cummeRbund installation fails
Entering edit mode
slanyrobert ▴ 30
Last seen 5.1 years ago

Hi Bioinfo Gurus:


I am having a serious problem installing cummeRbund on my machine:

I am using R on a recently updated Ubuntu 17:10

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
major          3                           
minor          4.1                         
year           2017                        
month          06                          
day            30                          
svn rev        72865                       
language       R                           
version.string R version 3.4.1 (2017-06-30)
nickname       Single Candle               

I installed cummeRbund through conda with:

conda install -c bioconda bioconductor-cummeRbund

which exited without any error. However, if I try to load cummeRbund in R it exits with an error as follows:

> library("cummeRbund")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append,, cbind, colMeans, colnames,
    colSums,, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax,, pmin,, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: RSQLite
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:


Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:


Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Error: package or namespace load failed for ‘Gviz’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘RMySQL’
Error: package ‘Gviz’ could not be loaded

I tried to install RMySQL directly under R from cran but it'll crash with some obscure error messages (I've no idea what it means).

A try to install cummeRbund directly under R also failed because of the RMySQL package.

Does anybody have the same problem? Is there an updated version of cummeRbund or any workaround? Wasn't it supposed that installation through the conda channels takes care of all dependencies?

Please, I don't want to become a computer coder, all I'd like is to use the program.

Any help is greatly appreciated.






bioconductor cummerbund software error GenomicFeatures • 1.3k views
Entering edit mode

Dear Martin,

thank you very much for your help. I tried to install the "RMySQL" through various ways (conda, Bioconductor and also directly with "install.packages("RMySQL", repos = "") but I always get exactly the same error as below.

I already updated RMariaDB and checked several solutions that I found in connection with RMySQL installation errors on the web, but to no avail! My problem is that I've no idea how to implement the suggested solution in the error message, because I've no idea how to include LIB_DIR and INCLUDE_DIR in my variables. What are these directories? How do I find them? (P.S. libmysqlclient is installed).

Any further help very welcome.


Robert --> error message below

* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Found mysql_config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/mariadb -I/usr/include/mariadb/mysql -g -O2 -fdebug-prefix-map=/build/mariadb-connector-c-ts5uYh/mariadb-connector-c-2.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wunused -Wno-uninitialized
Using PKG_LIBS=-L/usr/lib/x86_64-linux-gnu -lmariadb
------------------------- 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 ‘/home/slany/anaconda3/lib/R/library/RMySQL’


Entering edit mode

You're tackling this in the right way, by trying to install the underlying dependencies, but you'll have to tell us the 'obscure error' associated with RMySQL. Also, I personally would not use conda, but stick with standard Bioconductor installation procedures -- source(""); biocLite("RMySQL").

Entering edit mode
Last seen 3 days ago
United States

The error message indicates that the MySQL client library is not found. The solution is to install the client library. If your operating system is, for instance, Ubuntu 16.04, the command would be indicated in the error message. So

sudo apt-get install libmariadb-client-lgpl-dev

Note that one typically needs root (sudo) privileges to install system libraries. If you need more help we'll need to know what operating system you are using.

Entering edit mode

Dear Martin:

Thanks for the suggestion. I am on Ubuntu 17.10

lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 17.10
Release:    17.10
Codename:    artful

I tried to install libmariadb-client-lgpl-dev but it is already installed. However, in the new Ubuntu version the name of the program seems to have changed to libmariadb-dev.

sudo apt-get install libmariadb-client-lgpl-dev
[sudo] password for slany:
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting 'libmariadb-dev' instead of 'libmariadb-client-lgpl-dev'
libmariadb-dev is already the newest version (2.3.3-1).

Sorry, for being a nuisance but any further suggestions from the pros?


Entering edit mode

This issue might be relevant in your case; it points to a problem in RMySQL with a workaround at that might be ok until a fixed version is available.

Entering edit mode

Dear Martin,

thanks for this link, but -alas- no help in my case. See error report...

* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (devtools)

The downloaded source packages are in
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> devtools::install_github("alecuba16/RMySQL")
Downloading GitHub repo alecuba16/RMySQL@master
from URL
Installation failed: error in running command

Probably, I'll have just to wait till the error is fixed by the developers.

Thank you so much for trying.

Have a nice day




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