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Question: biocLite installs older version of SummarizedExperiment package
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gravatar for gaiusjaugustus
14 months ago by
University of Arizona
gaiusjaugustus0 wrote:

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

ADD COMMENTlink modified 14 months ago • written 14 months ago by gaiusjaugustus0
2
gravatar for Steve Lianoglou
14 months ago by
Genentech
Steve Lianoglou12k wrote:

biocLite is tied to your R version. To get the latest version of the packages you are trying to install, you need to make sure that you are running the latest version of R, ie. some flavor of R 3.3.x.

One way to check the version of R that you're running by looking at the output of sessionInfo()

 

ADD COMMENTlink written 14 months ago by Steve Lianoglou12k

Sorry, meant to mention that I checked my R version. I'm running 3.3.1.  And I have Bioconductor 3.2.

ADD REPLYlink written 14 months ago by gaiusjaugustus0

Please start a new R session in the terminal like so:

$ R --vanilla

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 --vanilla all the way to the output of sessionInfo() so that we can see exactly what's cooking

 

ADD REPLYlink modified 14 months ago • written 14 months ago by Steve Lianoglou12k

C:\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

ADD REPLYlink written 14 months ago by gaiusjaugustus0
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

ADD REPLYlink written 14 months ago by Martin Morgan ♦♦ 20k

If your BiocInstaller is current, when you load it it will sasy

Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
During startup - Warning message:
BiocInstaller version 3.2 is too old for R version 3.3.1; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller 

(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.

 

ADD REPLYlink written 14 months ago by Martin Morgan ♦♦ 20k

Thank you.  Following the instructions on the bioconductor troubleshooting page fixed the issue.

ADD REPLYlink written 14 months ago by gaiusjaugustus0
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