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

[Dan Tenenbaum]

On Tue, Feb 7, 2012 at 1:55 PM, Matthew Pettis <matthew.pettis at gmail.com> wrote:
> 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.
>

Did you put the graphviz bin directory in your PATH as instructed by
the README file?

http://bioconductor.org/packages/2.9/bioc/readmes/Rgraphviz/README

If this does not work, please send the output of sessionInfo() with
your response.

Dan


> 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”)
>
> _______________________________________________
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