Dear gRaphical models members
I am not sure if I'd better address my question to the Mac Port SIG.
I am trying to get Rgraphviz running on a mac ppc vers. 10.4.11.
The installation process doesn't complete successfully.
Graphviz is already installed and should be
at /usr/local/graphviz-2.14 on my machine,
but it seems that when installing Rgraphviz, Graphviz
can't be found. Can I tell it so
manually? Or, do you see any other way to get
it running properly?
Thanks a lot in advance.
Alex
> biocLite("Rgraphviz",depend=TRUE,type="source")
Running biocinstall version 2.4.10 with R version 2.9.0
Your version of R requires version 2.4 of Bioconductor.
versuche URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/
Rgraphviz_1.22.1.tar.gz'
Content type 'application/x-gzip' length 569867 bytes (556 Kb)
URL ge"offnet
==================================================
downloaded 556 Kb
* Installing *source* package 'Rgraphviz' ...
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 ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/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
checking for whether compiler has bool... yes
configure: No --with-graphviz option was specified. Trying to find
Graphviz using other methods.
checking for pkg-config... no
checking for dotneato-config... no
configure: dotneato-config not found in PATH.
configure: Using default directory /usr/local, consider specifiying --
with-graphviz
configure: error: /usr/local/bin/dot not found. Check Graphviz
installation.
Fehler: configuration failed f"ur Paket 'Rgraphviz'
* Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/
library/Rgraphviz'
* Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/
Resources/library/Rgraphviz'
The downloaded packages are in
'/private/tmp/RtmpnpndCY/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies, :
installation of package 'Rgraphviz' had non-zero exit status
[R--gR] installing Rgraphviz on mac
2 messages · Alex Biedermann, Achim Zeileis
On Fri, 5 Jun 2009, Alex Biedermann wrote:
Dear gRaphical models members I am not sure if I'd better address my question to the Mac Port SIG. I am trying to get Rgraphviz running on a mac ppc vers. 10.4.11. The installation process doesn't complete successfully. Graphviz is already installed and should be at /usr/local/graphviz-2.14 on my machine, but it seems that when installing Rgraphviz, Graphviz can't be found. Can I tell it so manually?
Yes, as the configure output says, there is the option --with-graphviz See also the README file in the Rgraphviz source package. It comments both on installation under Mac OSX and on installation from source. hth, Z
Or, do you see any other way to get it running properly? Thanks a lot in advance. Alex
biocLite("Rgraphviz",depend=TRUE,type="source")
Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. versuche URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Rgraphviz_1.22.1.tar.gz' Content type 'application/x-gzip' length 569867 bytes (556 Kb) URL ge"offnet ================================================== downloaded 556 Kb * Installing *source* package 'Rgraphviz' ... 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 ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/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 checking for whether compiler has bool... yes configure: No --with-graphviz option was specified. Trying to find Graphviz using other methods. checking for pkg-config... no checking for dotneato-config... no configure: dotneato-config not found in PATH. configure: Using default directory /usr/local, consider specifiying --with-graphviz configure: error: /usr/local/bin/dot not found. Check Graphviz installation. Fehler: configuration failed f"ur Paket 'Rgraphviz' * Removing '/Library/Frameworks/R.framework/Versions/2.9/Resources/library/Rgraphviz' * Restoring previous '/Library/Frameworks/R.framework/Versions/2.9/Resources/library/Rgraphviz' The downloaded packages are in '/private/tmp/RtmpnpndCY/downloaded_packages' Updating HTML index of packages in '.Library' Warning message: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Rgraphviz' had non-zero exit status
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