[R-sig-Fedora] [R] Failure to load X11 module in Fedora 13.

Carlo Tambuatco oraclmaster at gmail.com
Sun Jul 4 20:30:06 CEST 2010


On 07/04/2010 12:27 PM, Marc Schwartz wrote:
> On Jul 3, 2010, at 4:24 PM, Carlo Tambuatco wrote:
>
>    
>> On 07/03/2010 11:46 AM, Marc Schwartz wrote:
>>      
>>> On Jul 3, 2010, at 7:54 AM, Carlo Tambuatco wrote:
>>>
>>>
>>>        
>>>> I've googled around the archives for R-help and R-sig Fedora and found
>>>> that a lot of people have had the same errors I've gotten when
>>>> starting up the X11() module:
>>>>
>>>> Error in X11() : X11 module cannot be loaded
>>>> In addition: Warning message:
>>>> In X11() : unable to load shared library '/usr/lib/R/modules//R_X11.so':
>>>>   /usr/lib/libfontconfig.so.1: undefined symbol: FT_Select_Size
>>>>
>>>> But I have come across zero answers to this fundamental problem. (At
>>>> least none that make sense to a newbie user like me.)
>>>>
>>>> This is after a fresh install of R on Fedora 13 via Yum.
>>>>
>>>> I checked and /usr/lib/R/modules/R_X11.so indeed exists. But R somehow
>>>> doesn't care and fails to load it.
>>>>
>>>> So, what did anyone do to resolve this issue?
>>>>
>>>> Here's my sessionInfo():
>>>>
>>>> R version 2.11.1 (2010-05-31)
>>>> i386-redhat-linux-gnu
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>>          
>>>
>>> Carlo,
>>>
>>> What is the output of:
>>>
>>>    ldd /usr/lib/libfontconfig.so.1
>>>
>>>        
>>     linux-gate.so.1 =>   (0x004d9000)
>>     libfreetype.so.6 =>  /usr/lib/libfreetype.so.6 (0x009a8000)
>>     libexpat.so.1 =>  /lib/libexpat.so.1 (0x00941000)
>>     libc.so.6 =>  /lib/libc.so.6 (0x00110000)
>>     /lib/ld-linux.so.2 (0x00375000)
>>
>>
>>      
>>> and
>>>
>>>    ldd /usr/lib/R/modules/R_X11.so
>>>
>>>        
>>     linux-gate.so.1 =>   (0x00687000)
>>     libSM.so.6 =>  /usr/lib/libSM.so.6 (0x00527000)
>>     libICE.so.6 =>  /usr/lib/libICE.so.6 (0x00d68000)
>>     libpangocairo-1.0.so.0 =>  /usr/lib/libpangocairo-1.0.so.0 (0x00bfe000)
>>     libpango-1.0.so.0 =>  /usr/lib/libpango-1.0.so.0 (0x00110000)
>>     libgobject-2.0.so.0 =>  /lib/libgobject-2.0.so.0 (0x00dd7000)
>>     libgmodule-2.0.so.0 =>  /lib/libgmodule-2.0.so.0 (0x009cb000)
>>     libgthread-2.0.so.0 =>  /lib/libgthread-2.0.so.0 (0x00159000)
>>     librt.so.1 =>  /lib/librt.so.1 (0x002e2000)
>>     libglib-2.0.so.0 =>  /lib/libglib-2.0.so.0 (0x00395000)
>>     libX11.so.6 =>  /usr/lib/libX11.so.6 (0x0052f000)
>>     libpng12.so.0 =>  /usr/lib/libpng12.so.0 (0x0015e000)
>>     libz.so.1 =>  /lib/libz.so.1 (0x00766000)
>>     libcairo.so.2 =>  /usr/lib/libcairo.so.2 (0x0025e000)
>>     libXt.so.6 =>  /usr/lib/libXt.so.6 (0x0078f000)
>>     libXmu.so.6 =>  /usr/lib/libXmu.so.6 (0x00bcf000)
>>     libtiff.so.3 =>  /usr/lib/libtiff.so.3 (0x008a0000)
>>     libjpeg.so.62 =>  /usr/lib/libjpeg.so.62 (0x00cce000)
>>     libR.so =>  /usr/lib/R/lib/libR.so (0xb74af000)
>>     libm.so.6 =>  /lib/libm.so.6 (0x00ae3000)
>>     libpthread.so.0 =>  /lib/libpthread.so.0 (0x00186000)
>>     libc.so.6 =>  /lib/libc.so.6 (0xb7323000)
>>     libuuid.so.1 =>  /lib/libuuid.so.1 (0x00927000)
>>     libpangoft2-1.0.so.0 =>  /usr/lib/libpangoft2-1.0.so.0 (0x001a1000)
>>     libfreetype.so.6 =>  /usr/lib/libfreetype.so.6 (0x00688000)
>>     libfontconfig.so.1 =>  /usr/lib/libfontconfig.so.1 (0x00d2f000)
>>     libdl.so.2 =>  /lib/libdl.so.2 (0x00318000)
>>     /lib/ld-linux.so.2 (0x00375000)
>>     libxcb.so.1 =>  /usr/lib/libxcb.so.1 (0x00201000)
>>     libpixman-1.so.0 =>  /usr/lib/libpixman-1.so.0 (0x00495000)
>>     libXrender.so.1 =>  /usr/lib/libXrender.so.1 (0x0021f000)
>>     libXext.so.6 =>  /usr/lib/libXext.so.6 (0x00228000)
>>     libRblas.so =>  /usr/lib/R/lib/libRblas.so (0x00d03000)
>>     libgfortran.so.3 =>  /usr/lib/libgfortran.so.3 (0x00f20000)
>>     libreadline.so.6 =>  /lib/libreadline.so.6 (0x00808000)
