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

Tue Feb 7 23:26:35 CET 2012

On Tue, Feb 7, 2012 at 2:20 PM, Matthew Pettis <matthew.pettis at gmail.com> wrote:
> Hi Dan,
>
> I did, though perhaps I made some bad assumptions... here's what I have:
>
> I have Windows 7, x64.  I have a higher version of GraphViz than
> specified in the README, so I assumed I was OK.

> I further assumed
> that I did not need to rebuild from scratch, as Graphviz installed,
> and Windows 7 can accomodate 32-bit apps.  My PATH includes the path
> to the Graphviz bin (C:\Program Files (x86)\Graphviz2.26.3\bin),

This path suggests that you installed a 64-bit version of graphviz; is
that correct? If so, and if you want to use Rgraphviz in 32-bit mode
(which it looks like you do from your sessionInfo(), you need to
install the 32-bit version of graphviz and modify the PATH
accordingly.

and I
> assumed that paths with spaces in the name could be handled, but
> perhaps I am wrong about that... I don't see any mention about that in
> the README, but the example Path does not have any spaces (or `('
> characters in them, which mine does).

These are handled correctly.

>
> Do these assumptions jibe with what are in the README?  Perhaps I
> misunderstood this paragraph:
>
> ***
> Most users would want to use a binary (by which we mean pre-compiled)
> version of Graphviz. When preparing the binary version, it is assumed
> that a _specific_ version of Graphviz exists on the user's computer -
> using a different version of Graphviz will most likely cause Rgraphviz
> to fail. Rgraphviz will inform you of any version inconsistency when
> loaded.
> ***
>
> As I wrote, I do have a different version, but it is higher than this
> one, and I assumed it would work, and if it didn't, that "Rgraphviz
> will inform you of any version inconsistency when
> loaded", unless that is ultimately what the error is telling me.

No, the warning in this case is quite explicit.

>
>
> Further, I don't know where the .dll would be found... I don't have it
> in the Graphviz /bin directory, as these are the DLLs in there (see
> below).

Try the 32-bit version of graphviz.
The dll in question should be in the bin directory.
Dan

 The closest .dll to the one that seems to be erroring is
> cdt.dll, which I have.  I haven't installed the specific version of
> Graphviz mentioned in the README, but perhaps that has a different set
> of DLLs, one of which matches the one being requested in this error?
> I assumed
>
> GdiPlus.dll
> Pathplan.dll
> cdt.dll
> cgraph.dll
> glut32.dll
> graph.dll
> gvc.dll
> gvplugin_core.dll
> gvplugin_dot_layout.dll
> gvplugin_gd.dll
> gvplugin_gdiplus.dll
> gvplugin_neato_layout.dll
> gvplugin_pango.dll
> iconv.dll
> intl.dll
> jpeg62.dll
> libatk-1.0-0.dll
> libcairo-2.dll
> libexpat.dll
> libfontconfig-1.dll
> libfreetype-6.dll
> libgdk-win32-2.0-0.dll
> libgdk_pixbuf-2.0-0.dll
> libgdkglext-win32-1.0-0.dll
> libglade-2.0-0.dll
> libglib-2.0-0.dll
> libgmodule-2.0-0.dll
> libgobject-2.0-0.dll
> libgtk-win32-2.0-0.dll
> libgtkglext-win32-1.0-0.dll
> libltdl-3.dll
> libpango-1.0-0.dll
> libpangocairo-1.0-0.dll
> libpangoft2-1.0-0.dll
> libpangowin32-1.0-0.dll
> libpng12.dll
> libxml2.dll
> ltdl.dll
> regex_win32.dll
> vmalloc.dll
> zlib1.dll
>
>
>
> On Tue, Feb 7, 2012 at 4:04 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> 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”)
>>>
>>> _______________________________________________
>>> 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”)