Thanks Li and Robert for quick replies. I applied the version- specific fixes to common.h and graphvizVersion.c from 1.15.9 to the 1.14.1 distro, and it compiles/installs nicely against graphviz 2.14-1. I'll let you know if it doesn't work out somehow. /Emil > A correction: the nightly build is based on graphviz 2.12. From > what I > could see in testing with graphviz 2.14, I don't expect major > portability > issues on Mac OS. > > If you encounter additional problem with graphviz-2.14 in Rgraphviz > 1.15.9, please don't hesitate to let me know. > > Thanks, > > Li > >> >> This is done already for Rgraphviz. If you get latest codes, >> either from >> svn, source code download (1.15.9) or the upcoming official >> release in the >> beginning of Oct, you should be able to get it run with graphviz >> 2.14. >> The nightly build on Mac OS X (10.4.10) is all OK. >> >> Li >> >>> Hi all, >>> >>> I have trouble installing/compiling Rgraphviz 1.14.1 for BioC 2.0. >>> I'm on Mac OS X 10.4.1 server (Intel). This thread started on the >>> MacPorts mailing list (providers of the Graphviz package for OS X), >>> then took a side tour to the Graphviz developers, but I now believe >>> it belongs here. >>> >>> Response from macports-users: http://lists.macosforge.org/pipermail/ >>> macports-users/2007-September/005630.html >>> Response from graphviz-devel: https://mailman.research.att.com/ >>> pipermail/graphviz-devel/2007/000450.html >>> >>> The root of the problem is that graphviz >=2.14 is missing some >>> header files as compared to older versions. I assume this is due to >>> the cleanup of the code rather than missing functionality, but in >>> any >>> case, a revision of the Rgraphviz package is probably in order. >>> >>> Until an Rgraphviz update hits the trunk, do you have any tips on >>> how >>> I can get the current Rgraphviz to compile manually? Or dare I try >>> the OS X binary? Se below for compilation specifics. >>> >>> TIA, >>> >>> Emil Lundberg >>> MicroArray Datawarehouse Resource (MADR) >>> Linnaeus Centre for Bioinformatics (LCB) >>> Biomedical Centre (BMC) >>> Uppsala University >>> >>> >>> ********** >>> (manually in the Rgraphviz directory, or through bioclite >>> ("Rgraphviz")) >>> % R CMD INSTALL . >>> * Installing to library '/opt/local/lib/R/library' >>> * Installing *source* package 'Rgraphviz' ... >>> configure: No --with-graphviz option was specified. Trying to find >>> graphviz using other methods. >>> checking for pkg-config... /opt/local/bin/pkg-config >>> configure: Found graphviz 2.14.1 >>> configure: We have inferred the following flags for graphviz >>> configure: ..PKG_CPPFLAGS=-I/opt/local/include/graphviz >>> configure: ..PKG_LIBS=-L/opt/local/lib -lgvc >>> configure: creating ./config.status >>> config.status: creating src/Makevars >>> ** libs >>> /opt/local/bin/gcc-mp-4.2 -std=gnu99 -I/opt/local/lib/R/include -I/ >>> opt/local/lib/R/include -I/opt/local/include/graphviz - >>> DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -I/opt/local/include - >>> D__NO_MATH_INLINES -fPIC -O2 -c LL_funcs.c -o LL_funcs.o >>> In file included from /opt/local/include/graphviz/gvc.h:20, >>> from common.h:30, >>> from LL_funcs.c:1: >>> /opt/local/include/graphviz/types.h:27:1: warning: "TRUE" redefined >>> In file included from common.h:5, >>> from LL_funcs.c:1: >>> /opt/local/lib/R/include/Rdefines.h:148:1: warning: this is the >>> location of the previous definition >>> In file included from LL_funcs.c:1: >>> common.h:41:20: error: gvcint.h: No such file or directory >>> common.h:42:21: error: globals.h: No such file or directory >>> make: *** [LL_funcs.o] Error 1 >>> chmod: /opt/local/lib/R/library/Rgraphviz/libs/*: No such file or >>> directory >>> ERROR: compilation failed for package 'Rgraphviz' >>> ** Removing '/opt/local/lib/R/library/Rgraphviz' >>> >>> I've already tried removing the gvcint.h and globals.h includes from >>> common.h, but I then get: >>> >>> [...] >>> graphvizVersion.c: In function 'Rgraphviz_graphvizVersion': >>> graphvizVersion.c:24: error: dereferencing pointer to incomplete >>> type >>> >>> >>> ********** >>> >>> Thanks guys for adressing this. My graphviz (2.14-1 from >>> MacPorts) is >>> missing the following headers compared to Ryan's 2.12: >>> >>> aghdr.h >>> agxbuf.h >>> arith.h (back as of 2.14-3) >>> ast_common.h >>> dthdr.h >>> exgram.h >>> exlib.h >>> expr.h >>> globals.h (requested by Rgraphviz) >>> grammar.h >>> gvcint.h (requested by Rgraphviz) >>> libgraph.h >>> logic.h >>> malloc.h >>> parser.h >>> pathplan.h >>> pathutil.h >>> solvers.h >>> tri.h >>> triefa.h >>> vis.h >>> vispath.h >>> vmstub.h >>> >>> To clarify matters, the Rgraphviz is an external R package that >>> depends on the Bioconductor package, so the R developers might not >>> know about it. R builds fine using the current MacPorts version >>> (don't know about the devel), and so does Bioconductor, but neither >>> depend on graphviz as such. >>> >>> The maintainers of Rgraphviz have already made a good effort in that >>> package's header files to accomodate different versions of graphviz >>> (up to 2.10 at least), so this is hopefully what they need to >>> know to >>> update the Rgraphviz package. I'm forwarding this to the >>> bioconductor >>> mailing list. >>> >>> >>> best, >>> >>> /Emil >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >