Hi Li, Many thanks for your advises. According to your suggestions, I have modified the --configure-args='--with-graphviz=/usr/lib/graphviz' to look into executables in "/usr" instead, and it did the job. $ R CMD INSTALL Rgraphviz_1.16.0.tar.gz --configure-args='--with-graphviz=/usr' Thanks again, Amin. > On Fri, 2007-11-02 at 17:29 +0100, Li.Long at isb-sib.ch wrote: > > What the codes didn't get right is: GRAPHVIZ_MAJOR and GRAPHVIZ_MINOR in > > the following line: > > > > -------------------------------------------------------------------- > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include > > -I/usr/lib/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=1453: > > -DGRAPHVIZ_MINOR=1453: -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g > > -O2 -c agopen.c -o agopen.o > > -------------------------------------------------------------------- > > > > If you installed 2.12, they should be: GRAPHVIZ_MAJOR=2, GRAPHVIZ_MINOR=12. > > They are derived from running "dot -V" that gives something like: > > > > -------------------------------------------------------------------- > > dot - Graphviz version 2.12 (Fri Dec 15 14:34:55 UTC 2006) > > -------------------------------------------------------------------- > > > > You could try to see if you could run "dot -V" from your graphviz-2.12 > > installation. I suspect that your installation is incomplete for some > > reason: you only reference /usr/lib/graphviz, where are the executables? > > > > I don't think PKG_CONFIG_PATH is used any more (it doesn't hurt anything > > for you). I'll update the doc. > > > > Li > > > > > Dear Li, > > > Dear All, > > > > > > Many thanks for all your suggestions, I have upgraded the R to 2.6 and > > > tried to install the latest version of Rgraphviz but the problem still > > > exist and I don't know if it is actually related to bioconductor or > > > grphviz?? So any advise is appreciated. > > > > > > > > > I have installed : R version 2.6.0, Bioconductor version 2.1, Graphviz > > > version 2.12-4ubuntu3. > > > > > > The environment variable are configured as below : > > > > > > $export PKG_CONFIG_PATH="/usr/lib/pkgconfig" > > > > > > $whereis graphviz > > > graphviz: /usr/lib/graphviz /usr/include/graphviz /usr/share/graphviz > > > /usr/share/man/man7/graphviz.7.gz > > > > > > $export LD_LIBRARY_PATH=/usr/lib/graphviz > > > > > > $ R CMD INSTALL --configure-args='--with- graphviz=/usr/lib/graphviz' > > > Rgraphviz_1.16.0.tar.gz > > > * Installing to library '/home/moghadda/R/library26' > > > * Installing *source* package 'Rgraphviz' ... > > > configure: Using user specified graphviz root > > > directory /usr/lib/graphviz > > > ./configure: line 1459: test: 1453:: integer expression expected > > > configure: Found graphviz 1453: > > > ./configure: line 1481: test: 1453:: integer expression expected > > > ./configure: line 1481: test: 1453:: integer expression expected > > > configure: We have inferred the following flags for graphviz > > > configure: ..PKG_CPPFLAGS=-I/usr/lib/graphviz/include/graphviz > > > configure: ..PKG_LIBS=-L/usr/lib/graphviz/lib/graphviz > > > -L/usr/lib/graphviz/lib -lgvc > > > checking for whether compiler has bool... checking for gcc... gcc > > > checking for C compiler default output file name... a.out > > > checking whether the C compiler works... yes > > > checking whether we are cross compiling... no > > > checking for suffix of executables... > > > checking for suffix of object files... o > > > checking whether we are using the GNU C compiler... yes > > > checking whether gcc accepts -g... yes > > > checking for gcc option to accept ANSI C... none needed > > > checking how to run the C preprocessor... gcc -E > > > checking