Unable to install packages on MacOS
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Joe ▴ 10
@60535013
Last seen 6 weeks ago
United States

Hi...

I'm totally stumped as to what to do to install Bioconductor on a clean MacBook Air (Intel) MacOS system (version 10.15.7).

The R version is: Darwin Kernel Version 19.6.0: Mon Apr 12 20:57:45 PDT 2021; root:xnu-6153.141.28.1~1/RELEASE_X86_64

RStudio Version: 1.4.1106

.Renviron R_LIBS=/Users/bc/RPackages R_LIBS_SITE=/Users/bc/RPackages R_LIBS_USER=/Users/bc/RPackages

<h5>Now, I start up RStudio and this is what happens.</h5>

R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

```.libPaths() [1] "/Users/bc/RPackages"
[2] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"

```install.packages("BiocManager",lib="/Users/bc/RPackages")

There is a binary version available but the source version is later: binary source needs_compilation BiocManager 1.30.12 1.30.13 FALSE

installing the source package ‘BiocManager’

trying URL 'https://cran.rstudio.com/src/contrib/BiocManager_1.30.13.tar.gz'

Content type 'application/x-gzip' length 262030 bytes (255 KB)

downloaded 255 KB

  • installing source package ‘BiocManager’ ... package ‘BiocManager’ successfully unpacked and MD5 sums checked using staged installation R inst byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
  • DONE (BiocManager)

The downloaded source packages are in ‘/private/var/folders/mm/9w4wl11m8xl6y2006s7d5b100000gp/T/RtmpNuczkI/downloaded_packages’

NOW, I WANT TO INSTALL edgeR FROM BIOCONDUCTOR

```BiocManager::install("edgeR") Bioconductor version 3.12 (BiocManager 1.30.13), ?BiocManager::install for help 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.12 (BiocManager 1.30.13), R 4.0.5 (2021-03-31) Installing package(s) 'BiocVersion', 'edgeR' Installation paths not writeable, unable to update packages path: /Library/Frameworks/R.framework/Versions/4.0/Resources/library packages: boot, class, cluster, KernSmooth, lattice, MASS, Matrix, mgcv, nnet, spatial, survival

OK...THE QUESTIONS

  1. Why on earth does BiocManager need to get to:
     /Library/Frameworks/R.framework/Versions/4.0/Resources/library
    
    when this path is not available other than as a sudo user? Why does it need to modify these files?
  2. Any suggestions as to how to fix this?

Note: I did in fact attempt to run this install as su, but that equally failed.

Thanks in advance, Joe

sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.0.5 tools_4.0.5

macos installation • 402 views
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Entering edit mode
@kevin
Last seen 2 hours ago
Naas, Republic of Ireland

Can you check the suggested solution here? - Avoid upgrading BiocManager to 1.30.13; fix proposed

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Ahhh...that seemed to work. So far...

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