r - 验证安装到 docker 容器中的 R 包

Question

有没有人有任何最佳实践来验证 R 包是否已安装到 docker 容器中？我想将我的容器设置为在 CI 服务上运行，并验证我的包是否已安装，但由于我一直在本地构建它，所以日志似乎很难确定安装了哪些包，哪些没有安装。如果让 CI 服务为我做这件事，或者使用简单的批处理脚本来验证包是否已安装，那就太好了。

下面是我当前的 dockerfile:

FROM rocker/tidyverse:latest
RUN mkdir -p $HOME/.R
COPY R/Makevars /root/.R/Makevars

RUN apt-get update -qq \
    && apt-get -y --no-install-recommends install \
    liblzma-dev \
    libbz2-dev \
    ed \
    clang  \
    ccache \
    default-jdk \
    default-jre \
    && R CMD javareconf \
    && install2.r --error \
        ggstance ggrepel \
        rstan shinystan rstanarm \
        ###My pkgs
        tidytext janitor corrr officer devtools pacman
        tidyquant timetk tibbletime sweep broom prophet \
        forecast prophet lime sparklyr rsparkling \
        formattable httr rvest xml2 jsonlite \
        textclean ggthemes naniar \
    && Rscript -e 'devtools::install_github(c("hadley/multidplyr","jeremystan/tidyjson","ropenscilabs/skimr"))' \
    && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
    && rm -rf /var/lib/apt/lists/*

Answer 1

将其保存到类似 package_check.R 的文件中，然后通过 Rscript 运行它的 Docker 行:

c("tidytext", "janitor", "corrr", "officer", "devtools", "pacman", "tidyquant", 
  "timetk", "tibbletime", "sweep", "broom", "prophet", "forecast", "prophet", 
  "lime", "sparklyr", "rsparkling", "formattable", "httr", "rvest", "xml2", 
  "jsonlite", "textclean", "ggthemes", "naniar") -> chk_pkgs

suppressPackageStartupMessages(
  sapply(chk_pkgs, require, character.only=TRUE, quietly=FALSE, warn.conflicts=FALSE)
) -> ret

missing_pkgs <- sort(names(which(ret == FALSE)))

if (length(missing_pkgs) > 0) {
  warning("The following packages are not installed: %s", 
          paste0(sprintf("  - %s", missing_pkgs), collapse="\n"))
}

quit(save=FALSE, status=length(names) == 0, runLast = FALSE)

这会给你一个缺少列表的丢失包错误，并以非零退出状态退出脚本。