Rgraphviz installation problem

[Ram H. Sharma]

Dear experts

I installed Rgraphviz with the following command:


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

    biocLite("Rgraphviz")


But had a problem when I tried to load it.

This says that libcdt-4.dll is missing in your computer and the following
message in R window:

> library("Rgraphviz")
Loading required package: graph
Loading required package: grid
Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
  call: value[[3L]](cond)
  error: unable to load shared object
'C:/R/library/Rgraphviz/libs/i386/Rgraphviz.dll':
  LoadLibrary failure:  The specified module could not be found.


  Check that (1) graphviz is installed on your system; (2) the
  installed version of graphviz matches '2.20.3'; this is the version
  used to build this Rgraphviz package; (3) graphviz is accessible to
  R, e.g., the path to the graphviz 'bin' directory is in the system
  'PATH' variable.  See additional instructions in the 'README' file of
  the Rgraphviz 'source' distribution, available at

  http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html

  Ask further questions on the Bioconductor mailing list

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

Error: package/namespace load failed for 'Rgraphviz'


Help me please.


--

Ram H

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[Martin Morgan]

On 07/25/2011 06:05 AM, Ram H. Sharma wrote:

> Dear experts
>
> I installed Rgraphviz with the following command:
>
>
> source("http://www.bioconductor.org/biocLite.R")
>
>      biocLite("Rgraphviz")
>
>
> But had a problem when I tried to load it.
>
> This says that libcdt-4.dll is missing in your computer and the following
> message in R window:
>
>> library("Rgraphviz")
> Loading required package: graph
> Loading required package: grid
> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>    call: value[[3L]](cond)
>    error: unable to load shared object
> 'C:/R/library/Rgraphviz/libs/i386/Rgraphviz.dll':
>    LoadLibrary failure:  The specified module could not be found.
>
>
>    Check that (1) graphviz is installed on your system; (2) the

you need to install graphviz, as well as Rgraphviz.

>    installed version of graphviz matches '2.20.3'; this is the version
>    used to build this Rgraphviz package; (3) graphviz is accessible to

graphviz has to be a specific version.

>    R, e.g., the path to the graphviz 'bin' directory is in the system
>    'PATH' variable.  See additional instructions in the 'README' file of

your Windows system 'PATH' variable needs to be adjusted once you've
installed graphviz and before installing Rgraphviz

>    the Rgraphviz 'source' distribution, available at
>
>    http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html

additional details are at the url above. For instance, the specific
version of graphviz required is

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

>    Ask further questions on the Bioconductor mailing list
>
>    http://bioconductor.org/docs/mailList.html

if you have more questions, ask on the Bioconductor mailing list.

Martin

>
> Error: package/namespace load failed for 'Rgraphviz'
>
>
> Help me please.
>
>


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

Location: M1-B861
Telephone: [phone]

______________________________________________
[hidden email] 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.

[Ram H. Sharma]

Hi All

How can I adjust this path. My current path of Graphviz installation is:

C:\Program Files (x86)\Graphviz2.20\bin

and Rgraphviz is

C:\R\library\Rgraphviz\libs\i386

Please help me. I am new to Rgraphviz.

Ram




"your Windows system 'PATH' variable needs to be adjusted once you've
installed graphviz and before installing Rgraphviz"

---------- Forwarded message ----------
From: Martin Morgan <[hidden email]>
Date: Mon, Jul 25, 2011 at 9:25 AM
Subject: Re: [R] Rgraphviz installation problem
To: "Ram H. Sharma" <[hidden email]>
Cc: [hidden email]


On 07/25/2011 06:05 AM, Ram H. Sharma wrote:

> Dear experts
>
> I installed Rgraphviz with the following command:
>
>
> source("http://www.**bioconductor.org/biocLite.R<http://www.bioconductor.org/biocLite.R>
> ")
>
>     biocLite("Rgraphviz")
>
>
> But had a problem when I tried to load it.
>
> This says that libcdt-4.dll is missing in your computer and the following
> message in R window:
>
>  library("Rgraphviz")
>>
> Loading required package: graph
> Loading required package: grid
> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>   call: value[[3L]](cond)
>   error: unable to load shared object
> 'C:/R/library/Rgraphviz/libs/**i386/Rgraphviz.dll':
>   LoadLibrary failure:  The specified module could not be found.
>
>
>   Check that (1) graphviz is installed on your system; (2) the
>

you need to install graphviz, as well as Rgraphviz.


   installed version of graphviz matches '2.20.3'; this is the version
>   used to build this Rgraphviz package; (3) graphviz is accessible to
>

graphviz has to be a specific version.


