[Bioc-devel] Bioc Devel Version issue

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Fri Oct 27 17:26:48 CEST 2017

Are there any other locations where BiocInstaller might already be installed?


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

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

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

  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=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


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