How to install a bioconductor package RMySQL and specify R parameters
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mousheng xu ▴ 10
@mousheng-xu-2280
Last seen 6.7 years ago

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!

software error R • 1.8k views
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shepherl 3.9k
@lshep
Last seen 3 minutes ago
United States

When you run R CMD INSTALL --configure-vars='INCLUDE_DIR=/mydir/mariadb-connector-c' RMySQL , you need to be in a directory where RMySQL is present. So you can download the package here and then run or be in the directory whereever a local copy is.

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