   R, e.g., the path to the graphviz 'bin' directory is in the system
>   'PATH' variable.  See additional instructions in the 'README' file of
>

your Windows system 'PATH' variable needs to be adjusted once you've
installed graphviz and before installing Rgraphviz


   the Rgraphviz 'source' distribution, available at
>
>   http://bioconductor.org/**packages/release/bioc/html/**Rgraphviz.html<http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html>
>

additional details are at the url above. For instance, the specific version
of graphviz required is

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


   Ask further questions on the Bioconductor mailing list
>
>   http://bioconductor.org/docs/**mailList.html<http://bioconductor.org/docs/mailList.html>
>

if you have more questions, ask on the Bioconductor mailing list.

Martin



> Error: package/namespace load failed for 'Rgraphviz'
>
>
> Help me please.
>
>
>

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

Location: M1-B861
Telephone: [phone]



--

Ram H

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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]

On 07/25/2011 07:58 AM, Ram H. Sharma wrote:

> Hi All
>
> How can I adjust this path. My current path of Graphviz installation is:
>
> C:\Program Files (x86)\Graphviz2.20\bin
>
> and Rgraphviz is
>
> C:\R\library\Rgraphviz\libs\i386
>
> Please help me. I am new to Rgraphviz.

PATH is an environment variable. From the R FAQ for Windows

http://cran.fhcrc.org/bin/windows/base/rw-FAQ.html#How-do-I-set-environment-variables_003f

"For all applications via Windows. How you set an environment variable
is system specific: under Windows 2000/XP/Server 2003 you can use
`System' in the control panel or the properties of `My Computer' (under
the `Advanced' tab). Under Vista/7, go to `User Accounts' in the Control
Panel, and select your account and then `Change my environment variables'."

Create a 'New' user variable named PATH, with value

   C:\Program Files (x86)\Graphviz2.20\bin

If a value already exists for PATH, add the above, separated by a
semicolon ;. Restart R and check that the path is set correctly

   path <- strsplit(Sys.getenv("PATH"), ";")[[1]]
   dir(path[grepl("Graphviz2.20", path)])

should return several file names, including, e.g., libgraph-4.dll.
Install Rgraphviz with

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

>
> Ram
>
>
>
>
> "your Windows system 'PATH' variable needs to be adjusted once you've
> installed graphviz and before installing Rgraphviz"
>
> ---------- Forwarded message ----------
> From: Martin Morgan<[hidden email]>
> Date: Mon, Jul 25, 2011 at 9:25 AM
> Subject: Re: [R] Rgraphviz installation problem
> To: "Ram H. Sharma"<[hidden email]>
> Cc: [hidden email]
>
>
> On 07/25/2011 06:05 AM, Ram H. Sharma wrote:
>
>> Dear experts
>>
>> I installed Rgraphviz with the following command:
>>
>>
>> source("http://www.**bioconductor.org/biocLite.R<http://www.bioconductor.org/biocLite.R>
>> ")
>>
>>      biocLite("Rgraphviz")
>>
>>
>> But had a problem when I tried to load it.
>>
>> This says that libcdt-4.dll is missing in your computer and the following
>> message in R window:
>>
>>   library("Rgraphviz")
>>>
>> Loading required package: graph
>> Loading required package: grid
>> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>>    call: value[[3L]](cond)
>>    error: unable to load shared object
>> 'C:/R/library/Rgraphviz/libs/**i386/Rgraphviz.dll':
>>    LoadLibrary failure:  The specified module could not be found.
>>
>>
>>    Check that (1) graphviz is installed on your system; (2) the
>>
>
> you need to install graphviz, as well as Rgraphviz.
>
>
>     installed version of graphviz matches '2.20.3'; this is the version
>>    used to build this Rgraphviz package; (3) graphviz is accessible to
>>
>
> graphviz has to be a specific version.
>
>
>     R, e.g., the path to the graphviz 'bin' directory is in the system
>>    'PATH' variable.  See additional instructions in the 'README' file of
>>
>
> your Windows system 'PATH' variable needs to be adjusted once you've
> installed graphviz and before installing Rgraphviz
>
>
>     the Rgraphviz 'source' distribution, available at
>>
>>    http://bioconductor.org/**packages/release/bioc/html/**Rgraphviz.html<http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html>
>>
>
> additional details are at the url above. For instance, the specific version
> of graphviz required is
>
>   http://www.graphviz.org/pub/**graphviz/stable/windows/**
> graphviz-2.20.3.1.msi<http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi>
>
>
>     Ask further questions on the Bioconductor mailing list
>>
>>    http://bioconductor.org/docs/**mailList.html<http://bioconductor.org/docs/mailList.html>
>>
>
> if you have more questions, ask on the Bioconductor mailing list.
>
> Martin
>
>
>
>> Error: package/namespace load failed for 'Rgraphviz'
>>
>>
>> Help me please.
>>
>>
>>
>

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

Location: M1-B861
Telephone: [phone]

______________________________________________
[hidden email] 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.

[Ram H. Sharma]

Hi Martin

Thank you for help,  that helped me to come out the problem !

