[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 16:20:02 CET 2007
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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