Hi,

1. Rechecked Rgraphviz version, 1.12.3
2. My DYLD_LIBRARY_PATH does not seem to be visible to R, see the  
following (even after log-out/log-in):
 > system("export")
export AWK="awk"
export DISPLAY=":0"
export EDITOR="vi"
export EGREP="grep -E"
export HOME="/Users/danielk"
export LANG="en_GB.UTF-8"
export LN_S="ln -s"
export MAKE="make"
export OLDPWD
export PAGER="/usr/bin/less"
export PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
export PERL="/usr/bin/perl"
export PWD="/Users/danielk"
export R_ARCH="/i386"
export R_BROWSER="/usr/bin/open"
export R_DOC_DIR="/Library/Frameworks/R.framework/Versions/2.4/ 
Resources/doc"
export R_DVIPSCMD="/usr/local/teTeX/bin/i386-apple-darwin-current/dvips"
export R_GUI_APP_REVISION="4038"
export R_GUI_APP_VERSION="1.18"
export R_HOME="/Library/Frameworks/R.framework/Versions/2.4/Resources"
export R_INCLUDE_DIR="/Library/Frameworks/R.framework/Versions/2.4/ 
Resources/include"
export R_LATEXCMD="/usr/local/teTeX/bin/i386-apple-darwin-current/latex"
export R_LIBS="/Users/danielk/Library/R/library"
export R_MAKEINDEXCMD="/usr/local/teTeX/bin/i386-apple-darwin-current/ 
makeindex"
export R_PAPERSIZE="a4"
export R_PDFVIEWER="/usr/bin/open"
export R_PLATFORM="i386-apple-darwin8.8.1"
export R_PRINTCMD="lpr"
export R_RD4DVI="ae"
export R_RD4PDF="times,hyper"
export R_SESSION_TMPDIR="/tmp/RtmpGOVD7r"
export R_SHARE_DIR="/Library/Frameworks/R.framework/Versions/2.4/ 
Resources/share"
export R_UNZIPCMD="/usr/bin/unzip"
export R_USE_AQUA_SUBDIRS="yes"
export R_ZIPCMD="/usr/bin/zip"
export SECURITYSESSIONID="23431e90"
export SHELL="/bin/bash"
export SHLVL="1"	
export TAR="tar"
export USER="danielk"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"

however, running "export" in the terminal gives me the following:

danielk:~ danielk$ export
declare -x CLASSPATH="/usr/local/biojava/biojava-1.5-beta2.jar:/usr/ 
local/biojava/bytecode.jar:/usr/local/biojava/commons-cli.jar:/usr/ 
local/biojava/commons-collections-2.1.jar:/usr/local/biojava/commons- 
dbcp-1.1.jar:/usr/local/biojava/commons-pool-1.1.jar:/Users/danielk/ 
Documents/EclipseWorkspace/ELNServer/src/:/usr/local/mysql-java- 
connector-5.0.4/mysql-connector-java-5.0.4-bin.jar:"
declare -x DYLD
declare -x DYLD_LIBRARY_PATH="/usr/local/graphviz-2.12/lib"
declare -x HOME="/Users/danielk"
declare -x INFOPATH="/sw/share/info:/sw/info:/usr/share/info"
declare -x LOGNAME="danielk"
declare -x MANPATH="/sw/share/man:/usr/local/share/man:/usr/local/ 
mysql/man:/usr/share/man:/Library/TeX/Distributions/.DefaultTeX/ 
Contents/Man:/usr/X11R6/man:/sw/lib/perl5/5.8.6/man"
declare -x OLDPWD
declare -x PATH="/sw/bin:/sw/sbin:/usr/local/bin:/usr/local/sbin:/usr/ 
local/mysql/bin:/usr/local/blast-2.2.15/bin:/bin:/sbin:/usr/bin:/usr/ 
sbin:/usr/texbin:/usr/local/bin:/usr/X11R6/bin"
declare -x PERL5LIB="/sw/lib/perl5:/sw/lib/perl5/darwin:/sw/lib/perl5/ 
ensembl/modules"
declare -x PWD="/Users/danielk"
declare -x SECURITYSESSIONID="23431e90"
declare -x SHELL="/bin/bash"
declare -x SHLVL="1"
declare -x TERM="xterm-color"
declare -x TERM_PROGRAM="Apple_Terminal"
declare -x TERM_PROGRAM_VERSION="133"
declare -x USER="danielk"
declare -x __CF_USER_TEXT_ENCODING="0x1F5:0:0"
declare -x set

where DYLD_LIBRARY_PATH is present, but R doesn't seem to get the  
message.

3. No .so files are available in the given path, but lots of  
lib*.dylib files. Where would the .so files be loacted?

4. Running  nm lib*.dylib | grep agfstnode indeed gives
    U _agfstnode
          U _agfstnode
          U _agfstnode
          U _agfstnode
0000611c T _agfstnode
          U _agfstnode
          U _agfstnode
          U _agfstnode
          U _agfstnode
          U _agfstnode

and many more lines, all with the underscore ("_").

The error in R is still the same...

Best regards
Daniel

--

Contact information:

Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden

Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
E-mail: daniel@biotech.kth.se
E-mail: daniel@arrayadvice.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.ktharray.se/
Web: http://www.arrayadvice.se/
Fax: +46 8 5537 8481
MSN messenger: klevebring@msn.com


On 13 Apr 2007, at 12:43, Li.Long@isb-sib.ch wrote:

>
> Another thought:
>
> why do you have "_" in error msg:
>            Symbol not found: _agfstnode
> ?  In my Linux installation, it's only "agfstnode", without "_".
>
> I'd double-check to see which one you have in your graphviz  
> installation.
> In unix/linux, you can do somthing like:
>            nm lib*.so | grep agfstnode
>
> Li
>
>> Dear list,
>>
>> I am trying to load the package Rgraphviz on Mac OS X 10.4.9, and R
>> 2.4.1 using bioC 1.9 and Graphviz 2.12  and am running into the
>> following problem:
>>
>>> library(Rgraphviz)
>> Loading required package: graph
>> Loading required package: geneplotter
>> Loading required package: annotate
>> Loading required package: Biobase
>> Loading required package: tools
>>
>> Welcome to Bioconductor
>>
>>      Vignettes contain introductory material. To view, type
>>      'openVignette()' or start with 'help(Biobase)'. For details
>>      on reading vignettes, see the openVignette help page.
>>
>> KernSmooth 2.22 installed
>> Copyright M. P. Wand 1997
>> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>> 	unable to load shared library '/Users/danielk/Library/R/library/
>> Rgraphviz/libs/i386/Rgraphviz.so':
>>    dlopen(/Users/danielk/Library/R/library/Rgraphviz/libs/i386/
>> Rgraphviz.so, 6): Symbol not found: _agfstnode
>>    Referenced from: /Users/danielk/Library/R/library/Rgraphviz/libs/
>> i386/Rgraphviz.so
>>    Expected in: dynamic lookup
>> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
>> Error: package/namespace load failed for 'Rgraphviz'/usr/local/ 
>> graphviz-2.12/lib
>>
>> I have seen this problem posted before on the list, with the answer
>> to reinstalling the latest binary from bioC. I have tried this and it
>> didn't work. I have also seen something about setting the system
>> variable DYLD_LIBRARY_PATH, and I tried setting it in ~/.bashrc:
>> export DYLD_LIBRARY_PATH=/usr/local/graphviz-2.12/lib
>>
>> The same error as above still occurs. Does anyone know how to solve
>> this problem?
>>
>>> sessionInfo()
>> R version 2.4.1 (2006-12-18)
>> i386-apple-darwin8.8.1
>>
>> locale:
>> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"
>> "datasets"
>> [7] "methods"   "base"
>>
>> other attached packages:
>> geneplotter    annotate     Biobase       graph
>>     "1.12.0"    "1.12.0"    "1.12.2"    "1.12.1"
>>>
>>
>>
>> --
>>
>> Contact information:
>>
>> Daniel Klevebring
>> M. Sc. Eng., Ph.D. Student
>> Dept of Gene Technology
>> Royal Institute of Technology, KTH
>> SE-106 91 Stockholm, Sweden
>>
>> Visiting address: Roslagstullsbacken 21, B3
>> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
>> E-mail: daniel@biotech.kth.se
>> E-mail: daniel@arrayadvice.se
>> Phone: +46 8 5537 8337 (Office)
>> Phone: +46 704 71 65 91 (Mobile)
>> Web: http://www.ktharray.se/
>> Web: http://www.arrayadvice.se/
>> Fax: +46 8 5537 8481
>> MSN messenger: klevebring@msn.com
>>
>>
>>
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>>
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>


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