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.