在Docker中的R 3.3.2上安装rJava和nloptr

问题描述 投票：0回答：2

在rocker/tidyverse:3.3.2内部，即使我没有错误地安装r-cran-rjava r-cran-nloptr，在Q中缺少包rJAva和nloptr。任何想法为什么？

请参阅下面的Docker文件：

FROM rocker/tidyverse:3.3.2

RUN printf "deb http://archive.debian.org/debian/ jessie main\ndeb-src http://archive.debian.org/debian/ jessie main\ndeb http://security.debian.org jessie/updates main\ndeb-src http://security.debian.org jessie/updates main" > /etc/apt/sources.list

RUN apt-get update && apt-get install -y --no-install-recommends apt-utils

RUN apt-get -y update && apt-get install -y \
   default-jdk  r-cran-rjava  r-cran-nloptr libssh2-1-dev 
RUN R -e "library('rJava')" # Error in library("rJava") : there is no package called ‘rJava’
RUN R -e "library('nloptr')" # Error in library("nloptr") : there is no package called nloptr

谢谢

r docker rjava
2个回答
5
投票

这是因为您正在安装为最新稳定版R准备的软件包二进制文件，但您安装的R版本是旧版本，您不是要为要使用的R版本安装软件包。

1
投票

这是解决方案：

FROM openjdk:7-slim-jessie
RUN apt-get update
RUN apt-get install -y curl
RUN printf "deb http://deb.debian.org/debian jessie main\ndeb-src http://deb.debian.org/debian jessie main\ndeb http://security.debian.org/debian-security jessie/updates main\ndeb-src http://security.debian.org/debian-security jessie/updates main\n" > /etc/apt/sources.list
RUN apt-get update
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    bash-completion \
    ca-certificates \
    file \
    fonts-texgyre \
    g++ \
    gfortran \
    gsfonts \
    libblas-dev \
    libbz2-1.0 \
    libcurl3 \
    libicu52 \
    libjpeg62-turbo \
    libopenblas-dev \
    libpangocairo-1.0-0 \
    libpcre3 \
    libpng12-0 \
    libtiff5 \
    liblzma5 \
    locales \
    make \
    unzip \
    zip \
    zlib1g \
  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
  && locale-gen en_US.utf8 \
  && /usr/sbin/update-locale LANG=en_US.UTF-8 
RUN BUILDDEPS="curl \
 #   default-jdk \
    libbz2-dev \
    libcairo2-dev \
    libcurl4-openssl-dev \
    libpango1.0-dev \
    libjpeg-dev \
    libicu-dev \
    libpcre3-dev \
    libpng-dev \
    libreadline-dev \
    libtiff5-dev \
    liblzma-dev \
    libx11-dev \
    libxt-dev \
    perl \
    tcl8.5-dev \
    tk8.5-dev \
    texinfo \
    texlive-extra-utils \
    texlive-fonts-recommended \
    texlive-fonts-extra \
    texlive-latex-recommended \
    x11proto-core-dev \
    xauth \
    xfonts-base \
    xvfb \
    zlib1g-dev" \
  && apt-get install -y --no-install-recommends $BUILDDEPS 
RUN cd tmp/ \
  ## Download source code
  && curl -O https://cran.r-project.org/src/base/R-3/R-3.2.3.tar.gz \
  ## Extract source code
  && tar -xf R-3.2.3.tar.gz \
  && cd R-3.2.3 \
  ## Set compiler flags
  && R_PAPERSIZE=letter \
    R_BATCHSAVE="--no-save --no-restore" \
    R_BROWSER=xdg-open \
    PAGER=/usr/bin/pager \
    PERL=/usr/bin/perl \
    R_UNZIPCMD=/usr/bin/unzip \
    R_ZIPCMD=/usr/bin/zip \
    R_PRINTCMD=/usr/bin/lpr \
    LIBnn=lib \
    AWK=/usr/bin/awk \
    CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
    CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" \
  ## Configure options
  ./configure --enable-R-shlib \
               --enable-memory-profiling \
               --with-readline \
               --with-blas \
               --with-tcltk \
               --disable-nls \
               --with-recommended-packages \
  ## Build and install
  && make \
  && make install 
  ## Add a default CRAN mirror

RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
  ## Add a library directory (for user-installed packages)
  && mkdir -p /usr/local/lib/R/site-library \
  && chown root:staff /usr/local/lib/R/site-library \
  && chmod g+wx /usr/local/lib/R/site-library \
  ## Fix library path
  && echo "R_LIBS_USER='/usr/local/lib/R/site-library'" >> /usr/local/lib/R/etc/Renviron \
  && echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron \
  ## install packages from date-locked MRAN snapshot of CRAN
  && [ -z "$BUILD_DATE" ] && BUILD_DATE=$(TZ="America/Los_Angeles" date -I) || true \
  && MRAN=https://mran.microsoft.com/snapshot/${BUILD_DATE} \
  && echo MRAN=$MRAN >> /etc/environment \
  && export MRAN=$MRAN \
  && echo "options(repos = c(CRAN='$MRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site \
  ## Use littler installation scripts
  && Rscript -e "install.packages(c('littler', 'docopt'), repo = '$MRAN')" \
  && ln -s /usr/local/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
  && ln -s /usr/local/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
  && ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r \
  ## Clean up from R source install
  && cd / \
  && rm -rf /tmp/* \
  && apt-get remove --purge -y $BUILDDEPS \
  && apt-get autoremove -y \
  && apt-get autoclean -y \
&& rm -rf /var/lib/apt/lists/*
RUN echo "options(repos = c(CRAN='https://mran.microsoft.com/snapshot/2016-10-10'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site




RUN printf "deb http://snapshot.debian.org/archive/debian/20161010T101527Z/ jessie main\ndeb-src http://snapshot.debian.org/archive/debian/20161010T101527Z/ jessie main\ndeb http://snapshot.debian.org/archive/debian/20161010T101527Z/ jessie-backports main\ndeb-src http://snapshot.debian.org/archive/debian/20161010T101527Z/ jessie-backports main\n" > /etc/apt/sources.list

#RUN apt-get -y -o Acquire::Check-Valid-Until=false update && apt-get install -y \
#    r-cran-rjava  r-cran-nloptr libssh2-1-dev
RUN apt-get -y -o Acquire::Check-Valid-Until=false update
RUN printf "deb http://deb.debian.org/debian jessie main\ndeb-src http://deb.debian.org/debian jessie main\ndeb http://security.debian.org/debian-security jessie/updates main\ndeb-src http://security.debian.org/debian-security jessie/updates main\n" > /etc/apt/sources.list
RUN apt-get -y -o Acquire::Check-Valid-Until=false update
RUN apt-get install -y libxml2-dev 
#RUN apt-get install -y r-cran-xml2 
#RUN apt-get install -y r-base-dev
RUN apt-get install -y libbz2-dev  libicu-dev  liblzma-dev 
#RUN echo "install.packages('rJava', repos='http://www.rforge.net/', configure.args='--disable-Xrs')" | R --no-save
RUN apt-get install -y libnlopt-dev libnlopt-guile0 libnlopt0
RUN R -e "install.packages('xml2')" 
RUN R -e "install.packages('rJava')"    

RUN R -e "install.packages('xml2')" 
RUN R -e "install.packages('ReporteRs')"

RUN R -e "install.packages('nloptr')"
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