Hi Has anyone had this problem installing BioConductor on linux (RH 9.0) and R 1.7.1? I just grabbed the source tarball because I want to put it on a few machines. It worked fine until it hit Rgraphviz. Could it be gcc 3.2.2? Regards Peter Installation problem --------------------- * Installing *source* package 'Rgraphviz' ... ** libs gcc -I/usr/local/lib/R/include `dotneato-config --cflags` -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o /bin/sh: line 1: dotneato-config: command not found In file included from Rgraphviz.c:1: common.h:19:20: render.h: No such file or directory common.h:20:19: graph.h: No such file or directory common.h:21:22: dotprocs.h: No such file or directory common.h:22:24: neatoprocs.h: No such file or directory common.h:23:20: adjust.h: No such file or directory In file included from Rgraphviz.c:1: common.h:37: parse error before '*' token common.h:38: parse error before '*' token many warnings deleted Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) make: *** [Rgraphviz.o] Error 1 ERROR: compilation failed for package 'Rgraphviz' Details of system ----------------- ** Redhat 9.0 all rpms updated $ uname -a Linux hostname_here 2.4.20-18.9smp #1 SMP Thu May 29 06:55:05 EDT 2003 i686 i686 i386 GNU/Linux $ gcc --version gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) ** R 1.7.1 built from source: > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 1 minor 7.1 year 2003 month 06 day 16 language R -- Dr Peter Baker, Statistician (Bioinformatics/Genetics), CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct 306 Carmody Road, St Lucia Qld 4067. Australia. Email: <peter.baker@csiro.au> WWW: http://www.cmis.csiro.au/Peter.Baker/ Phone:+61 7 3214 2210 Fax:+61 7 3214 2900

Have you installed graphviz (a recent version)? "Peter Baker (CMIS, St Lucia)" <peter.baker@csiro.au> writes: > Hi > > Has anyone had this problem installing BioConductor on linux (RH 9.0) > and R 1.7.1? > > I just grabbed the source tarball because I want to put it on a few > machines. It worked fine until it hit Rgraphviz. > > Could it be gcc 3.2.2? > > Regards > Peter > > > Installation problem > --------------------- > > * Installing *source* package 'Rgraphviz' ... > ** libs > gcc -I/usr/local/lib/R/include `dotneato-config --cflags` -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o > /bin/sh: line 1: dotneato-config: command not found > In file included from Rgraphviz.c:1: > common.h:19:20: render.h: No such file or directory > common.h:20:19: graph.h: No such file or directory > common.h:21:22: dotprocs.h: No such file or directory > common.h:22:24: neatoprocs.h: No such file or directory > common.h:23:20: adjust.h: No such file or directory > In file included from Rgraphviz.c:1: > common.h:37: parse error before '*' token > common.h:38: parse error before '*' token > > many warnings deleted > > Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) > make: *** [Rgraphviz.o] Error 1 > ERROR: compilation failed for package 'Rgraphviz' > > Details of system > ----------------- > ** Redhat 9.0 all rpms updated > > $ uname -a > Linux hostname_here 2.4.20-18.9smp #1 SMP Thu May 29 06:55:05 EDT 2003 i686 i686 i386 GNU/Linux > $ gcc --version > gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) > > > ** R 1.7.1 built from source: >> version > _ > platform i686-pc-linux-gnu > arch i686 > os linux-gnu > system i686, linux-gnu > status > major 1 > minor 7.1 > year 2003 > month 06 > day 16 > language R > > > > -- > Dr Peter Baker, Statistician (Bioinformatics/Genetics), > CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct > 306 Carmody Road, St Lucia Qld 4067. Australia. > Email: <peter.baker@csiro.au> > WWW: http://www.cmis.csiro.au/Peter.Baker/ > Phone:+61 7 3214 2210 Fax:+61 7 3214 2900 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- A.J. Rossini / rossini@u.washington.edu / rossini@scharp.org http://software.biostat.washington.edu/ UNTIL IT MOVES IN JULY. Biomedical and Health Informatics, University of Washington Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center. FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}

Hi Toni I have now installed graphviz: thanks! However, after either source or rpm install of graphviz, while I get a lot less warnings it still appears to crash at the same spot in comilation. Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) Rgraphviz.c:511: (Each undeclared identifier is reported only once Rgraphviz.c:511: for each function it appears in.) make: *** [Rgraphviz.o] Error 1 ERROR: compilation failed for package 'Rgraphviz' Is there an easy way to drop this package out of the install? Thanks Cheers Peter On Wed, 18 Jun 2003 rossini@blindglobe.net wrote: > >Have you installed graphviz (a recent version)? > > >"Peter Baker (CMIS, St Lucia)" <peter.baker@csiro.au> writes: > >> Hi >> >> Has anyone had this problem installing BioConductor on linux (RH 9.0) >> and R 1.7.1? >> many warnings deleted >> >> Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) >> make: *** [Rgraphviz.o] Error 1 >> ERROR: compilation failed for package 'Rgraphviz' >> >> Details of system >> ----------------- >> ** Redhat 9.0 all rpms updated >> >> $ uname -a >> Linux hostname_here 2.4.20-18.9smp #1 SMP Thu May 29 06:55:05 EDT 2003 i686 i686 i386 GNU/Linux >> $ gcc --version >> gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) >> >> >> ** R 1.7.1 built from source: >>> version >> _ >> platform i686-pc-linux-gnu >> arch i686 >> os linux-gnu >> system i686, linux-gnu >> status >> major 1 >> minor 7.1 >> year 2003 >> month 06 >> day 16 >> language R >> >> >> >> -- >> Dr Peter Baker, Statistician (Bioinformatics/Genetics), >> CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct >> 306 Carmody Road, St Lucia Qld 4067. Australia. >> Email: <peter.baker@csiro.au> >> WWW: http://www.cmis.csiro.au/Peter.Baker/ >> Phone:+61 7 3214 2210 Fax:+61 7 3214 2900

