You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package

Based on your success I thought I would try again. I am not sure why I
had more success this time but this time I got this far even though I
did not change my path at all or make any system changes from what I
had before. ?I did reinstall Rgraphviz but used the previously
installed graphviz. ? I tried this code taken from the Rgrpahviz
vignette:

library("Rgraphviz")

Loading required package: graph
Loading required package: grid

set.seed(123)
V <- letters[1:10]
M <- 1:4
g1 <- randomGraph(V, M, 0.2)
g1

A graphNEL graph with undirected edges
Number of Nodes = 10
Number of Edges = 16


but when I tried to plot it R crashed.

plot(g1)

It did produce this message on the Windows console (not the R console):

Error: Layout type: "dot" not recognized. Use one of:

There was nothing after the of:

R.version.string

[1] "R version 2.10.1 Patched (2010-03-10 r51276)"

win.version()

[1] "Windows Vista (build 6002) Service Pack 2"

packageDescription("Rgraphviz")$Version

[1] "1.24.0"

graphvizVersion()

$installed_version
[1] ?2.20.3?

$build_version
[1] ?2.20.3?




On Wed, Mar 31, 2010 at 9:56 AM, HU,ZHENGJUN <hhu at ufl.edu> wrote:

Hi Martin,

?It is really a 'PATH' problem. After adding C:\Program
Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz
package can be loaded without any error messages.

?Sorry that I ONLY set my 'PATH' environment variable correctly for R but
not for Graphviz.

?Thank you and Duncan so much for your great help.
?Howard


On Tue Mar 30 18:12:54 EDT 2010, Martin Morgan <mtmorgan at fhcrc.org> wrote:

On 03/30/2010 03:06 PM, HU,ZHENGJUN wrote:

Hi Martin,

?I am 100% sure that I set my 'PATH' environment variable correctly
because all other packages can loaded correctly as well as because R can
be run correctly under both MS DOS and MS Windows XP. Also, I can create
some simple R packages correctly.

The PATH must be set correctly to include graphviz, as in my example
below. Copy and paste the output of

?strsplit(Sys.getenv("PATH"), ";")

and

?list.files(strsplit(Sys.getenv("PATH"), ";")[[1]][[14]], "dll")

Martin

?Thanks.
?Howard


On Tue Mar 30 16:58:55 EDT 2010, Martin Morgan <mtmorgan at fhcrc.org>
wrote:

On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote:

Hi Martin,

?I uninstalled graphviz-2.26.3.msi and then installed
graphviz-2.20.3.1.msi. Then installed the
Rgraphviz package again. As expected, I got the same error messages as
before:

"Error in inDL(x, as.logical(local), as.logical(now), ...) :
?unable to load shared library
'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll':
?LoadLibrary failure: ?The specified module could not be found."

'LoadLibrary' is being vague, the 'specified modules' are the DLLs from
graphviz.

Have you checked that your 'PATH' environment variable is set correctly?
In R

?> strsplit(Sys.getenv("PATH"), ";")
$PATH
?...
?[14] "C:\\Program Files\\Graphviz2.20\\bin"
...

The relevant files in this directory might look like

list.files(strsplit(Sys.getenv("PATH"), ";")[[1]][[14]], "dll")

