[Bioc-devel] Bioc Devel Version issue
Are there any other locations where BiocInstaller might already be installed? .libPaths() Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of MikeMorgan <mm33 at sanger.ac.uk>
Sent: Friday, October 27, 2017 9:37:54 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Bioc Devel Version issue
Sent: Friday, October 27, 2017 9:37:54 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Bioc Devel Version issue
Dear Bioc-Developers,
I am trying to switch to Bioc Devel (R version 3.4.2). There is a
versioning issue with Bioconductor:
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> useDevel()
Error: 'devel' version already in use
> remove.packages("BiocInstaller")
Removing package from ?/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4?
(as ?lib? is unspecified)
Error in find.package(pkgs, lib) :
there is no package called ?BiocInstaller?
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning message:
Bioconductor version 3.4 is too old for R version 3.4.2; see
https://bioconductor.org/install/#troubleshoot-biocinstaller
I have followed the instructions in the URL and this does not provide a
solution. I am attempting to specifically update to use
SingleCellExperiment and the github version of scran.
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.24.0
loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2
>
One of my colleagues currently has the same issue on a Mac with Sierra
10.12.6 running R 3.4.1.
Best wishes
Mike
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