for egrep... grep -E > > > checking for ANSI C header files... yes > > > checking for sys/types.h... yes > > > checking for sys/stat.h... yes > > > checking for stdlib.h... yes > > > checking for string.h... yes > > > checking for memory.h... yes > > > checking for strings.h... yes > > > checking for inttypes.h... yes > > > checking for stdint.h... yes > > > checking for unistd.h... yes > > > checking for stdbool.h that conforms to C99... yes > > > checking for _Bool... yes > > > yes > > > configure: creating ./config.status > > > config.status: creating src/Makevars > > > ** libs > > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include > > > -I/usr/lib/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=1453: > > > -DGRAPHVIZ_MINOR=1453: -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g > > > -O2 -c agopen.c -o agopen.o > > > In file included from agopen.c:1: > > > common.h:17:5: error: ':' without preceding '?' > > > In file included from agopen.c:1: > > > common.h:52: error: expected ???=???, ???,???, ???;???, ???asm??? or > > > ???__attribute__??? > > > before ???*??? token > > > common.h:55:5: error: ':' without preceding '?' > > > common.h:60: error: expected ???=???, ???,???, ???;???, ???asm??? or > > > ???__attribute__??? > > > before ???*??? token > > > In file included from agopen.c:2: > > > util.h:18: error: expected ???)??? before ???*??? token > > > agopen.c:4: error: expected ???=???, ???,???, ???;???, ???asm??? or > > > ???__attribute__??? > > > before ???*??? token > > > agopen.c: In function ???Rgraphviz_agopen???: > > > agopen.c:54: error: ???Agraph_t??? undeclared (first use in this function) > > > agopen.c:54: error: (Each undeclared identifier is reported only once > > > agopen.c:54: error: for each function it appears in.) > > > agopen.c:54: error: ???g??? undeclared (first use in this function) > > > agopen.c:54: error: ???tmpGraph??? undeclared (first use in this function) > > > agopen.c:55: error: ???sgs??? undeclared (first use in this function) > > > agopen.c:56: error: ???Agnode_t??? undeclared (first use in this function) > > > agopen.c:56: error: ???head??? undeclared (first use in this function) > > > agopen.c:56: error: ???tail??? undeclared (first use in this function) > > > agopen.c:56: error: ???tmp??? undeclared (first use in this function) > > > agopen.c:57: error: ???Agedge_t??? undeclared (first use in this function) > > > agopen.c:57: error: ???curEdge??? undeclared (first use in this function) > > > agopen.c:80: warning: implicit declaration of function ???aginit??? > > > agopen.c:82: warning: implicit declaration of function ???agopen??? > > > agopen.c:86: warning: implicit declaration of function > > > ???setDefaultAttrs??? > > > agopen.c:89: error: expected expression before ???)??? token > > > agopen.c:107: warning: implicit declaration of function ???agsubg??? > > > agopen.c:109: warning: implicit declaration of function ???free??? > > > agopen.c:118: warning: implicit declaration of function ???agset??? > > > agopen.c:142: warning: implicit declaration of function ???agnode??? > > > agopen.c:170: warning: implicit declaration of function ???agfindnode??? > > > agopen.c:180: warning: implicit declaration of function ???agedge??? > > > agopen.c:194: warning: implicit declaration of function ???buildRagraph??? > > > agopen.c:194: warning: return makes pointer from integer without a cast > > > make: *** [agopen.o] Error 1 > > > chmod: cannot access `/home/moghadda/R/library26/Rgraphviz/libs/*': No > > > such file or directory > > > ERROR: compilation failed for package 'Rgraphviz' > > > ** Removing '/home/moghadda/R/library26/Rgraphviz' > > > ** Restoring previous '/home/moghadda/R/library26/Rgraphviz' > > > > > > > > > =================== > > > > > >> sessionInfo() > > > R version 2.6.0 (2007-10-03) > > > i486-pc-linux-gnu > > > > > > locale: > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE =en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER= en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US .UTF-8;LC_IDENTIFICATION=C > > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > > > > loaded via a namespace (and not attached): > > > [1] rcompgen_0.1-17 > > > > > > > > > > > > Regards, > > > Amin. