[BioC] Rgraphviz: cannot allocate memory block of size 3.4 Gb

Matthew Pettis matthew.pettis at gmail.com
Tue Feb 7 21:24:26 CET 2012


Hi,

I installed graphviz from the directions given at:

http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html

which is just to execute these two statements:
==============================================================
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
==============================================================

However, I am not able to load the library due to the error below.
But it seems a strange error... why should this package be trying to
allocate 3.4Gb of memory?

I am running:

R: 2.12.2
Graphviz: 2.26.3


Thanks for any help.
Matt


Here is the R console output for the getting of the package and trying
to load the library:


This is the output to the R console:
==============================================================
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
> biocLite("Rgraphviz")
Using R version 2.12.2, biocinstall version 2.7.7.
Installing Bioconductor version 2.7 packages:
[1] "Rgraphviz"
Please wait...

Installing package(s) into ‘C:\Users\U0008998\Documents/R/win-library/2.12’
(as ‘lib’ is unspecified)
trying URL 'http://bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/Rgraphviz_1.28.0.zip'
Content type 'application/zip' length 1065188 bytes (1.0 Mb)
opened URL
downloaded 1.0 Mb

package 'Rgraphviz' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Users\U0008998\AppData\Local\Temp\Rtmpck6fS3\downloaded_packages
==============================================================


When I try to load the library, I get:
==============================================================
> library('Rgraphviz')
Error in get(hookname, envir = env, inherits = FALSE) :
  cannot allocate memory block of size 3.4 Gb
Error: package/namespace load failed for 'Rgraphviz'
==============================================================


--
Do not seek to follow in the footsteps of the wise men of old. Seek
what they sought.

- Matsuo Munefusa (”Basho”)


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