Are you making sure that you are getting a very recent (i.e. from the Lucent/Bell Labs wwwsite http://www.graphviz.org/, I think?) version? I suspect that the rpm install won't do the trick. best, -tony "Peter Baker (CMIS, St Lucia)" <peter.baker@csiro.au> writes: > Hi Toni > > I have now installed graphviz: thanks! > > However, after either source or rpm install of graphviz, while I get a > lot less warnings it still appears to crash at the same spot in > comilation. > > Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) > Rgraphviz.c:511: (Each undeclared identifier is reported only once > Rgraphviz.c:511: for each function it appears in.) > make: *** [Rgraphviz.o] Error 1 > ERROR: compilation failed for package 'Rgraphviz' > > Is there an easy way to drop this package out of the install? > > Thanks > > Cheers > Peter > > On Wed, 18 Jun 2003 rossini@blindglobe.net wrote: > >> >>Have you installed graphviz (a recent version)? >> >> >>"Peter Baker (CMIS, St Lucia)" <peter.baker@csiro.au> writes: >> >>> Hi >>> >>> Has anyone had this problem installing BioConductor on linux (RH 9.0) >>> and R 1.7.1? >>> many warnings deleted >>> >>> Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) >>> make: *** [Rgraphviz.o] Error 1 >>> ERROR: compilation failed for package 'Rgraphviz' >>> >>> Details of system >>> ----------------- >>> ** Redhat 9.0 all rpms updated >>> >>> $ uname -a >>> Linux hostname_here 2.4.20-18.9smp #1 SMP Thu May 29 06:55:05 EDT 2003 i686 i686 i386 GNU/Linux >>> $ gcc --version >>> gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) >>> >>> >>> ** R 1.7.1 built from source: >>>> version >>> _ >>> platform i686-pc-linux-gnu >>> arch i686 >>> os linux-gnu >>> system i686, linux-gnu >>> status >>> major 1 >>> minor 7.1 >>> year 2003 >>> month 06 >>> day 16 >>> language R >>> >>> >>> >>> -- >>> Dr Peter Baker, Statistician (Bioinformatics/Genetics), >>> CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct >>> 306 Carmody Road, St Lucia Qld 4067. Australia. >>> Email: <peter.baker@csiro.au> >>> WWW: http://www.cmis.csiro.au/Peter.Baker/ >>> Phone:+61 7 3214 2210 Fax:+61 7 3214 2900 > > -- A.J. Rossini / rossini@u.washington.edu / rossini@scharp.org http://software.biostat.washington.edu/ UNTIL IT MOVES IN JULY. Biomedical and Health Informatics, University of Washington Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center. FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}

Yep, you need a newer version of graphviz; the one that I am using is graphviz-1.9.20030616.0415 unfortunately on the graphviz site they label it as: graphviz-current.tar.gz which is rather unfortunate because you can't tell which it is until you get it (there is a bug as well in that version - which may have already been fixed, I reported it earlier this week), Robert On Thu, Jun 19, 2003 at 05:13:50PM +1000, Peter Baker (CMIS, St Lucia) wrote: > Hi Toni > > I have now installed graphviz: thanks! > > However, after either source or rpm install of graphviz, while I get a > lot less warnings it still appears to crash at the same spot in > comilation. > > Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) > Rgraphviz.c:511: (Each undeclared identifier is reported only once > Rgraphviz.c:511: for each function it appears in.) > make: *** [Rgraphviz.o] Error 1 > ERROR: compilation failed for package 'Rgraphviz' > > Is there an easy way to drop this package out of the install? > > Thanks > > Cheers > Peter > > On Wed, 18 Jun 2003 rossini@blindglobe.net wrote: > > > > >Have you installed graphviz (a recent version)? > > > > > >"Peter Baker (CMIS, St Lucia)" <peter.baker@csiro.au> writes: > > > >> Hi > >> > >> Has anyone had this problem installing BioConductor on linux (RH 9.0) > >> and R 1.7.1? > >> many warnings deleted > >> > >> Rgraphviz.c:511: `twopi_nodesize' undeclared (first use in this function) > >> make: *** [Rgraphviz.o] Error 1 > >> ERROR: compilation failed for package 'Rgraphviz' > >> > >> Details of system > >> ----------------- > >> ** Redhat 9.0 all rpms updated > >> > >> $ uname -a > >> Linux hostname_here 2.4.20-18.9smp #1 SMP Thu May 29 06:55:05 EDT 2003 i686 i686 i386 GNU/Linux > >> $ gcc --version > >> gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) > >> > >> > >> ** R 1.7.1 built from source: > >>> version > >> _ > >> platform i686-pc-linux-gnu > >> arch i686 > >> os linux-gnu > >> system i686, linux-gnu > >> status > >> major 1 > >> minor 7.1 > >> year 2003 > >> month 06 > >> day 16 > >> language R > >> > >> > >> > >> -- > >> Dr Peter Baker, Statistician (Bioinformatics/Genetics), > >> CSIRO Mathematical & Information Sciences, Queensland Bioscience Precinct > >> 306 Carmody Road, St Lucia Qld 4067. Australia. > >> Email: <peter.baker@csiro.au> > >> WWW: http://www.cmis.csiro.au/Peter.Baker/ > >> Phone:+61 7 3214 2210 Fax:+61 7 3214 2900 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+