Just wanted to point out that S4Vectors blocks regular Matrix package operations. Matrix is, perhaps, the most popular sparse matrix package for R, and it would be nice if S4Vectors (which is required by many/most of Bioconductor packages) wouldn't break it. Specific example of how masked colSums() call breaks things is shown below. Perhaps there's some way of doing whatever S4Vectors needs to do without masking common functions.
> m <- matrix(sample(c(0,1),1e2,replace=T),nrow=10) > library(Matrix) > sm <- Matrix(m,sparse=T) > colSums(sm)  6 7 7 7 6 2 4 5 6 7 > library(S4Vectors) Loading required package: stats4 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, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:Matrix’: colMeans, colSums, expand, rowMeans, rowSums The following objects are masked from ‘package:base’: colMeans, colSums, expand.grid, rowMeans, rowSums > colSums(sm) Error in colSums(sm) : 'x' must be an array of at least two dimensions > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats4 stats graphics grDevices utils datasets  methods base other attached packages:  S4Vectors_0.10.3 BiocGenerics_0.18.0 Matrix_1.2-7.1 loaded via a namespace (and not attached):  grid_3.3.1 lattice_0.20-34 >