On Mon, Jul 25, 2011 at 11:46 AM, Martin Morgan <[hidden email]> wrote:

> On 07/25/2011 07:58 AM, Ram H. Sharma wrote:
>
>> Hi All
>>
>> How can I adjust this path. My current path of Graphviz installation is:
>>
>> C:\Program Files (x86)\Graphviz2.20\bin
>>
>> and Rgraphviz is
>>
>> C:\R\library\Rgraphviz\libs\**i386
>>
>> Please help me. I am new to Rgraphviz.
>>
>
> PATH is an environment variable. From the R FAQ for Windows
>
> http://cran.fhcrc.org/bin/**windows/base/rw-FAQ.html#How-**
> do-I-set-environment-**variables_003f<http://cran.fhcrc.org/bin/windows/base/rw-FAQ.html#How-do-I-set-environment-variables_003f>
>
> "For all applications via Windows. How you set an environment variable is
> system specific: under Windows 2000/XP/Server 2003 you can use `System' in
> the control panel or the properties of `My Computer' (under the `Advanced'
> tab). Under Vista/7, go to `User Accounts' in the Control Panel, and select
> your account and then `Change my environment variables'."
>
> Create a 'New' user variable named PATH, with value
>
>
>  C:\Program Files (x86)\Graphviz2.20\bin
>
> If a value already exists for PATH, add the above, separated by a semicolon
> ;. Restart R and check that the path is set correctly
>
>  path <- strsplit(Sys.getenv("PATH"), ";")[[1]]
>  dir(path[grepl("Graphviz2.20", path)])
>
> should return several file names, including, e.g., libgraph-4.dll. Install
> Rgraphviz with
>
>  source("http://bioconductor.**org/biocLite.R<http://bioconductor.org/biocLite.R>
> ")
>  biocLite('Rgraphviz")
>
>
>> Ram
>>
>>
>>
>>
>> "your Windows system 'PATH' variable needs to be adjusted once you've
>> installed graphviz and before installing Rgraphviz"
>>
>> ---------- Forwarded message ----------
>> From: Martin Morgan<[hidden email]>
>> Date: Mon, Jul 25, 2011 at 9:25 AM
>> Subject: Re: [R] Rgraphviz installation problem
>> To: "Ram H. Sharma"<[hidden email]**>
>> Cc: [hidden email]
>>
>>
>> On 07/25/2011 06:05 AM, Ram H. Sharma wrote:
>>
>>  Dear experts
>>>
>>> I installed Rgraphviz with the following command:
>>>
>>>
>>> source("http://www.**bioconduc**tor.org/biocLite.R<http://bioconductor.org/biocLite.R>
>>> <http://www.**bioconductor.org/biocLite.R<http://www.bioconductor.org/biocLite.R>
>>> >
>>>
>>> ")
>>>
>>>     biocLite("Rgraphviz")
>>>
>>>
>>> But had a problem when I tried to load it.
>>>
>>> This says that libcdt-4.dll is missing in your computer and the following
>>> message in R window:
>>>
>>>  library("Rgraphviz")
>>>
>>>>
>>>>  Loading required package: graph
>>> Loading required package: grid
>>> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>>>   call: value[[3L]](cond)
>>>   error: unable to load shared object
>>> 'C:/R/library/Rgraphviz/libs/****i386/Rgraphviz.dll':
>>>   LoadLibrary failure:  The specified module could not be found.
>>>
>>>
>>>   Check that (1) graphviz is installed on your system; (2) the
>>>
>>>
>> you need to install graphviz, as well as Rgraphviz.
>>
>>
>>    installed version of graphviz matches '2.20.3'; this is the version
>>
>>>   used to build this Rgraphviz package; (3) graphviz is accessible to
>>>
>>>
>> graphviz has to be a specific version.
>>
>>
>>    R, e.g., the path to the graphviz 'bin' directory is in the system
>>
>>>   'PATH' variable.  See additional instructions in the 'README' file of
>>>
>>>
>> your Windows system 'PATH' variable needs to be adjusted once you've
>> installed graphviz and before installing Rgraphviz
>>
>>
>>    the Rgraphviz 'source' distribution, available at
>>
>>>
>>>   http://bioconductor.org/****packages/release/bioc/html/****
>>> Rgraphviz.html<http://bioconductor.org/**packages/release/bioc/html/**Rgraphviz.html>
>>> <http://**bioconductor.org/packages/**release/bioc/html/Rgraphviz.**html<http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html>
>>> >
>>>
>>>
>> additional details are at the url above. For instance, the specific
>> version
>> of graphviz required is
>>
>>  http://www.graphviz.org/pub/****graphviz/stable/windows/**<http://www.graphviz.org/pub/**graphviz/stable/windows/**>
>> graphviz-2.20.3.1.msi<http://**www.graphviz.org/pub/graphviz/**
>> stable/windows/graphviz-2.20.**3.1.msi<http://www.graphviz.org/pub/graphviz/stable/windows/graphviz-2.20.3.1.msi>
>> >
>>
>>
>>
>>    Ask further questions on the Bioconductor mailing list
>>
>>>
>>>   http://bioconductor.org/docs/****mailList.html<http://bioconductor.org/docs/**mailList.html>
>>> <http://**bioconductor.org/docs/**mailList.html<http://bioconductor.org/docs/mailList.html>
>>> >
>>>
>>>
>> if you have more questions, ask on the Bioconductor mailing list.
>>
>> Martin
>>
>>
>>
>>  Error: package/namespace load failed for 'Rgraphviz'
>>>
>>>
>>> Help me please.
>>>
>>>
>>>
>>>
>>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: [phone]
>

