rjags cannot find JAGS-4.0.0

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rjags cannot find JAGS-4.0.0

Margaret Donald
1. Despite being in R with administrative rights  the library "rjags" loads
in a temporary location.

> install.packages("rjags", dependencies=TRUE,
+       lib= "C:/Users/Margaret Donald/Documents/R/win-library/3.2")
trying URL 'https://cran.r-project.org/bin/windows/contrib/3.2/rjags_4-4.zip
'
Content type 'application/zip' length 525871 bytes (513 KB)
downloaded 513 KB

package ‘rjags’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\Margaret
Donald\AppData\Local\Temp\RtmpMzv76s\downloaded_packages
#-----------------------------------------------------------------------------------------------------------------

2. Cannot find JAGS-4.0.0 which is in C;\programs\JAGS\JAGS-4.0.0.  How do
I get R to see JAGS-4.0.0
> library(rjags)
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: Failed to locate any version of JAGS version 4

The rjags package is just an interface to the JAGS library
Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
http://www.sourceforge.net/projects/mcmc-jags/files

Error: package or namespace load failed for ‘rjags’
> library(R2jags)
Loading required package: rjags
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: Failed to locate any version of JAGS version 4

The rjags package is just an interface to the JAGS library
Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
http://www.sourceforge.net/projects/mcmc-jags/files

Error: package ‘rjags’ could not be loaded
>

Regards,
Margaret Donald
--
Margaret Donald
Post Doctoral researcher
University of New South Wales
[hidden email]
0405 834 550

        [[alternative HTML version deleted]]

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Re: rjags cannot find JAGS-4.0.0

David Winsemius

> On Nov 26, 2015, at 4:59 PM, Margaret Donald <[hidden email]> wrote:
>
> 1. Despite being in R with administrative rights  the library "rjags" loads
> in a temporary location.
>
>> install.packages("rjags", dependencies=TRUE,
> +       lib= "C:/Users/Margaret Donald/Documents/R/win-library/3.2")
> trying URL 'https://cran.r-project.org/bin/windows/contrib/3.2/rjags_4-4.zip
> '
> Content type 'application/zip' length 525871 bytes (513 KB)
> downloaded 513 KB
>
> package ‘rjags’ successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
>        C:\Users\Margaret
> Donald\AppData\Local\Temp\RtmpMzv76s\downloaded_packages

That’s not an indication of an error. The installation process always does that.


> #-----------------------------------------------------------------------------------------------------------------
>
> 2. Cannot find JAGS-4.0.0 which is in C;\programs\JAGS\JAGS-4.0.0.  How do
> I get R to see JAGS-4.0.0

You might try to use Sys.setenv to create a properly directed JAGS_HOME

Sys.setenv(JAGS_HOME=“C:\programs\JAGS\JAGS-4.0.0”)

(I corrected the semi-colon.)
>> library(rjags)
> Error : .onLoad failed in loadNamespace() for 'rjags', details:
>  call: fun(libname, pkgname)
>  error: Failed to locate any version of JAGS version 4
>
> The rjags package is just an interface to the JAGS library
> Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
> http://www.sourceforge.net/projects/mcmc-jags/files

I’m was having a perhaps similar problem on a Mac. The binary version 3-15 of rjags installed today from CRAN was trying to access /usr/local/lib/libjags.3.dylib, but since I have installed JAGS version 4.0.1 installed from the SourceForge repository, there is no ligjags.3.dylib, but instead there was only a /usr/local/lib/libjags.4.dylib


Going back to SourceForge and tracking down the older version of JAGS and installing version 3.4.0 was successful in getting rjags to load correctly. I suspect that with the release of JAGS v4 that there is some mismatch among the various editions of rjags and JAGS.


