[BioC] cant install Rgraphviz

[Anders Stegmann]

Can't install ”Rgraphviz_1.18.1” on Ubuntu 7.10, with R version 2.5.1 (2007-06-27), BioC 2.2 and graphviz-2.20.2 


When typing this in R:



>source("http://bioconductor.org/biocLite.R")

>biocLite("Rgraphviz")



I get the following output:



Running biocinstall version 2.0.8 with R version 2.5.1 

Your version of R requires version 2.0 of Bioconductor.

Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  : 

         argument 'lib' is missing: using '/usr/local/lib/R/site-library'

trying URL 'http://bioconductor.org/packages/2.0/bioc/src/contrib/Rgraphviz_1.14.1.tar.gz'

Content type 'application/x-gzip' length 1521762 bytes

opened URL

==================================================

downloaded 1486Kb



* Installing *source* package 'Rgraphviz' ...

configure: No --with-graphviz option was specified. Trying to find graphviz using other methods.

checking for pkg-config... /usr/bin/pkg-config

configure: Found graphviz 2.20.2

configure: We have inferred the following flags for graphviz

configure: ..PKG_CPPFLAGS=-I/usr/local/include/graphviz  

configure: ..PKG_LIBS=-L/usr/local/lib -lgvc -lgraph -lcdt  

configure: creating ./config.status

config.status: creating src/Makevars

** libs

gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -I/usr/local/include/graphviz    -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20     -fpic  -g -O2 -c agopen.c -o agopen.o

I filen inkluderet af agopen.c:1:

common.h:41:20: error: gvcint.h: No such file or directory

common.h:42:21: error: globals.h: No such file or directory

make: *** [agopen.o] Fejl 1

chmod: kan ikke tilgå '/usr/local/lib/R/site-library/Rgraphviz/libs/*': No such file or directory

ERROR: compilation failed for package 'Rgraphviz'

** Removing '/usr/local/lib/R/site-library/Rgraphviz'

** Restoring previous '/usr/local/lib/R/site-library/Rgraphviz'



The downloaded packages are in

        /tmp/RtmptAYLaf/downloaded_packages

Warning message:

installation of package 'Rgraphviz' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, 



I have the files ”gvcint.h” and ”globals.h” as I've installed ”graphviz-dev” as well.


When installing ”Rgraphviz_1.18.1.tar.gz” manually and trying to configure ”Rgraphviz” with ”./configure”, I get following output:

configure: No --with-graphviz option was specified. Trying to find graphviz using other methods.

checking for pkg-config... /usr/bin/pkg-config

configure: Found graphviz 2.20.2

configure: We have inferred the following flags for graphviz

configure: ..PKG_CPPFLAGS=-I/usr/local/include/graphviz  

configure: ..PKG_LIBS=-L/usr/local/lib -lgvc -lgraph -lcdt  

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



After this I type ”make” and gets output:

make: *** Ingen angivne mål og ingen makefil fundet. Stop.

It didn't find a makefile.

What now?




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