[Bioc-devel] Installing EBImage with custom packages dir?

[Shepherd, Lori]

If you are able to set environment variables or have a .bash_aliases,  you could set the R_LIBS or R_LIBS_USER environment variables to your desired path "~/.R/x86_64-pc-linux-gnu-library/3.1.2".  When these are set it should become the default path in .libPaths() when you start R.


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 Guillaume MULLER <gm at presans.com>
Sent: Monday, April 3, 2017 5:45:22 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Installing EBImage with custom packages dir?

Hi,

I've been installing EBImage several time these past months on multiple machines, using instructions at: http://bioconductor.org/packages/release/bioc/html/EBImage.html.

I've noticed a few strange things with the installer:

- When the installer installs the dependencies and one of them fails (e.g. "tiff" or "png", because the headers are not installed on the system), and I run again biocLite("EBImage"), then even the dependencies that previously installed successfully (I saw the "DONE (xxx)" line in the logs) are re-downloaded and re-installed...

- The script asks if I want to upgrade my packages. If I says yes, then the system-wide installation fails because I'm not root, thus the biocLite() asks if I want to install the packages in my "personal library". If I answer "yes", it installs the packages in the default personal library location ("~/R/x86_64-pc-linux-gnu-library/3.2"), whereas I've hardcoded my personal library location by using (.libPaths("~/.R/x86_64-pc-linux-gnu-library/3.1.2" in my .Rprofile)... Also, I'm not sure the script does not takes into account the packages already installed installed in my personal library, thus redundantly (re)-installs some packages in the default location.

Is there any work-around so that I don't have to move all the (redundantly) installed packages into my actual personal library?

Cheers


GM
--
Guillaume MULLER, PhD
PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
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