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

Martin Morgan mtmorgan at fhcrc.org
Wed Feb 8 01:06:46 CET 2012 

On 02/07/2012 02:26 PM, Dan Tenenbaum wrote:
> 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 am a little rusty on my graphviz, but I think you _do_ want the exact 
version; the DLL is found by name, and the name / organization of the 
DLL's change with version -- libcdt-4.dll != cdt.dll. Martin

>
>> 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”)
>
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