HU,ZHENGJUN
2010-Mar-31 15:44 UTC
[R] You are right and the problem is solved. Re: about the possible errors in Rgraphviz Package
Hi Gabor,
I just used your R code below and the code worked properly
without any error messages. Attached is the output graph, which
may be the one you expected.
library("Rgraphviz")
set.seed(123)
V <- letters[1:10]
M <- 1:4
g1 <- randomGraph(V, M, 0.2)
g1
plot(g1)
Thanks.
Howard
On Wed Mar 31 11:18:25 EDT 2010, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
> By the way, just in case you did not read the entire message R
> crashed
> when I tried to run the code from the vignette.
>
> On Wed, Mar 31, 2010 at 10:52 AM, Gabor Grothendieck
> <ggrothendieck at gmail.com> wrote:
>> 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
>>>>>>>>>>>
>>>>>>>>>>>
______________________________________________
>>>>>>>>>>> R-help at r-project.org mailing
list
>>>>>>>>>>>
https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>>>>>> PLEASE do read the posting guide
>>>>>>>>>>>
http://www.R-project.org/posting-guide.html
>>>>>>>>>>> and provide commented, minimal,
self-contained,
>>>>>>>>>>> reproducible code.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -- HU,ZHENGJUN
>>>>>>>>>
>>>>>>>>>
______________________________________________
>>>>>>>>> R-help at r-project.org mailing list
>>>>>>>>>
https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>>>> PLEASE do read the posting guide
>>>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>>>> and provide commented, minimal,
self-contained,
>>>>>>>>> reproducible code.
>>>>>>>>
>>>>>>>>
>>>>>>>> -- 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
>>>
>>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible
>> code.
>>
>
>
--
HU,ZHENGJUN
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