Question: Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
0
gravatar for YaGalbi
18 months ago by
YaGalbi20
MRC Harwell Institute, Oxford, UK
YaGalbi20 wrote:

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 • 523 views
ADD COMMENTlink modified 18 months ago by Mike Smith3.9k • written 18 months ago by YaGalbi20
Answer: Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remov
2
gravatar for Mike Smith
18 months ago by
Mike Smith3.9k
EMBL Heidelberg / de.NBI
Mike Smith3.9k wrote:

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 COMMENTlink modified 18 months ago • written 18 months ago by Mike Smith3.9k

You legend .. That worked! :) 

Any chance of a job? ;) haha 

ADD REPLYlink written 18 months ago by YaGalbi20
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