So, this may be pretty big problem that may affect many packages, including mine. I hope others are not having the same issue, but I cannot get GenomicRanges to load because it wants a newer version of S4Vectors than exists on Bioconductor(see https://bioconductor.org/packages/release/bioc/html/S4Vectors.html, at the bottom, it's version 0.22.1). It's probably a quick fix, but I thought I would bring it to your attention.
> library(GenomicRanges) 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, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, 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, which, which.max, which.min Error: package ‘S4Vectors’ 0.22.1 was found, but >= 0.23.19 is required by ‘GenomicRanges’
To show that the old version is still being installed by default:
> BiocManager::install("S4Vectors") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'S4Vectors' trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/S4Vectors_0.22.1.tar.gz' Content type 'application/x-gzip' length 637005 bytes (622 KB) downloaded 622 KB
This is a problem for me because I have Bioconductor dependencies on my package and now my installation instructions will fail (as will basically any package installation attempt).
> sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_rt.so Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding 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:  BiocGenerics_0.30.0 ggplot2_3.2.1 loaded via a namespace (and not attached):  Rcpp_1.0.2 XVector_0.24.0 GenomeInfoDb_1.20.0  pillar_1.4.2 compiler_3.6.0 prettyunits_1.0.2  progress_1.2.2 zlibbioc_1.30.0 bitops_1.0-6  tools_3.6.0 biomaRt_2.40.5 zeallot_0.1.0  digest_0.6.21 bit_1.1-14 RSQLite_2.1.2  memoise_1.1.0 tibble_2.1.3 gtable_0.3.0  pkgconfig_2.0.3 rlang_0.4.0 DBI_1.0.0  GenomeInfoDbData_1.2.1 httr_1.4.1 stringr_1.4.0  withr_2.1.2 dplyr_0.8.3 hms_0.5.1  Biostrings_2.52.0 IRanges_2.18.3 S4Vectors_0.22.1  vctrs_0.2.0 bit64_0.9-7 grid_3.6.0  tidyselect_0.2.5 glue_1.3.1 Biobase_2.44.0  R6_2.4.0 AnnotationDbi_1.46.1 XML_3.98-1.20  purrr_0.3.2 blob_1.2.0 magrittr_1.5  GenomicRanges_1.37.16 scales_1.0.0 backports_1.1.5  assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3  RCurl_1.95-4.12 lazyeval_0.2.2 munsell_0.5.0  crayon_1.3.4 >