Hello All, I'm hoping someone here can help me out. I am trying to run a web application using RApache, that I have running on a test machine, but am having difficulty with on the actual service machine. This application depends on Rgraphviz to generate figures as output. I have installed graphviz 2.2-6, as well as Rgraphviz 1.26.0, and can run "example(layoutGraph) with only X11 font problems (old system, not relevant to generated output) either as a regular user, the apache user, or as root. However, when I try and load the Rgraphviz library in my web application, I get the following error: RApache Warning/Error!!! Loading required package: Rgraphviz RApache Warning/Error!!! Loading required package: graph RApache Warning/Error!!! Loading required package: grid RApache Warning/Error!!! Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: call: value[[3L]](cond) error: unable to load shared library '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so': libdotneato.so.0: cannot open shared object file: No such file or directory Check that (1) graphviz is installed on your system; (2) the installed version of graphviz matches '2.2'; this is the version used to build this Rgraphviz package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin' directory is in the system 'PATH' variable. See additional instructions in the 'README' file of the Rgraphviz 'source' distribution, available at http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask further questions on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html I can't really figure out where this is looking for "libdotneato.so.0", because when I run R I have no problems. I did make a symbolic link to the actual file, could this be part of the problem? I could really use some direction on this. Thanks, -Robert R version 2.11.1 (2010-05-31) x86_64-unknown-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 Rapache 1.1.9 Rgraphviz 1.26.0 graphviz 2.2-6 Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.flight at louisville.edu EM rflight79 at gmail.com Williams and Holland's Law: ? ? ?? If enough data is collected, anything may be proven by statistical methods.

So that others might know, the problem was that regular users had a different $LD_LIBRARY_PATH than the apache daemon, and therefore the libraries could not be found when the application was being run as a web user. -Robert On Tue, Oct 19, 2010 at 12:01, Robert M. Flight <rflight79 at="" gmail.com=""> wrote: > Hello All, > I'm hoping someone here can help me out. > I am trying to run a web application using RApache, that I have > running on a test machine, but am having difficulty with on the actual > service machine. This application depends on Rgraphviz to generate > figures as output. I have installed graphviz 2.2-6, as well as > Rgraphviz 1.26.0, and can run "example(layoutGraph) with only X11 font > problems (old system, not relevant to generated output) either as a > regular user, the apache user, or as root. > However, when I try and load the Rgraphviz library in my web > application, I get the following error: > > RApache Warning/Error!!! > > Loading required package: Rgraphviz > RApache Warning/Error!!! > > Loading required package: graph > RApache Warning/Error!!! > > Loading required package: grid > RApache Warning/Error!!! > > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > call: value[[3L]](cond) error: unable to load shared library > '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so': > libdotneato.so.0: cannot open shared object file: No such file or > directory Check that (1) graphviz is installed on your system; (2) the > installed version of graphviz matches '2.2'; this is the version used > to build this Rgraphviz package; (3) graphviz is accessible to R, > e.g., the path to the graphviz 'bin' directory is in the system 'PATH' > variable. See additional instructions in the 'README' file of the > Rgraphviz 'source' distribution, available at > http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask > further questions on the Bioconductor mailing list > http://bioconductor.org/docs/mailList.html > > I can't really figure out where this is looking for > "libdotneato.so.0", because when I run R I have no problems. I did > make a symbolic link to the actual file, could this be part of the > problem? I could really use some direction on this. > > Thanks, > > -Robert > > R version 2.11.1 (2010-05-31) > x86_64-unknown-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 > > > Rapache 1.1.9 > Rgraphviz 1.26.0 > graphviz 2.2-6 > > > Robert M. Flight, Ph.D. > University of Louisville Bioinformatics Laboratory > University of Louisville > Louisville, KY > > PH 502-852-0467 > EM robert.flight at louisville.edu > EM rflight79 at gmail.com > > Williams and Holland's Law: > ? ? ?? If enough data is collected, anything may be proven by > statistical methods. >