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

[Shepherd, Lori]

You can always use biocLite(pkg  , lib="path/to/library") .  The lib path in 
biocLite defaults to the .libPaths()[1].  When you do .libPaths() upon opening 
R does your path appear that you set with the environment variables?



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Guillaume MULLER <g...@presans.com>
Sent: Tuesday, April 11, 2017 8:28:34 AM
To: Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Installing EBImage with custom packages dir?

Hi,

Thanks for your answer.

The R_LIBS and R_LIBS_USER environment variables are already set in my 
~/.Renviron . They point to the correct location. But this latter is not 
selected when installing packages with biocLite()...

Cheers

GM
--
Guillaume MULLER, PhD
PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
http://www.presans.com
http://feeds.feedburner.com/OYI/fr


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

[Guillaume MULLER]

Hi,

Thanks for your answer.

The R_LIBS and R_LIBS_USER environment variables are already set in my 
~/.Renviron . They point to the correct location. But this latter is not 
selected when installing packages with biocLite()...

Cheers

GM
-- 
Guillaume MULLER, PhD
PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
http://www.presans.com
http://feeds.feedburner.com/OYI/fr

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Re: [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  on behalf of Guillaume 
MULLER 
Sent: Monday, April 3, 2017 5:45:22 AM
To: bioc-devel@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
http://www.presans.com
http://feeds.feedburner.com/OYI/fr

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