Re: [R] rjags cannot find JAGS-4.0.0

[Martyn Plummer]

On Fri, 2015-11-27 at 11:27 -0800, David Winsemius wrote:
> > On Nov 26, 2015, at 4:59 PM, Margaret Donald  
> > 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
> > margaret.don...@unsw.edu.au
> > 0405 834 550
> > 
> > [[alternative HTML version deleted]]
> > 
> > __
> > R-help@r-project.org 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
> 

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] rjags cannot find JAGS-4.0.0

[David Winsemius]

> On Nov 26, 2015, at 4:59 PM, Margaret Donald  
> 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
> margaret.don...@unsw.edu.au
> 0405 834 550
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org 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

__
R-help@r-project.org 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.

Re: [R] rjags cannot find JAGS-4.0.0

[David Winsemius]

> On Nov 27, 2015, at 11:27 AM, David Winsemius  wrote:
> 
>> 
>> On Nov 26, 2015, at 4:59 PM, Margaret Donald  
>> 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
>> margaret.don...@unsw.edu.au
>> 0405 834 550
>> 
>>  [[alternative HTML version deleted]]
>> 
>> __
>> R-help@r-project.org 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
> 
> __
> R-help@r-project.org 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

__
R-help@r-project.org 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.

[R] 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
margaret.don...@unsw.edu.au
0405 834 550

[[alternative HTML version deleted]]

__
R-help@r-project.org 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.