r：加载共享库时出错：libR.so：无法打开共享对象文件：没有这样的文件或目录

Question

我在 rocker/rstudio:4.3.1 中安装软件包时遇到问题 使用 CRAN_REPO 快照

https://packagemanager.posit.co/cran/__linux__/jammy/2024-02-01/

和 BIOC_REPO

https://ftp.gwdg.de/pub/misc/bioconductor/

install2.r --deps NA --error --skipinstalled --ncpus -1 BiocManager rstudioapi remotes languageserver aws.s3 usethis
r: error while loading shared libraries: libR.so: cannot open shared object file: No such file or directory
ERROR: process "/bin/sh -c /install_scripts/setup_r.sh" did not complete successfully: exit code: 127

Dockerfile

FROM rocker/rstudio:4.3.1

ENV \
    # R repositories and versions \
    CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/jammy/2024-02-01/" \
    BIOC_REPO="https://ftp.gwdg.de/pub/misc/bioconductor/" \
    BIOC_VERSION="3.18" \

COPY ./install_scripts/setup_r.sh /install_scripts/setup_r.sh
RUN /install_scripts/setup_r.sh

安装脚本/setup_r.sh

#!/bin/bash
# setup R and install Bioconductor

set -e # exit script on error (non-zero exit status)
set -x # print command trace
set -u # exit when undeclared variables are used

# build ARGs
NCPUS=${NCPUS:--1}

# set the RStudio Package Manager repositories for CRAN (overrides CRAN set
# by rocker) and bioconductor and increase download timeout
echo "options(repos = c(CRAN = '${CRAN_REPO}'), BioC_mirror = '${BIOC_REPO}',
      download.file.method = 'libcurl', timeout = 600)" >> \
          ${R_HOME}/etc/Rprofile.site

# update all base R packages
/usr/local/lib/R/site-library/littler/examples/update.r --ncpus ${NCPUS:--1}

# setup bioconductor
install2.r --deps "NA" --error --skipinstalled --ncpus ${NCPUS:--1} \
    BiocManager \
    rstudioapi \
    remotes \
    languageserver \
    aws.s3 \
    usethis

在其他版本的 CRAN_REPO 版本（例如 2023-10-30）中，这有效。

Answer 1

🗎

Dockerfile

FROM rocker/rstudio:4.3.1

ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/jammy/2024-02-01/"
ENV BIOC_REPO="https://ftp.gwdg.de/pub/misc/bioconductor/"
ENV BIOC_VERSION="3.18"

ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/R/lib

RUN apt-get update && \
    apt-get install -y libxml2-dev

COPY ./install_scripts/setup_r.sh /install_scripts/setup_r.sh
RUN chmod u+x /install_scripts/setup_r.sh && \
    /install_scripts/setup_r.sh

🗎

install_scripts/setup_r.sh

#!/bin/bash

set -e
set -x
set -u

NCPUS=${NCPUS:--1}

cat <<END >$R_HOME/etc/Rprofile.site
options(
    repos = c(CRAN = '${CRAN_REPO}'),
    BioC_mirror = '${BIOC_REPO}',
    download.file.method = 'libcurl'
)
END

/usr/local/lib/R/site-library/littler/examples/update.r --ncpus ${NCPUS:--1}

install2.r --deps "NA" --error --skipinstalled --ncpus ${NCPUS:--1} \
    BiocManager \
    rstudioapi \
    remotes \
    languageserver \
    aws.s3 \
    usethis