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           
status                                     
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, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, 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’:

    hclust

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’:

    expand.grid

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.

Thanks

Robert

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.