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

[Matthew Pettis]

Hi,

I upgraded R to 2.14.1.  I again followed the directions at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html .
The install seemed to go smoothly, I had to update some packages like
`boot', but all of the checksums passed.  However, when executing:

library('Rgraphviz')

I get:

The program can't start because libcdt-4.dll is missing from your
computer.  Try reinstalling the program to fix this problem.

Any help is appreciated.

Thanks,
Matt

On Tue, Feb 7, 2012 at 3:35 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> This is a rather old version of R.  Please upgrade to 2.14, the current
> released version, and if you have further problems, please send the output
> of sessionInfo() with your query.
>
> On Tue, Feb 7, 2012 at 3:24 PM, Matthew Pettis <matthew.pettis at gmail.com>
> wrote:
>>
>> 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”)
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>



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

- Matsuo Munefusa (”Basho”)