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

Tue Feb 7 23:20:42 CET 2012

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), 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).

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.

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).  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”)