I don't get that message when loading cummeRbund. Are you using a current version of R/Bioconductor?
> 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, basename, cbind, colMeans,
colnames, colSums, dirname, 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
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
Matrix products: default
BLAS: /data/oldR/R-3.5.0/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-3.5.0/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] cummeRbund_2.22.0 Gviz_1.24.0 rtracklayer_1.40.1
[4] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0 IRanges_2.14.4
[7] S4Vectors_0.18.1 fastcluster_1.1.24 reshape2_1.4.3
[10] ggplot2_2.2.1 RSQLite_2.1.1 BiocGenerics_0.26.0
[13] BiocInstaller_1.30.0
loaded via a namespace (and not attached):
[1] Biobase_2.40.0 httr_1.3.1
[3] bit64_0.9-7 splines_3.5.0
[5] Formula_1.2-3 assertthat_0.2.0
[7] latticeExtra_0.6-28 blob_1.1.1
[9] BSgenome_1.48.0 GenomeInfoDbData_1.1.0
[11] Rsamtools_1.32.0 progress_1.1.2
[13] pillar_1.2.2 backports_1.1.2
[15] lattice_0.20-35 biovizBase_1.28.0
[17] digest_0.6.15 RColorBrewer_1.1-2
[19] XVector_0.20.0 checkmate_1.8.5
[21] colorspace_1.3-2 htmltools_0.3.6
[23] Matrix_1.2-14 plyr_1.8.4
[25] XML_3.98-1.11 GetoptLong_0.1.6
[27] biomaRt_2.36.0 zlibbioc_1.26.0
[29] scales_0.5.0 BiocParallel_1.14.1
[31] tibble_1.4.2 htmlTable_1.11.2
[33] AnnotationFilter_1.4.0 GenomicFeatures_1.32.0
[35] SummarizedExperiment_1.10.0 nnet_7.3-12
[37] lazyeval_0.2.1 survival_2.42-3
[39] magrittr_1.5 memoise_1.1.0
[41] foreign_0.8-70 data.table_1.11.0
[43] tools_3.5.0 prettyunits_1.0.2
[45] GlobalOptions_0.0.13 matrixStats_0.53.1
[47] ComplexHeatmap_1.18.0 stringr_1.3.0
[49] munsell_0.4.3 cluster_2.0.7-1
[51] DelayedArray_0.6.0 ensembldb_2.4.1
[53] AnnotationDbi_1.42.0 Biostrings_2.48.0
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