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

Matthew Pettis matthew.pettis at gmail.com
Wed Feb 8 16:49:15 CET 2012 

SOLVED.

Thank you to all that helped, I really appreciate it.

The solution that worked for me was to upgrade to R 2.14.1, and to
install the 2.20 version of Graphviz.  For the record, since there
were 3 options at the link that Dan sent me, I chose this installer,
and it worked:

http://graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi

I also, per the docs, put the path to graphviz on my system path.  I
have 2 versions of Graphviz on my computer, with one being newer, and
to be safe, I put the path to the \bin directory of v2.20 BEFORE the
path to the newer Graphviz version.  I could probably just take out
the path to the newer version, though, as it will for all practical
purposes never get accessed.

Thank you all again,
Matt

On Tue, Feb 7, 2012 at 6:06 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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”)
>>
>>
>> _______________________________________________
>> 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
>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
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-- 
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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