David

>
> Error: package or namespace load failed for ‘rjags’
>> library(R2jags)
> Loading required package: rjags
> Error : .onLoad failed in loadNamespace() for 'rjags', details:
>  call: fun(libname, pkgname)
>  error: Failed to locate any version of JAGS version 4
>
> The rjags package is just an interface to the JAGS library
> Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
> http://www.sourceforge.net/projects/mcmc-jags/files
>
> Error: package ‘rjags’ could not be loaded
>>
>
> Regards,
> Margaret Donald
> --
> Margaret Donald
> Post Doctoral researcher
> University of New South Wales
> [hidden email]
> 0405 834 550
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

David Winsemius
Alameda, CA, USA

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.
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Re: rjags cannot find JAGS-4.0.0

David Winsemius

> On Nov 27, 2015, at 11:27 AM, David Winsemius <[hidden email]> wrote:
>
>>
>> On Nov 26, 2015, at 4:59 PM, Margaret Donald <[hidden email]> wrote:
>>
>> 1. Despite being in R with administrative rights  the library "rjags" loads
>> in a temporary location.
>>
>>> install.packages("rjags", dependencies=TRUE,
>> +       lib= "C:/Users/Margaret Donald/Documents/R/win-library/3.2")
>> trying URL 'https://cran.r-project.org/bin/windows/contrib/3.2/rjags_4-4.zip
>> '
>> Content type 'application/zip' length 525871 bytes (513 KB)
>> downloaded 513 KB
>>
>> package ‘rjags’ successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>       C:\Users\Margaret
>> Donald\AppData\Local\Temp\RtmpMzv76s\downloaded_packages
>
> That’s not an indication of an error. The installation process always does that.
>
>
>> #-----------------------------------------------------------------------------------------------------------------
>>
>> 2. Cannot find JAGS-4.0.0 which is in C;\programs\JAGS\JAGS-4.0.0.  How do
>> I get R to see JAGS-4.0.0
>
> You might try to use Sys.setenv to create a properly directed JAGS_HOME
>
> Sys.setenv(JAGS_HOME=“C:\programs\JAGS\JAGS-4.0.0”)

Er ,,,, being a Mac user I forgot that this should have been (but I don’t really know whether `rjags` checks this environment variable, so am unsure if it was the correct notion in the first place)::

Sys.setenv(JAGS_HOME=“C:\\programs\\JAGS\\JAGS-4.0.0”)

Or:

Sys.setenv(JAGS_HOME=“C:/programs/JAGS/JAGS-4.0.0”)


David.

>
> (I corrected the semi-colon.)
>>> library(rjags)
>> Error : .onLoad failed in loadNamespace() for 'rjags', details:
>> call: fun(libname, pkgname)
>> error: Failed to locate any version of JAGS version 4
>>
>> The rjags package is just an interface to the JAGS library
>> Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
>> http://www.sourceforge.net/projects/mcmc-jags/files
>
> I’m was having a perhaps similar problem on a Mac. The binary version 3-15 of rjags installed today from CRAN was trying to access /usr/local/lib/libjags.3.dylib, but since I have installed JAGS version 4.0.1 installed from the SourceForge repository, there is no ligjags.3.dylib, but instead there was only a /usr/local/lib/libjags.4.dylib
>
>
> Going back to SourceForge and tracking down the older version of JAGS and installing version 3.4.0 was successful in getting rjags to load correctly. I suspect that with the release of JAGS v4 that there is some mismatch among the various editions of rjags and JAGS.
>
> —
> David
>>
>> Error: package or namespace load failed for ‘rjags’
>>> library(R2jags)
>> Loading required package: rjags
>> Error : .onLoad failed in loadNamespace() for 'rjags', details:
>> call: fun(libname, pkgname)
>> error: Failed to locate any version of JAGS version 4
>>
>> The rjags package is just an interface to the JAGS library
>> Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
>> http://www.sourceforge.net/projects/mcmc-jags/files
>>
>> Error: package ‘rjags’ could not be loaded
>>>
>>
>> Regards,
>> Margaret Donald
>> --
>> Margaret Donald
>> Post Doctoral researcher
>> University of New South Wales
>> [hidden email]
>> 0405 834 550
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
> David Winsemius
> Alameda, CA, USA
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

David Winsemius
Alameda, CA, USA

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.
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Re: rjags cannot find JAGS-4.0.0

Martyn Plummer-3
In reply to this post by David Winsemius
On Fri, 2015-11-27 at 11:27 -0800, David Winsemius wrote:

> > On Nov 26, 2015, at 4:59 PM, Margaret Donald <[hidden email]> wrote:
> >
> > 1. Despite being in R with administrative rights  the library "rjags" loads
> > in a temporary location.
> >
> >> install.packages("rjags", dependencies=TRUE,
> > +       lib= "C:/Users/Margaret Donald/Documents/R/win-library/3.2")
> > trying URL 'https://cran.r-project.org/bin/windows/contrib/3.2/rjags_4-4.zip
> > '
> > Content type 'application/zip' length 525871 bytes (513 KB)
> > downloaded 513 KB
> >
> > package ‘rjags’ successfully unpacked and MD5 sums checked
> >
> > The downloaded binary packages are in
> >        C:\Users\Margaret
> > Donald\AppData\Local\Temp\RtmpMzv76s\downloaded_packages
>
> That’s not an indication of an error. The installation process always does that.
>
>
> > #-----------------------------------------------------------------------------------------------------------------
> >
> > 2. Cannot find JAGS-4.0.0 which is in C;\programs\JAGS\JAGS-4.0.0.  How do
> > I get R to see JAGS-4.0.0

The Windows installer writes some keys in the Windows registry. These
keys are then read by the rjags package when it is loaded to locate the
JAGS DLL.

I don't know why this is not working in your case. You might try
uninstalling and reinstalling JAGS (and by this I mean that the user who
installed it should uninstall it from the Control Panel).

Otherwise, as David says, you can set the environment variable
JAGS_HOME. Note that if you previously set JAGS_HOME in .Rprofile and
have upgraded to a new version of JAGS, then JAGS_HOME will be pointing
to the wrong place. This might explain why rjags cannot find JAGS and
this is why I do not recommend this solution except as a last resort.

> You might try to use Sys.setenv to create a properly directed JAGS_HOME
>
> Sys.setenv(JAGS_HOME=“C:\programs\JAGS\JAGS-4.0.0”)
>
> (I corrected the semi-colon.)
> >> library(rjags)
> > Error : .onLoad failed in loadNamespace() for 'rjags', details:
> >  call: fun(libname, pkgname)
> >  error: Failed to locate any version of JAGS version 4
> >
> > The rjags package is just an interface to the JAGS library
> > Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
> > http://www.sourceforge.net/projects/mcmc-jags/files
>
> I’m was having a perhaps similar problem on a Mac. The binary version
> 3-15 of rjags installed today from CRAN was trying to
> access /usr/local/lib/libjags.3.dylib, but since I have installed JAGS
> version 4.0.1 installed from the SourceForge repository, there is no
> ligjags.3.dylib, but instead there was only
> a /usr/local/lib/libjags.4.dylib

rjags_4-4 requires JAGS 4.x.y and the previous version rjags_3-15 is not
compatible with JAGS 4.0.0. Unfortunately the Mac OS X binaries on CRAN
are not up to date. I have no control over this but Matt Denwood has
made a binary for Mavericks or later available on Sourceforge:

http://sourceforge.net/projects/mcmc-jags/files/rjags/4/rjags_4-4.tgz

Martyn

> Going back to SourceForge and tracking down the older version of JAGS
> and installing version 3.4.0 was successful in getting rjags to load
> correctly. I suspect that with the release of JAGS v4 that there is
> some mismatch among the various editions of rjags and JAGS.
>
> —
> David
> >
> > Error: package or namespace load failed for ‘rjags’
> >> library(R2jags)
> > Loading required package: rjags
> > Error : .onLoad failed in loadNamespace() for 'rjags', details:
> >  call: fun(libname, pkgname)
> >  error: Failed to locate any version of JAGS version 4
> >
> > The rjags package is just an interface to the JAGS library
> > Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
> > http://www.sourceforge.net/projects/mcmc-jags/files
> >
> > Error: package ‘rjags’ could not be loaded
> >>
> >
> > Regards,
> > Margaret Donald
> > --
> > Margaret Donald
> > Post Doctoral researcher
> > University of New South Wales
> > [hidden email]
> > 0405 834 550
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
> David Winsemius
> Alameda, CA, USA
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.