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

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Tue Apr 11 13:59:13 CEST 2017

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?


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?


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

Bioc-devel at r-project.org mailing list

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]]

More information about the Bioc-devel mailing list