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, 2007-10-19 at 15:40 +0200, Li.Long at isb-sib.ch wrote: > > >> It's the combination of different version of R/Rgraphviz and graphviz > > >> that's causing the problem. > > >> > > >> graphviz 2.14.1 was released AFTER R 2.4.1 (and its matching > > >> bioconductor > > >> release), therefore, the old Rgraphviz doesn't know what to do with the > > >> newer graphviz. > > >> > > >> You could upgrade your R to 2.6.0, along with bioconductor 2.1, its > > >> matching Rgraphviz handles graphviz 2.14.1. > > >> > > >> Or if you have to stick with older version of R/bioconductor, you have > > >> to > > >> back port the necessary changes in Rgraphviz to your older version. > > >> This > > >> is reported and accomplished already (you could find info in the mail > > >> archive) > > >> > > >> We don't have resource to make all older version of bioconductor > > >> compatible with newer software releases. > > >> > > >> Thanks, > > >> > > >> Li > > >> > > >> > > > >> > Dear Tony, > > >> > Thanks for your quick reply, here is my sessioninfo : > > >> > > > >> >> sessionInfo() > > >> > R version 2.4.1 (2006-12-18) > > >> > i686-pc-linux-gnu > > >> > > > >> > locale: > > >> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLL ATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAP ER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en _US.UTF-8;LC_IDENTIFICATION=C > > >> > > > >> > attached base packages: > > >> > [1] "stats" "graphics" "grDevices" "utils" "datasets" > > >> > "methods" > > >> > [7] "base" > > >> >> > > >> > > > >> > > > >> > Cheers, > > >> > Amin. > > >> > > > >> > > > >> > On Fri, 2007-10-19 at 13:46 +0100, Tony Chiang wrote: > > >> >> Hi Amin, > > >> >> > > >> >> Can you please send the list the output of your sessionInfo(). It > > >> will > > >> >> help us to try and reproduce the error you get. > > >> >> > > >> >> Best, > > >> >> --Tony > > >> >> > > >> >> On 10/19/07, Amin Moghaddasi <a.moghaddasi at="" gmail.com=""> wrote: > > >> >> Dear All, > > >> >> > > >> >> I have some problem installing Rgraphgviz on my system with > > >> >> the > > >> >> following specification. > > >> >> > > >> >> My system is Suse 9.2 , i386 GNU/Linux > > >> >> I have installed graphviz-2.14.1 from source > > >> >> I have gcc version 3.3.4 (pre 3.3.5 20040809) > > >> >> I also set the LD_LIBRARY_PATH= > > >> >> $LD_LIBRARY_PATH:/usr/local/lib/graphviz > > >> >> R version 2.4.1 (2006-12-18) > > >> >> > > >> >> 1 - When I try to install from bash command, I'll get the > > >> >> following > > >> >> error: > > >> >> > R CMD INSTALL Rgraphviz_1.5.0.tar.gz > > >> >> * Installing *source* package 'Rgraphviz' ... > > >> >> checking for graphviz... checking for dotneato- config... not > > >> >> found > > >> >> failed > > >> >> configure: error: please specify a valid path to > > >> >> 'dotneato-config' > > >> >> version >= 1.12 using --with-graphviz=DIR > > >> >> ERROR: configuration failed for package 'Rgraphviz' > > >> >> ** Removing '/home/bkp- moghadda/lib/R/library/Rgraphviz' > > >> >> > > >> >> 2 - using biocLite in R gives another error: > > >> >> > source("http://bioconductor.org/biocLite.R") > > >> >> Warning