[BioC] Rgraphviz installation issue

[Luo Weijun]

Hi Krishna,
Rgraphviz is not really a dependency of gage, but rather one for pathview since gage imports one function from pathview. R forces to install all secondary dependencies somehow, even though it is just for a single imported function and those are not really needed. Of course, I would still appreciate Kasper’s taking care of the Rgraphviz installation problem since that’s needed for other packages.

To help users like you to install and use gage more smoothly, I just updated gage and removed that single import from pathview. Therefore, now you don’t have to install all the secondary dependencies like Rgraphviz. You shall see the new version (2.12.1) in the following page the next day or so. Let me know if you still don’t see the update by next Monday.
http://bioconductor.org/packages/release/bioc/html/gage.html

HTH, 
Weijun


--------------------------------------------
On Thu, 12/19/13, km wrote:

Hi all,

I am unable to install Rgraphviz as a dependency for gage package.
I am using R (3.0.2)  and bioconductor 2.13.

>
biocLite('Rgraphviz')

BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'Rgraphviz'
trying URL '
http://bioconductor.org/packages/2.13/bioc/src/contrib/Rgraphviz_2.6.0.tar.gz
'
Content type 'application/x-gzip' length 7451849 bytes (7.1 Mb)
opened URL
...
...
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o
Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o
buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o
libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a
libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
gcc: error: libxdot.a: No such file or directory
gcc: error: libgvplugin_dot_layout.a: No such file or directory
gcc: error: libgvplugin_neato_layout.a: No such file or directory
gcc: error: libgvplugin_core.a: No such file or directory
gcc: error: libgvc.a: No such file or directory
gcc: error: libpathplan.a: No such file or directory
gcc: error: libgraph.a: No such file or directory
gcc: error: libcdt.a: No such file or directory
make: *** [Rgraphviz.so] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/home/km/lib64/R/library/Rgraphviz’

The downloaded source packages are in
        ‘/tmp/RtmpOFdCuI/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘Rgraphviz’ had non-zero exit status



> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


Regards,
Krishna