?[1] "iconv.dll" ? ? ? ? ? ? ? ? ? ? ?"intl.dll"
?[3] "jpeg62.dll" ? ? ? ? ? ? ? ? ? ? "libcairo-2.dll"
?[5] "libcdt-4.dll" ? ? ? ? ? ? ? ? ? "libcgraph-4.dll"
?[7] "libexpat.dll" ? ? ? ? ? ? ? ? ? "libfontconfig-1.dll"
?[9] "libfreetype-6.dll" ? ? ? ? ? ? ?"libgdk_pixbuf-2.0-0.dll"
[11] "libglib-2.0-0.dll" ? ? ? ? ? ? ?"libgmodule-2.0-0.dll"
[13] "libgobject-2.0-0.dll" ? ? ? ? ? "libgraph-4.dll"
[15] "libgvc-4.dll" ? ? ? ? ? ? ? ? ? "libgvplugin_core-5.dll"
[17] "libgvplugin_dot_layout-5.dll" ? "libgvplugin_gd-5.dll"
[19] "libgvplugin_neato_layout-5.dll" "libgvplugin_pango-5.dll"
[21] "libltdl-3.dll" ? ? ? ? ? ? ? ? ?"libpango-1.0-0.dll"
[23] "libpangocairo-1.0-0.dll" ? ? ? ?"libpangoft2-1.0-0.dll"
[25] "libpangowin32-1.0-0.dll" ? ? ? ?"libpathplan-4.dll"
[27] "libpng12.dll" ? ? ? ? ? ? ? ? ? "libxml2.dll"

Martin

?Thank you.
?Howard


On Tue Mar 30 15:36:05 EDT 2010, Martin Morgan <mtmorgan at fhcrc.org>
wrote:

On 03/30/2010 10:24 AM, HU,ZHENGJUN wrote:

Hi Duncan,

(They are pretty hard to find, but I think you can find them on the
Bioconductor site.) ?It is > not enough to install the Rgraphviz
package, you also need to install Graphviz.

?Yes I did. Before installing the Rgraphviz package successfully,
(1) I
downloaded graphviz-2.26.3.msi for MS Windows (XP) and installed it
successfully and (2) I also installed the packages from
Bioconductor by:
(Note: I use MS Windows XP and R 2.10.1 version)

This is a bioconductor package so please ask on the Bioconductor
mailing
list

http://bioconductor.org/docs/mailList.html

See the 'README' file in the 'tar.gz' file at


?http://bioconductor.org/packages/release/Software.html
?http://bioconductor.org/packages/2.5/bioc/html/Rgraphviz.html




http://bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz



which says


o. install Graphviz ***2.20.3.1*** Windows ***binary*** distribution
from



http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi


you must use this version of graphviz. File paths must be correct.

Martin

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

?I got those error messages:

"Error in inDL(x, as.logical(local), as.logical(now), ...) :
?unable to load shared library
'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll':
?LoadLibrary failure: ?The specified module could not be found."

?Obviously, it seems it is the package problem because it should go
to
'C:/PROGRA~1/R/R-2.10.1/library/Rgraphviz/libs/Rgraphviz.dll'
instead of
'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll'

?Thank you for the reply. Howard


On Tue Mar 30 12:50:44 EDT 2010, Duncan Murdoch
<murdoch at stats.uwo.ca>
wrote:

On 30/03/2010 10:44 AM, HU,ZHENGJUN wrote:

Hi All,

?I tried to install the package of Rgraphviz in the following two
ways successfully:

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


install.packages(pkgs="C:/Progra~1/R/lib_download/Rgraphviz_1.24.0.zip",


lib="C:/Progra~1/R/R-2.10.1/library", repos=NULL)

but when I loaded the package though library(Rgraphviz) or
library("Rgraphviz"), and got the same error message below:

"Error in inDL(x, as.logical(local), as.logical(now), ...) :
?unable to load shared library
'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll':
?LoadLibrary failure: ?The specified module could not be found."

Most likely the problem is that you haven't followed the
installation
instructions. ?(They are pretty hard to find, but I think you can
find
them on the Bioconductor site.) ?It is not enough to install the
Rgraphviz package, you also need to install Graphviz.

Duncan Murdoch

I think that it is the error in the package because it should go to
'C:/PROGRA~1/R/R-2.10.1/library/Rgraphviz/libs/Rgraphviz.dll'
instead
of 'C:/PROGRA~1/R/R-210~1.1/library/Rgraphviz/libs/Rgraphviz.dll'

Could anyone help me to solve to problem?
Thank you very much for the help. Howard

-- HU,ZHENGJUN

-- Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

-- HU,ZHENGJUN

-- Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

-- HU,ZHENGJUN

-- Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

--
HU,ZHENGJUN