Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
1
0
Entering edit mode
YaGalbi ▴ 20
@yagalbi-11519
Last seen 23 months ago
MRC Harwell Institute, Oxford, UK

Hi all,

 

I had ChIPpeakanno installed and working on the last versions of R and Rstudio. I recently updated to the latest version or R and Rstudio. Just now I tried to run ChIPpeakAnno and it was not installed.

I tried installing with 

source("https://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")
------------------------- 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=...'
----------------------------------------------------------------

I then tried to install libmysqlclient with :

source("https://bioconductor.org/biocLite.R")
biocLite("libmariadb-client-lgpl-dev")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘libmariadb-client-lgpl-dev’
installation path not writeable, unable to update packages: codetools, lattice, Matrix, spatial
Warning message:
package ‘libmariadb-client-lgpl-dev’ is not available (for R version 3.4.3) 

 

So now Im thinking I have to uninstall R version 3.4.3 and install an older version.

Has anyone got a better soluction?

 

Thanks in advance

Kenneth

ChIPpeakAnno • 816 views
ADD COMMENT
2
Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 7 hours ago
EMBL Heidelberg / de.NBI

The error message and suggested installation instructions related to a system library, rather than a missing R package. 

Exactly what you need to do depends upon your operating system, with suggestions given in the brackets in the message.  For example, if you're running Ubuntu 16.04 you want to run something like this in a terminal:

apt-get install libmariadb-client-lgpl-dev

Or if you're running Mac OSX then something like the following (possibly after reading https://brew.sh/ )

brew install mariadb-connector-c

We can't give more specific help without details of the system you're running, which you can provide by running the R command sessionInfo() and including it here.

ADD COMMENT
0
Entering edit mode

You legend .. That worked! :) 

Any chance of a job? ;) haha 

ADD REPLY

Login before adding your answer.

Traffic: 275 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6