[BioC] cant install Rgraphviz

[Robert Gentleman]

Hi Anders,
   First let me suggest that you get a more recent R, we are at 2.7.1 
now, yours is about one year out of date - and lots has changed since. 
Also your Ubuntu is old, 8.04 seems to be the current one.  Most folks 
are not going to be willing to help fix things in outdated releases that 
work in current releases.

More comments below.

Anders Stegmann wrote:
> 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.
> 

   Are they in /usr/local/include/graphviz, as that seems to be the only 
place Rgraphviz is looking. If not installing graphviz either by hand or 
configuring graphviz-dev to put them into the right place (I don't use 
Ubuntu so you need to ask someone else how to do this)

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

That is not how you do this.  Please read the R Extensions manual for 
how to pass configure flags to R packages at install time.

R CMD INSTALL --configure-args='--with-graphviz=/whereeveryouputit/'

is more like the incantation needed.  I am not sure how you hit on the 
method you used, but if it is suggested somewhere in R's documentation 
could you please let me know where as it likely needs some modification.

Robert




> 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?
> 
> 
> 
> 
>       Find din nye laptop på kelkoo.dk. Se de gode tilbud her - http://dk.yahoo.com/r/pat/mm
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org