Entering edit mode
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:
[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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocGenerics_0.30.0 ggplot2_3.2.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 XVector_0.24.0 GenomeInfoDb_1.20.0
[4] pillar_1.4.2 compiler_3.6.0 prettyunits_1.0.2
[7] progress_1.2.2 zlibbioc_1.30.0 bitops_1.0-6
[10] tools_3.6.0 biomaRt_2.40.5 zeallot_0.1.0
[13] digest_0.6.21 bit_1.1-14 RSQLite_2.1.2
[16] memoise_1.1.0 tibble_2.1.3 gtable_0.3.0
[19] pkgconfig_2.0.3 rlang_0.4.0 DBI_1.0.0
[22] GenomeInfoDbData_1.2.1 httr_1.4.1 stringr_1.4.0
[25] withr_2.1.2 dplyr_0.8.3 hms_0.5.1
[28] Biostrings_2.52.0 IRanges_2.18.3 S4Vectors_0.22.1
[31] vctrs_0.2.0 bit64_0.9-7 grid_3.6.0
[34] tidyselect_0.2.5 glue_1.3.1 Biobase_2.44.0
[37] R6_2.4.0 AnnotationDbi_1.46.1 XML_3.98-1.20
[40] purrr_0.3.2 blob_1.2.0 magrittr_1.5
[43] GenomicRanges_1.37.16 scales_1.0.0 backports_1.1.5
[46] assertthat_0.2.1 colorspace_1.4-1 stringi_1.4.3
[49] RCurl_1.95-4.12 lazyeval_0.2.2 munsell_0.5.0
[52] crayon_1.3.4
>
Here's the requested output in the comment.
The remainder of the BiocManager::valid() output is below (it was over 5000 characters).
If you're wanting to use the devel version of Bioconductor, then indicate that with BiocManager
and then re-run
BiocManager::valid()-- it will indicate that there are a few packages that are out-of-date, and you should then update them.If you're wanting to use the release version of Bioconductor, then copy and paste the command above into your R session (and take a break for coffee!).
If you want to have two different installations of Bioconductor, then follow the instructions in the vignette.