN apt-get install -y python3 python3-dev python3-pip
RUN pip3 install bs4
RUN pip3 install requests
RUN chmod 777 run.sh

# PROBLEM AREA (everything above works great)
RUN apt-get -y install r-base
RUN apt-get -y install libcurl4-openssl-dev
RUN apt-get install libcurl4-openssl-dev

#setup R configs

FROM r-base:latest
RUN Rscript -e "install.packages('tidyverse', repos = 'http://cran.us.r-project.org')"
RUN Rscript -e "install.packages('httr', repos = 'http://cran.us.r-project.org')"
RUN Rscript -e "install.packages('rvest', repos = 'http://cran.us.rproject.org')"

USER nifi

ENTRYPOINT ["./run.sh"]

问题点肯定是安装R本身以及我想要的软件包。如何正确格式化R软件包安装？我最初从此链接中提取了格式，但不确定Rscript是否正确。

在这里，rvest似乎是一个特别棘手的问题。

更新：

当我尝试在docker构建/运行后运行我的脚本时，我得到了这个错误：

Error in library(httr) : there is no package called ‘httr’
Execution halted

ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/usr/local/lib/R/site-library/httr’

为什么会发生这种情况？我是通过docker安装的。

以下是一些错误信息：

The downloaded source packages are in
'/tmp/RtmpykICxP/downloaded_packages'
Warning messages:
1: In install.packages("rvest", repos = "http://cran.us.r-project.org") :
installation of package 'openssl' had non-zero exit status
2: In install.packages("rvest", repos = "http://cran.us.r-project.org") :
installation of package 'xml2' had non-zero exit status
3: In install.packages("rvest", repos = "http://cran.us.r-project.org") :
installation of package 'httr' had non-zero exit status
4: In install.packages("rvest", repos = "http://cran.us.r-project.org") :
installation of package 'rvest' had non-zero exit status

And:

ERROR: configuration failed for package ‘xml2’
* removing ‘/usr/local/lib/R/site-library/xml2’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/usr/local/lib/R/site-library/httr’
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’
* removing ‘/usr/local/lib/R/site-library/rvest’

And:

ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’

在通过终端爬行并构建图像后，我发现了这些错误。

- papelr

1个回答

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原文链接

- bruce.moran · Accepted Answer

您需要为操作系统安装xml2，openssl软件包。

RUN apt-get -y install xml2 openssl

请注意，-y指定了对apt-get install的肯定回答，因此您可以删除。

RUN apt-get install libcurl4-openssl-dev

与前一行相同，您可能还需要安装R包的依赖项。

例如，您可能希望为R软件包安装依赖项。

RUN Rscript -e "install.packages('tidyverse', repos = 'http://cran.us.r-project.org', dependencies=TRUE)"

希望这有所帮助。