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在 Ubuntu 中使用 R 3.5.1 安装 RODBC 时出现问题

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在 Ubuntu 中使用 R 3.5.1 安装 RODBC 时出现问题

线程这里关于 RODBC 已经过时了，大约 7 年前，他们的解决方案安装r-cran-odbc后libiodbc2-dev不起作用。从 R 3.5.1 开始，我得到了与 7 年前相同的错误

install.packages("RODBC", keep_outputs = T)

configure: error: "ODBC headers sql.h and sqlext.h not found"
ERROR: configuration failed for package ‘RODBC’
* removing ‘/opt/conda/lib/R/library/RODBC’

尽管已经安装了上述软件包。因此

如何在 R 3.5.1（R 和 Ubuntu 的最新版本）中在 Ubuntu 中安装 RODBC？

最小可复制基础（Dockerfile）

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
ARG BASE_CONTAINER=jupyter/minimal-notebook
FROM $BASE_CONTAINER

LABEL maintainer="Jupyter Project <[email protected]>"

USER root

# R pre-requisites
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    fonts-dejavu \
    tzdata \
    libiodbc2-dev \
    r-cran-rodbc \
    gfortran \
    gcc && \
    rm -rf /var/lib/apt/lists/*

USER $NB_UID

# R packages
RUN conda install --quiet --yes \
    'r-base=3.5.1' \
    'r-irkernel=0.8*' \
    'r-plyr=1.8*' \
    'r-devtools=1.13*' \
    'r-tidyverse=1.2*' \
    'r-shiny=1.2*' \
    'r-rmarkdown=1.11*' \
    'r-forecast=8.2*' \
    'r-rsqlite=2.1*' \
    'r-reshape2=1.4*' \
    'r-nycflights13=1.0*' \
    'r-caret=6.0*' \
    'r-rcurl=1.95*' \
    'r-crayon=1.3*' \
    'r-randomforest=4.6*' \
    'r-htmltools=0.3*' \
    'r-sparklyr=0.9*' \
    'r-htmlwidgets=1.2*' \
    'r-hexbin=1.27*' && \
    conda clean -tipsy && \
    fix-permissions $CONDA_DIR

以下软件包libiodbc2-dev无法解决r-cran-rodbc问题。

眼镜

$ uname -a
Linux 370485a13e40 4.9.93-linuxkit-aufs #1 SMP Wed Jun 6 16:55:56 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

sql.h 位于以下位置

$ apt-file sql.h

libdballe-dev: /usr/include/dballe/sql/sql.h
libiodbc2-dev: /usr/include/iodbc/sql.h
libmailutils-dev: /usr/include/mailutils/sql.h
libwine-dev: /usr/include/wine/windows/sql.h
libwine-development-dev: /usr/include/wine-development/wine/windows/sql.h
mingw-w64-common: /usr/share/mingw-w64/include/sql.h
mingw-w64-i686-dev: /usr/i686-w64-mingw32/include/sql.h
mingw-w64-x86-64-dev: /usr/x86_64-w64-mingw32/include/sql.h
pike7.8-core: /usr/lib/pike7.8/include/sql.h
pike8.0-core: /usr/lib/pike8.0/include/sql.h
unixodbc-dev: /usr/include/sql.h

和

# apt-file search /sqlext.h
libiodbc2-dev: /usr/include/iodbc/sqlext.h
libwine-dev: /usr/include/wine/windows/sqlext.h
libwine-development-dev: /usr/include/wine-development/wine/windows/sqlext.h
mingw-w64-common: /usr/share/mingw-w64/include/sqlext.h
mingw-w64-i686-dev: /usr/i686-w64-mingw32/include/sqlext.h
mingw-w64-x86-64-dev: /usr/x86_64-w64-mingw32/include/sqlext.h
unixodbc-dev: /usr/include/sqlext.h

答案1

可以通过从 conda 安装包来解决缺少标头的问题r-rodbc，如下所示

RUN conda install --quiet --yes \
    'r-base=3.5.1' \
    'r-rodbc=1.3*' \

然后你就会得到以下错误

hecking for library containing SQLTables... no
configure: error: "no ODBC driver manager found"
ERROR: configuration failed for package ‘RODBC’
* removing ‘/opt/conda/lib/R/library/RODBC’
* restoring previous ‘/opt/conda/lib/R/library/RODBC’

你需要r-cran-odbc，unixodbc以及 apt 中的 'unixodbc-dev'（只有 unixodbc 是不够的），这样你的 Dockerfile 就变成了

# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
ARG BASE_CONTAINER=jupyter/minimal-notebook
FROM $BASE_CONTAINER

LABEL maintainer="Jupyter Project <[email protected]>"

USER root

# R pre-requisites
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    fonts-dejavu \
    tzdata \
    unixodbc \
    unixodbc-dev \
    r-cran-rodbc \
    gfortran \
    gcc && \
    rm -rf /var/lib/apt/lists/*

USER $NB_UID

# R packages
RUN conda install --quiet --yes \
    'r-base=3.5.1' \
    'r-rodbc=1.3*' \
    'unixodbc=2.3.*' \
    'r-irkernel=0.8*' \
    'r-plyr=1.8*' \
    'r-devtools=1.13*' \
    'r-tidyverse=1.2*' \
    'r-shiny=1.2*' \
    'r-rmarkdown=1.11*' \
    'r-forecast=8.2*' \
    'r-rsqlite=2.1*' \
    'r-reshape2=1.4*' \
    'r-nycflights13=1.0*' \
    'r-caret=6.0*' \
    'r-rcurl=1.95*' \
    'r-crayon=1.3*' \
    'r-randomforest=4.6*' \
    'r-htmltools=0.3*' \
    'r-sparklyr=0.9*' \
    'r-htmlwidgets=1.2*' \
    'r-hexbin=1.27*' && \
    conda clean -tipsy && \
    fix-permissions $CONDA_DIR

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