I am trying to install CopywriteR, which failed at updating a dependent package RMySQL. The error I got was as follows:

    ------------------------- ANTICONF ERROR ---------------------------
    
    Configuration failed because libmysqlclient was not found. Try installing:
    
     * deb: libmariadb-client-lgpl-dev (Debian, Ubuntu 16.04)
    
            libmariadbclient-dev (Ubuntu 14.04)
    
     * rpm: mariadb-devel | mysql-devel (Fedora, CentOS, RHEL)
    
     * csw: mysql56_dev (Solaris)
    
     * brew: mariadb-connector-c (OSX)
    
    If libmysqlclient is already installed, check that 'pkg-config' is in your
    
    PATH and PKG_CONFIG_PATH contains a libmysqlclient.pc file. If pkg-config
    
    is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
    
    R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
    
    --------------------------------------------------------------------

My question is: where can I specify  --configure-vars='INCLUDE_DIR=... LIB_DIR=...'? I cannot do this at command line because RMySQL is installed through bioconductor. If I do

 R CMD INSTALL --configure-vars='INCLUDE_DIR=/mydir/mariadb-connector-c' RMySQL

I will get:

    --------------------------------------------------------
    
    Warning: invalid package ‘RMySQL’
    
    Error: ERROR: no packages specified
    
    --------------------------------------------------------

Thanks in advance!

I was able to install CopywriteR after the following steps:

 1. Download CopyhelpeR_1.0.2.tar.gz

 2. sudo R CMD INSTALL CopyhelpeR*.tar.gz

 3. sudo R CMD INSTALL CopywriteR*.tar.gz

This somehow bypassed the RMySQL installation. Part of the problem might come from the R version: I was using R 3.2.3, while CopywriteR was built under R version 3.4.2.