Forum: help

RE: cannot load Vennerable 3.0 on Mac OS [ Reply ] By: Jonathan Swinton on 2015-12-15 14:16	[forum:42800]
I still do not have access to a Mac so I can't offer any advice, but I would appreciate it if anyone that has had success installing Vennerable on a Mac lets us know here. Please note that active development of Vennerable has moved to https://github.com/js229/Vennerable Please also note success was reported here: https://r-forge.r-project.org/forum/message.php?msg_id=39774&group_id=474

RE: cannot load Vennerable 3.0 on Mac OS [ Reply ]
By: Sara Meyer on 2013-11-19 00:17

[forum:40084]

I'm a novice at R and so I'm not entirely sure if all that I had to load/install was necessary but the basic R install was not nearly enough. Vennerable is my first quest with R.

I have OS X 10.7.5 and R 3.0.0

I had to load in Package Manager (if these are not listed go install them from BioConductor or CRAN in Package Installer):
BiocGenerics, compiler, tools, utils, plyr, the list goes on and on…every time I tried to Install something else it said I needed other dependencies (as an example…...ERROR: dependency ‘BiocGenerics’ is not available for package ‘graph’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/graph’)

Eventually I figured out all these dependencies I could find in Installer or Manager.

Then things started finally rolling downhill.
I was able to install and load RBGL then graph (not the other way around).

But the URL that Fong posted for Other Repository link still did not allow install of Vennerable. It required other dependencies so I installed:
RColorBrewer, gtools, and reshape and loaded those.

Then finally was able to install and load Vennerable….hopefully it works I have not tried it yet (4 hours later).

RE: cannot load Vennerable 3.0 on Mac OS [ Reply ]
By: Fong Koh on 2013-08-09 19:03

[forum:39776]

I'm a noob on a Mac running R64 v2.15. I had to jump through a few hoops to get Vennerable installed, so I'm documenting the process below to help others in the same situation.

1. A fresh OS X install does not come with command line tools, which contains gcc required to compile from source. Download from Apple Developers website by searching for Command Line Tools.
https://developer.apple.com/downloads/index.action
Latest: Command Line Tools (OS X Mountain Lion) for Xcode - April 2013

2. Install dependencies.
a) Using the R Package Installer, looking into the BioConductor (binary) repository, install "graph" package (current version 1.36.2). (not sure if there're any dependencies, but I check Install Dependencies by default)

b) Download the package source from BioC for RBGL.
http://www.bioconductor.org/packages/release/bioc/html/RBGL.html

The installation of this package is a little tricky for me because it requires the libraries of both i386 and x86_64 architectures, but a simple installation of one will overwrite the other.

This is the error I'll get if I install normally.
*** arch - i386
Error : package ‘RBGL’ is not installed for 'arch=i386'
Error: loading failed
Execution halted

To avoid that error, use both of these commands in Terminal to install RBGL (I'm preferring R64 over R):
R --arch=x86_64 CMD INSTALL /path/to/file/RBGL_1.36.2.tar.gz
R --arch=i386 CMD INSTALL --libs-only /path/to/file/RBGL_1.36.2.tar.gz

3. Going back to the R Package Installer, putting "http://r-forge.r-project.org/" into Other Repository, and selecting Binary Format Packages, you should now be able to install Vennerable.

Hope this helps someone out there. Cheers!

RE: cannot load Vennerable 3.0 on Mac OS [ Reply ] By: Jonathan Swinton on 2013-08-07 16:56	[forum:39775]
Having actually read the reported error message (!) the problem is that you need to install the packages RBGL and graph (available I believe from the bioconductor repository). Another thread reports success in this way.

RE: cannot load Vennerable 3.0 on Mac OS [ Reply ] By: Jonathan Swinton on 2013-08-07 16:40	[forum:39773]
R-Forge is no longer building binaries for MacOS. Nothing to do with Vennerable so I can't do anything about it. There is no reason I am aware of why you should not be able to install the package from source. Hints for this are in nearby threads. If you try to do this, please let me, and other potential users, know of your success or failure.

cannot load Vennerable 3.0 on Mac OS [ Reply ]
By: Yu Fan on 2013-08-02 17:05

[forum:39772]

the R studio warning:
Warning in install.packages :
package ‘~/Downloads/Vennerable_3.0.tar.gz’ is not available (for R version 3.0.1)
ERROR: dependencies ‘graph’, ‘RBGL’ are not available for package ‘Vennerable’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Vennerable’
Warning in install.packages :
installation of package ‘/Users/***/Downloads/Vennerable_3.0.tar.gz’ had non-zero exit status

the graph, and RBGL were not available in mac recently, can you offer resolution about this problem?