[BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"
Amin Moghaddasi
a.moghaddasi at gmail.com
Fri Nov 2 17:46:07 CET 2007
Hi Li,
The "dot -V" gives the following response for me as well.
$ dot -V
dot - Graphviz version 2.12 (Tue Sep 4 16:56:48 UTC 2007)
$ which dot
/usr/bin/dot
$ which dotty
/usr/bin/dotty
$ which neato
/usr/bin/neato
$ which twopi
/usr/bin/twopi
I have also took the pkg_conf_path out of the env variables, however the
error still there.
Best Regards,
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_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"
> >> > [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/contrib/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
> >> >
> >>
> >
>
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