[BioC] Rgraphviz installation problem on " chmod: cannot access '~/library/Rgraphviz/libs/*': No such file or directory"
Li.Long at isb-sib.ch
Li.Long at isb-sib.ch
Fri Nov 2 17:29:05 CET 2007
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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