Entering edit mode
Hi,
Trying to install TCGAbiolinks, which has version 1.2.3 of SummarizedExperiments. When I install via biocLite(), I get version 1.0.2. I tried checking out the Github repo, but didn't see any more information there.
I also tried removing the package and reinstalling it, with no improvement.
R version: 3.3.1
Bioconductor Version: 3.2
What am I missing?
Any help would be nice,
Gaius
Sorry, meant to mention that I checked my R version. I'm running 3.3.1. And I have Bioconductor 3.2.
Please start a new R session in the terminal like so:
Then at the R prompt type:
R> source("https://bioconductor.org/biocLite.R") R> biocLite("SummarizedExperiment") R> library("SummarizedExperiment") R> sessionInfo()Please copy and paste the entire R session from right after you launch
R --vanillaall the way to the output ofsessionInfo()so that we can see exactly what's cookingC:\Program Files\R\R-3.3.1\bin>R.exe --vanilla
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
> biocLite("SummarizedExperiment")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.1 (2016-06-21).
Installing package(s) 'SummarizedExperiment'
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.3/S
ummarizedExperiment_1.0.2.zip'
Content type 'application/zip' length 2629971 bytes (2.5 MB)
downloaded 2.5 MB
package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\gaugustus\AppData\Local\Temp\RtmpeGh994\downloaded_packages
Old packages: 'curl', 'irlba', 'spdep', 'foreign', 'lattice', 'Matrix', 'mgcv',
'survival'
Update all/some/none? [a/s/n]: n
> library("SummarizedExperiment")
Loading required package: GenomicRanges
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, as.vector, 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, unlist, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.0.2 Biobase_2.30.0
[3] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[5] IRanges_2.4.8 S4Vectors_0.8.11
[7] BiocGenerics_0.16.1 BiocInstaller_1.20.3
loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 XVector_0.10.0 tools_3.3.1
It is still the case that your BiocInstaller package is out-of-date -- remove it following the directions at https://bioconductor.org/install/#troubleshoot-biocinstaller
If your BiocInstaller is current, when you load it it will sasy
(Hmm, it's not that BiocInstaller version 3.2 is too old, but that Bioconductor version 3.2 is too old...; it's also possible under some circumstances that you don't have a recent enough version of BiocInstaller to see the message...) Follow the instructions at the link in the message.
Thank you. Following the instructions on the bioconductor troubleshooting page fixed the issue.