messages: > > >> >> 1: Redefining 'biocinstall' in: safeSource() > > >> >> 2: Redefining 'biocinstall.affyPkgs' in: safeSource() > > >> >> 3: Redefining 'biocinstall.allPkgs' in: safeSource() > > >> >> 4: Redefining 'biocinstall.defaultPkgs' in: safeSource() > > >> >> 5: Redefining 'biocinstall.graphPkgs' in: safeSource() > > >> >> 6: Redefining 'biocinstall.litePkgs' in: safeSource() > > >> >> 7: Redefining 'biocinstall.monographPkgs' in: safeSource() > > >> >> > biocLite("Rgraphviz") > > >> >> Running biocinstall version 1.9.9 with R version 2.4.1 > > >> >> Your version of R requires version 1.9 of Bioconductor. > > >> >> Warning in install.packages(pkgs = pkgs, repos = repos, > > >> >> dependencies = > > >> >> dependencies, : > > >> >> argument 'lib' is missing: > > >> >> using /home/bkp-moghadda/lib/R/library > > >> >> trying URL > > >> >> 'http://bioconductor.org/packages/1.9/bioc/src/contr ib/Rgraphviz_1.12.3.tar.gz' > > >> >> Content type 'application/x-gzip' length 1504829 bytes > > >> >> opened URL > > >> >> ================================================== > > >> >> downloaded 1469Kb > > >> >> > > >> >> * Installing *source* package 'Rgraphviz' ... > > >> >> checking for pkg-config... /usr/local/bin/pkg-config > > >> >> configure: Found graphviz 2.14.1 > > >> >> configure: creating ./config.status > > >> >> config.status : creating src/Makevars > > >> >> ** libs > > >> >> gcc -std=gnu99 -I/usr/lib/R/include -I/usr/lib/R/include > > >> >> -I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 > > >> >> -DGRAPHVIZ_MINOR=14 > > >> >> -I/usr/local/include -fpic -c Rgraphviz.c -o Rgraphviz.o > > >> >> In file included from /usr/local/include/graphviz/gvc.h:20, > > >> >> from common.h:38, > > >> >> from Rgraphviz.c:1: > > >> >> /usr/local/include/graphviz/types.h:27:1: warning: "TRUE" > > >> >> redefined > > >> >> In file included from common.h:8, > > >> >> from Rgraphviz.c:1: > > >> >> /usr/lib/R/include/Rdefines.h:148:1: warning: this is the > > >> >> location of > > >> >> the previous definition > > >> >> In file included from Rgraphviz.c:1: > > >> >> common.h:42:20: gvcint.h: No such file or directory > > >> >> common.h:43:21: globals.h: No such file or directory > > >> >> Rgraphviz.c: In function `getListElement': > > >> >> Rgraphviz.c:51: warning: implicit declaration of function > > >> >> `Rf_type2char' > > >> >> Rgraphviz.c: In function `Rgraphviz_graphvizVersion': > > >> >> Rgraphviz.c:1042: error: dereferencing pointer to incomplete > > >> >> type > > >> >> make: *** [Rgraphviz.o] Error 1 > > >> >> chmod: cannot access > > >> >> `/home/bkp-moghadda/lib/R/library/Rgraphviz/libs/*': No such > > >> >> file or > > >> >> directory > > >> >> ERROR: compilation failed for package 'Rgraphviz' > > >> >> ** Removing '/home/bkp- moghadda/lib/R/library/Rgraphviz' > > >> >> > > >> >> The downloaded packages are in > > >> >> /tmp/Rtmpmnucc7/downloaded_packages > > >> >> Warning messages: > > >> >> 1: installation of package 'Rgraphviz' had non-zero exit > > >> >> status in: > > >> >> install.packages(pkgs = pkgs, repos = repos, dependencies = > > >> >> dependencies, > > >> >> 2: cannot create HTML package index in: > > >> >> tools:::unix.packages.html(.Library) > > >> >> > > >> >> I would be much appreciated if someone can help me to figure > > >> >> out where > > >> >> the problem is. > > >> >> > > >> >> Regards, > > >> >> Amin. > > >> >> > > >> >> _______________________________________________ > > >> >> 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 > > >> >> > > >> > > > >> > _______________________________________________ > > >> > 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 > > >> > > > >> > > > > > > >