>>     libpcre.so.0 =>  /lib/libpcre.so.0 (0x0031d000)
>>     libbz2.so.1 =>  /lib/libbz2.so.1 (0x00239000)
>>     libicuuc.so.42 =>  /usr/lib/libicuuc.so.42 (0xb71c7000)
>>     libicui18n.so.42 =>  /usr/lib/libicui18n.so.42 (0xb7002000)
>>     libexpat.so.1 =>  /lib/libexpat.so.1 (0x00b7b000)
>>     libXau.so.6 =>  /usr/lib/libXau.so.6 (0x001cb000)
>>     libtinfo.so.5 =>  /lib/libtinfo.so.5 (0x002eb000)
>>     libicudata.so.42 =>  /usr/lib/libicudata.so.42 (0xb60bb000)
>>     libstdc++.so.6 =>  /usr/lib/libstdc++.so.6 (0xb5fce000)
>>     libgcc_s.so.1 =>  /lib/libgcc_s.so.1 (0x0034d000)
>>
>>
>>      
>>> I noted the double forward slash in your output above for the second module, which is a bit confusing, but I don't think that should affect anything.
>>>
>>> This is something that should work "out of the box". That you are having a fundamental problem here with X11 begins to point in the direction of a packaging issue or a version conflict with the R RPMs on F13.
>>>
>>> Just in case, I am cc'ing Tom on this thread to solicit any comments that he might have.
>>>
>>> Also, just for the heck of it, that you are having problems both on Fedora and on OSX with display related things, please verify that these are two separate computers. You are not running some virtual machine (eg. VMWare, VirtualBox, Parallels) with Fedora and OSX running at the same time on the same computer?
>>>
>>>        
>> Fedora and OS X are not running at the same time, but they are on the same computer (my MacBook Pro). It's not a virtual machine.
>>      
> So a dual-boot system then.
>
> Thanks for the clarification. That should hopefully obviate any VM associated issues.
>
> When you get a minute, please run 'yum update' as root to be sure that your system is fully updated. Depending upon whether you have run that since installing F13, it could take a while to download and install any RPM updates. Once you have done that, re-check R for any errors.
>
> Also, please run the following command at the CLI:
>
>    rpm -qi freetype
>
> That should display version information for the freetype RPM that is installed. If you post back, be sure to note whether you run that before or after running the 'yum update' command so as to avoid confusion. The most recent version is freetype-2.3.11-3.fc13.
>
> The original error messages suggest a version link conflict between libfontconfig and freetype, so presuming that you have not manually installed or removed something that might result in the conflict, this would tend to further support a packaging issue AFAICS. So we might have to wait for Tom to comment.
>
> Regards,
>
> Marc
>
>    

From: rpm -qi freetype

Run after 'sudo yum update'

X11() module still fails to load in R.


Name        : freetype                     Relocations: (not relocatable)
Version     : 2.3.11                            Vendor: Fedora Project
Release     : 3.fc13                        Build Date: Wed 03 Mar 2010 
05:32:03 PM EST
Install Date: Wed 09 Jun 2010 02:04:00 PM EDT      Build Host: 
xb-01.phx2.fedoraproject.org
Group       : System Environment/Libraries   Source RPM: 
freetype-2.3.11-3.fc13.src.rpm
Size        : 814191                           License: FTL or GPLv2+
Signature   : RSA/8, Wed 03 Mar 2010 05:46:21 PM EST, Key ID 
7edc6ad6e8e40fde
Packager    : Fedora Project
URL         : http://www.freetype.org
Summary     : A free and portable font rendering engine
Description :
The FreeType engine is a free and portable font rendering
engine, developed to provide advanced font support for a variety of
platforms and environments. FreeType is a library which can open and
manages font files as well as efficiently load, hint and render
individual glyphs. FreeType is not a font server or a complete
text-rendering library.



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