Krdytkyu

The thread here about RODBC is old, about 7 years old, their solution about installing r-cran-odbc and libiodbc2-dev do not work. As of R 3.5.1, I am getting the same error as 7 years ago

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’

despite having the mentioned packages installed. So

How to get the RODBC installed in Ubuntu as of R 3.5.1 (latest versions of R and Ubuntu)?

Minimal reproducible base (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 <jupyter@googlegroups.com>"



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

where the following packages libiodbc2-dev and r-cran-rodbc won't resolve the issue.

Specs

$ 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 is located in the following

$ 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

and

# 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

The missing headers problem can be solved by installing the r-rodbc package from conda such that

RUN conda install --quiet --yes 

    'r-base=3.5.1' 

    'r-rodbc=1.3*' 

and then after that you will get the following error

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’

for which you need r-cran-odbc, unixodbc and 'unixodbc-dev' (just unixodbc is not enough) from apt so your Dockerfile becomes

# 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 <jupyter@googlegroups.com>"



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