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.sheph...@roswellpark.org<mailto:lori.sheph...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of MikeMorgan <m...@sanger.ac.uk<mailto:m...@sanger.ac.uk>> Sent: Friday, October 27, 2017 9:37:54 AM To: bioc-devel@r-project.org<mailto:bioc-devel@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@r-project.org<mailto:Bioc-devel@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]]
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