How to install a bioconductor package RMySQL and specify R parameters

Question

[moxu]

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!

[Sej Modha]

If you are using R CMD INSTALL --configure-vars='INCLUDE_DIR=/mydir/mariadb-connector-c' RMySQL*.tar.gz then you'd need to download relevant version of RMySQL from https://cran.r-project.org/web/packages/RMySQL/index.html

[moxu]

Thanks a lot for the input. I got almost identical errors after downloading the package. Weird because "mariadb-connector-c" is already installed by brew in the specified dir and the location is given at the command line. How come it still cannot find it?

The command line:

R CMD INSTALL --configure-vars='INCLUDE_DIR=/mydir/.linuxbrew/opt/mariadb-connector-c LIB_DIR=/ark/home/mx010/.linuxbrew/opt/mariadb-connector-c' RMySQL_0.10.13.tar.gz

The errors:

* installing to library ‘/ark/home/mx010/R/x86_64-pc-linux-gnu-library/3.2’
* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Found INCLUDE_DIR and/or LIB_DIR!
Using PKG_CFLAGS=-I/ark/home/mx010/.linuxbrew/opt/mariadb-connector-c 
Using PKG_LIBS=-L/ark/home/mx010/.linuxbrew/opt/mariadb-connector-c -lmysqlclient
------------------------- 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=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘RMySQL’
* removing ‘/ark/home/mx010/R/x86_64-pc-linux-gnu-library/3.2/RMySQL’

[Sej Modha]

I am sorry but I won't be able to help any further as I don't have those specific tools installed on my system, I found this stackoverflow thread that might help: https://stackoverflow.com/questions/41947213/trouble-installing-rmysql-on-osx-sierra

Answer 1

[moxu]

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.