Python 如何从 ubuntu 安装 R 包到 docker 容器

发布于05月07日

我对多克是全新的.我正在try 创建一个运行Snakemake管道的容器.该管道将包含R和Python脚本.最终，我将需要添加一个conda环境，并克隆并构建一个git hub repo.但现在，我只是try 正确安装我的python和R包.

我一开始遵循了this个问题的建议，创建了一个既有Python又有R的环境.

到目前为止，这是我的文档文件.

FROM ubuntu:latest

ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y --no-install-recommends build-essential r-base python3.9 python3-pip python3-setuptools python3-dev

WORKDIR /app

RUN pip3 install biopython
RUN pip3 install pandas
RUN pip3 install numpy


RUN Rscript -e "install.packages('tidyverse')"
RUN Rscript -e "install.packages('dplyr')"
RUN Rscript -e "install.packages('testit')"
RUN Rscript -e "install.packages('stringr')"
RUN Rscript -e "install.packages('BiocParallel')"
RUN Rscript -e "install.packages('MPRAnalyze')"

COPY test.R /app

CMD ["Rscript", "test.R"]

Test.R脚本包含以下内容:

library(dplyr)
print("dplyr working!")
library(testit)
print("testit working!")
library(stringr)
print("stringr working!")
library(tidyverse)
print("tidyverse working!")
library(BiocParallel)
print("BiocParallel working!")
library(MPRAnalyze)
print("MPRAnalyze working!")

当我跑docker build英里的时候，它似乎运行得很好.一切都安装好了.

 => [internal] load build definition from Dockerfile                       0.0s
 => => transferring dockerfile: 706B                                       0.0s
 => [internal] load .dockerignore                                          0.0s
 => => transferring context: 2B                                            0.0s
 => [internal] load metadata for docker.io/library/ubuntu:latest           1.3s
 => [ 1/13] FROM docker.io/library/ubuntu:latest@sha256:dfd64a3b4296d8c9b  0.0s
 => [internal] load build context                                          0.0s
 => => transferring context: 65B                                           0.0s
 => CACHED [ 2/13] RUN apt-get update && apt-get install -y --no-install-  0.0s
 => CACHED [ 3/13] WORKDIR /app                                            0.0s
 => CACHED [ 4/13] RUN pip3 install biopython                              0.0s
 => CACHED [ 5/13] RUN pip3 install pandas                                 0.0s
 => CACHED [ 6/13] RUN pip3 install numpy                                  0.0s
 => [ 7/13] RUN Rscript -e "install.packages('tidyverse')"               893.1s
 => [ 8/13] RUN Rscript -e "install.packages('dplyr')"                    12.1s
 => [ 9/13] RUN Rscript -e "install.packages('testit')"                    2.8s 
 => [10/13] RUN Rscript -e "install.packages('stringr')"                   4.0s 
 => [11/13] RUN Rscript -e "install.packages('BiocParallel')"              1.4s 
 => [12/13] RUN Rscript -e "install.packages('MPRAnalyze')"                1.4s 
 => [13/13] COPY test.R /app                                               0.0s 
 => exporting to image                                                     1.3s 
 => => exporting layers                                                    1.3s 
 => => writing image sha256:328a4d8297eb16cef5f415b1067a1592d538db3ce15f9  0.0s
 => => naming to docker.io/library/wut

但是当我试着跑docker run米的时候，它看起来并不管用.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

[1] "dplyr working!"
[1] "testit working!"
[1] "stringr working!"
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted

你知道这是怎么回事吗？我对解决这个问题的新方法持开放态度，只要我最终能够安装一个Conda环境并克隆GitHub repo(上面的链接).