--

Ram H

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.

[slipkid90515]

Martin -- I know this is about a year late, but I have to thank you for taking the time to answer Ram's question in this thread.  It helped me get Rgraphviz up and running.  I've been struggling with this for about 90 minutes, so thank you so much!  

And to anyone else who may run upon this thread with the same issues, I found this link helpful:  https://wiki.duke.edu/display/DUKER/Install+RGraphviz+under+Windows

Thanks,
Jess

[gerostathos]

Dear Martin
thanks for your comprehensive instructions, had I found them earlier I would have saved at least 3 hours of problems...
Everyone copies: "your Windows system 'PATH' variable needs to be adjusted once you've
installed graphviz and before installing Rgraphviz "
What if Rgraphviz is already installed? Trying every step proposed does not seem to work any more (I get "character (0)" when I try your check in R). How can I remove Rgraphviz from R in order to start everything again? Or are there other solutions to that?

Thanks in advance

Anton Gerostathos

[Uwe Ligges-3]

On 24.06.2012 16:54, gerostathos wrote:

> Dear Martin
> thanks for your comprehensive instructions, had I found them earlier I would
> have saved at least 3 hours of problems...
> Everyone copies: "your Windows system 'PATH' variable needs to be adjusted
> once you've
> installed graphviz and before installing Rgraphviz "
> What if Rgraphviz is already installed? Trying every step proposed does not
> seem to work any more (I get "character (0)" when I try your check in R).
> How can I remove Rgraphviz from R in order to start everything again? Or are
> there other solutions to that?
>

You can always reinstall via install.packages()
and if you really want to remove before, use remove.packages().

Uwe Ligges

> Thanks in advance
>
> Anton Gerostathos
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Rgraphviz-installation-problem-tp3692733p4634332.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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.
>

______________________________________________
[hidden email] 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.

[gerostathos]

Thank you
removing everything and reinstalling while respecting every instruction did
not change anything...
evidently, I was too optimistic when thinking that the problem was caused by
something so simple... I continue to strive with it but, at least, I know
where not to look for the solution.
Regards

Anton Gerostathos

-----Message d'origine-----
From: Uwe Ligges
Sent: Sunday, June 24, 2012 5:22 PM
To: gerostathos
Cc: [hidden email]
Subject: Re: [R] Fwd: Rgraphviz installation problem



On 24.06.2012 16:54, gerostathos wrote:

> Dear Martin
> thanks for your comprehensive instructions, had I found them earlier I
> would
> have saved at least 3 hours of problems...
> Everyone copies: "your Windows system 'PATH' variable needs to be adjusted
> once you've
> installed graphviz and before installing Rgraphviz "
> What if Rgraphviz is already installed? Trying every step proposed does
> not
> seem to work any more (I get "character (0)" when I try your check in R).
> How can I remove Rgraphviz from R in order to start everything again? Or
> are
> there other solutions to that?
>

You can always reinstall via install.packages()
and if you really want to remove before, use remove.packages().

Uwe Ligges

> Thanks in advance
>
> Anton Gerostathos
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/Rgraphviz-installation-problem-tp3692733p4634332.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] 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.
>

______________________________________________
[hidden email] 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.