[Bioc-devel] Bioc Devel Version issue

[Michael Morgan]

Hi Lori,
It looks like there are additional locations:

> .libPaths()
[1] "/home/mikemorgan/R/x86_64-pc-linux-gnu-library/3.4" "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library" "/usr/lib/R/library”

I’ve switched to just a single local library path by setting R_LIBS_SITE in my .Renviron file.

Thanks for the clue!

Best
Mike

On 27 Oct 2017, at 16:26, Shepherd, Lori <Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

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<mailto:bioc-devel-bounces at r-project.org>> on behalf of MikeMorgan <mm33 at sanger.ac.uk<mailto:mm33 at sanger.ac.uk>>
Sent: Friday, October 27, 2017 9:37:54 AM
To: bioc-devel at r-project.org<mailto: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<mailto: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.




-- 
 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. 



	[[alternative HTML version deleted]]