[Bioc-devel] Bioc Devel Version issue

[Shepherd, Lori]

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

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



--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]