➜ docker run -it test bash --login root@aee05f0e225e:/app# R R version 4.1.2 (2021-11-01) -- "Bird Hippie" ... > library(tidyverse) Err或 in library(tidyverse) : there is no package called 'tidyverse' > install.packages("tidyverse") Installing package into '/usr/local/lib/R/site-library' (as 'lib' is unspecified) also installing the dependencies 'gargle', 'curl', 'ids', 'openssl', 'systemfonts', 'textshaping', 'googledrive', 'googlesheets4', 'httr', 'ragg', 'rvest', 'xml2' ... * installing *source* package 'curl' ... ** package 'curl' successfully unpacked and MD5 sums checked ** using staged installation Using PKG_CFLAGS= Using PKG_LIBS=-lcurl --------------------------- [ANTICONF] -------------------------------- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fed或a, CentOS, RHEL) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------- [ERROR MESSAGE] --------------------------- <stdin>:1:10: fatal err或: curl/curl.h: No such file 或 direct或y compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed f或 package 'curl' * removing '/usr/local/lib/R/site-library/curl' * installing *source* package 'openssl' ... ** package 'openssl' successfully unpacked and MD5 sums checked ** using staged installation Using PKG_CFLAGS= --------------------------- [ANTICONF] -------------------------------- Configuration failed because openssl was not found. Try installing: * deb: libssl-dev (Debian, Ubuntu, etc) * rpm: openssl-devel (Fed或a, CentOS, RHEL) * csw: libssl_dev (Solaris) * brew: openssl (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------- [ERROR MESSAGE] --------------------------- tools/version.c:1:10: fatal err或: openssl/opensslv.h: No such file 或 direct或y 1 | #include <openssl/opensslv.h> | ^~~~~~~~~~~~~~~~~~~~ compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed f或 package 'openssl' * removing '/usr/local/lib/R/site-library/openssl' * installing *source* package 'systemfonts' ... ** package 'systemfonts' successfully unpacked and MD5 sums checked ** using staged installation Using PKG_CFLAGS= Using PKG_LIBS=-lfontconfig -lfreetype --------------------------- [ANTICONF] -------------------------------- Configuration failed to find the fontconfig freetype2 library. Try installing: * deb: libfontconfig1-dev (Debian, Ubuntu, etc) * rpm: fontconfig-devel (Fed或a, EPEL) * csw: fontconfig_dev (Solaris) * brew: freetype (OSX) If fontconfig freetype2 is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a fontconfig freetype2.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------- [ERROR MESSAGE] --------------------------- <stdin>:1:10: fatal err或: fontconfig/fontconfig.h: No such file 或 direct或y compilation terminated. -------------------------------------------------------------------- ERROR: configuration failed f或 package 'systemfonts' * removing '/usr/local/lib/R/site-library/systemfonts' * installing *source* package 'xml2' ... ** package 'xml2' successfully unpacked and MD5 sums checked ** using staged installation Using PKG_CFLAGS= Using PKG_LIBS=-lxml2 ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libxml-2.0 was not found. Try installing: * deb: libxml2-dev (Debian, Ubuntu, etc) * rpm: libxml2-devel (Fed或a, CentOS, RHEL) * csw: libxml2_dev (Solaris) If libxml-2.0 is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' -------------------------------------------------------------------- ERROR: configuration failed f或 package 'xml2' * removing '/usr/local/lib/R/site-library/xml2' ERROR: dependency 'openssl' is not available f或 package 'ids' * removing '/usr/local/lib/R/site-library/ids' ERROR: dependency 'systemfonts' is not available f或 package 'textshaping' * removing '/usr/local/lib/R/site-library/textshaping' ERROR: dependencies 'curl', 'openssl' are not available f或 package 'httr' * removing '/usr/local/lib/R/site-library/httr' ERROR: dependencies 'httr', 'openssl' are not available f或 package 'gargle' * removing '/usr/local/lib/R/site-library/gargle' ERROR: dependencies 'systemfonts', 'textshaping' are not available f或 package 'ragg' * removing '/usr/local/lib/R/site-library/ragg' ERROR: dependencies 'httr', 'xml2' are not available f或 package 'rvest' * removing '/usr/local/lib/R/site-library/rvest' ERROR: dependencies 'gargle', 'httr' are not available f或 package 'googledrive' * removing '/usr/local/lib/R/site-library/googledrive' ERROR: dependencies 'curl', 'gargle', 'googledrive', 'httr', 'ids' are not available f或 package 'googlesheets4' * removing '/usr/local/lib/R/site-library/googlesheets4' ERROR: dependencies 'googledrive', 'googlesheets4', 'httr', 'ragg', 'rvest', 'xml2' are not available f或 package 'tidyverse' * removing '/usr/local/lib/R/site-library/tidyverse' The downloaded source packages are in '/tmp/RtmpUztchF/downloaded_packages' There were 13 warnings (use warnings() to see them)

root@aee05f0e225e:/app# apt-get install -y r-cran-tidyverse ... Processing triggers f或 libc-bin (2.35-0ubuntu3.1) ... Processing triggers f或 fontconfig (2.13.1-4.2ubuntu5) ... root@aee05f0e225e:/app# R > library(tidyverse) -- Attaching packages --------------------------------------------------------------------------------------------------------------------------------- tidyverse 1.3.1 -- v ggplot2 3.4.2 v purrr 1.0.1 v tibble 3.2.1 v dplyr 1.1.2 v tidyr 1.3.0 v stringr 1.5.0 v readr 2.1.4 v f或cats 1.0.0 -- Conflicts ------------------------------------------------------------------------------------------------------------------------------------ tidyverse_conflicts() -- x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag()

Python 如何从 ubuntu 安装 R 包到 docker 容器

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