Question: installation of "GenomicFeatures"
0
gravatar for krwyaong.ju
14 months ago by
krwyaong.ju0 wrote:

installation of "GenomicFeatures" failed; pls say how to figure it out?

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("GenomicFeatures")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘GenomicFeatures’
also installing the dependency ‘RMySQL’

trying URL 'https://cloud.r-project.org/src/contrib/RMySQL_0.10.14.tar.gz'
Content type 'application/x-gzip' length 52703 bytes (51 KB)
==================================================
downloaded 51 KB

trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/GenomicFeatures_1.30.3.tar.gz'
Content type 'application/x-gzip' length 893759 bytes (872 KB)
==================================================
downloaded 872 KB

* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lmysqlclient
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because no mysql client library was found. Try installing:
 * deb: libmariadbclient-dev | libmariadb-client-lgpl-dev (Debian, Ubuntu)
 * rpm: mariadb-connector-c-devel | mariadb-devel | mysql-devel (Fedora, CentOS, RHEL)
 * csw: mysql56_dev (Solaris)
 * brew: mariadb-connector-c (OSX)
If you already have a mysql client library installed, verify that either
mariadb_config or mysql_config is on your PATH. If these are unavailable
you can also set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘RMySQL’
* removing ‘/usr/local/lib/R/site-library/RMySQL’
ERROR: dependency ‘RMySQL’ is not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’

The downloaded source packages are in
    ‘/tmp/RtmpHwrOi7/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RMySQL’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
>

 

genomicfeatures • 398 views
ADD COMMENTlink modified 14 months ago by James W. MacDonald50k • written 14 months ago by krwyaong.ju0
Answer: installation of "GenomicFeatures"
1
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald50k wrote:

You have an error that tells you what you need to do:

Configuration failed because no mysql client library was found. Try installing:
 * deb: libmariadbclient-dev | libmariadb-client-lgpl-dev (Debian, Ubuntu)
 * rpm: mariadb-connector-c-devel | mariadb-devel | mysql-devel (Fedora, CentOS, RHEL)
 * csw: mysql56_dev (Solaris)
 * brew: mariadb-connector-c (OSX)

Since you are installing a source package, I assume you are on a Linux variant. If you have sudo privileges, you can follow the instructions that pertain to your Linux distro. If you don't have sudo privileges (most likely if you are on a Linux computer that is not your own), then you will need to ask whoever is your system administrator to install mariadb for you.

ADD COMMENTlink written 14 months ago by James W. MacDonald50k
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