[R] JAGS 4.x, rjags 4.x problems

Discussion:

[R] JAGS 4.x, rjags 4.x problems | Linux

Evan Cooch

2015-11-04 19:08:47 UTC

Greetings --

This has also been posted on the jags forum, but since I suspect the
problem is more 'R-related' than jags, will aos post here.

Decided to 'upgrade' from jags 3.x.x to 4.x.x today, on my GNU/Linux
boxes (which run latest RHEL). Here are the basic details:

1\ used R 3.2.2 compiled from source. 64-bit -- nothing fancy, other
than the fact that I used OpenBLAS instead of 'generic'. Works fine.

2\ downloaded and compiled JAGS 4.0.1 from source (nothing fancy,
./configure & make & make install) -- no errors. Runs fine as a
standalone app from CLI.

3\ Downloaded rjags_4-3.tar.gz, and installed from R CLI (within R --
usual R CMD INSTALL approach). Again, no errors reported.

However, when I fire up R, and try something simple like

library(R2jags)

I get a whole slew of error messages - following is reproducible on all
my machines:

Loading required package: rjags
Loading required package: coda
Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/usr/lib64/R/library/rjags/libs/rjags.so':
libjags.so.3: cannot open shared object file: No such file or directory
Error: package ‘rjags’ could not be loaded

Meaning, what? I checked, and rjags.so is where its supposed to be.If I run

R CMD ldd /usr/lib64/R/library/rjags/libs/rjags.so

no failures at any point.

Suggestions? Pointers to the obvious?

Thanks very much in advance.

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Rainer Hurling

2015-11-04 20:05:05 UTC

Permalink

On FreeBSD, I get the following, when I try to load package R2jags:

library(R2jags)
Lade nötiges Paket: rjags
Lade nötiges Paket: coda
Linked to JAGS 4.0.0
Loaded modules: basemod,bugs
Attache Paket: ‘R2jags’
The following object is masked from ‘package:coda’:
traceplot

So, in principle, it should work on Unix alike platforms.

I suggest, your next step should be to rebuild packages coda, basemod
and bugs, and of course, package R2jags_0.5-7?

Sorry, no other clue so far.

Greetings,
Rainer

Post by Evan Cooch
I get a whole slew of error messages - following is reproducible on all
Loading required package: rjags
Loading required package: coda
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
libjags.so.3: cannot open shared object file: No such file or directory
Error: package ‘rjags’ could not be loaded
Meaning, what? I checked, and rjags.so is where its supposed to be.If I run
R CMD ldd /usr/lib64/R/library/rjags/libs/rjags.so
no failures at any point.
Suggestions? Pointers to the obvious?
Thanks very much in advance.

______________________________________________
R-***@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, re

Yvan Richard

2015-11-04 20:31:37 UTC

Permalink

Hi Evan

The last version of rjags on CRAN is 4.4. Have you tried it?
http://cran.stat.auckland.ac.nz/web/packages/rjags/index.html
I did have the same problem before updating it, but it now works on my
Ubuntu with the new JAGS version.

Cheers,
-Yvan

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Yvan Richard

2015-11-04 21:24:17 UTC

Permalink

According to the README file in the rjags source code (in the tar.gz
file), you can apparently pass options to the configure script to
specify where JAGS is installed.
I'm confident you can solve your problem by following the instructions
in that README file.

I wonder if this is the problem -- on my system(s), R is installed to
/usr/lib64/R, whereas JAGS and associated files is in /usr/local/lib/JAGS. I
have a hunch that the problem relates to where rjags expects to find things
during install/compile, given how R was compiled, and where it is installed.
Seem reasonable? Not sure what to do about it, but...

Post by Yvan Richard
Hi Evan
The last version of rjags on CRAN is 4.4. Have you tried it?
http://cran.stat.auckland.ac.nz/web/packages/rjags/index.html
I did have the same problem before updating it, but it now works on my
Ubuntu with the new JAGS version.
Cheers,
-Yvan

yes, but when I do, I get the following during the install (which fails).
checking version of JAGS library... wrong version
configure: error: rjags requires JAGS version 4.x.y
ERROR: configuration failed for package ‘rjags’
* removing ‘/usr/lib64/R/library/rjags’
* restoring previous ‘/usr/lib64/R/library/rjags’
which makes no sense, because I have JAGS 4.0.01 on the system, and in the
path
Welcome to JAGS 4.0.1 on Wed Nov 4 15:41:46 2015
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok
.

--
Yvan Richard

DRAGONFLY Science

Physical address: Level 5, 158 Victoria St, Te Aro, Wellington
Postal address: PO Box 27535, Wellington 6141
New Zealand
Ph: 04.385.9285
web page

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Evan Cooch

2015-11-04 20:36:01 UTC

Permalink

Post by Evan Cooch
Greetings --
This has also been posted on the jags forum, but since I suspect the
problem is more 'R-related' than jags, will aos post here.
Decided to 'upgrade' from jags 3.x.x to 4.x.x today, on my GNU/Linux
1\ used R 3.2.2 compiled from source. 64-bit -- nothing fancy, other
than the fact that I used OpenBLAS instead of 'generic'. Works fine.
2\ downloaded and compiled JAGS 4.0.1 from source (nothing fancy,
./configure & make & make install) -- no errors. Runs fine as a
standalone app from CLI.
3\ Downloaded rjags_4-3.tar.gz, and installed from R CLI (within R --
usual R CMD INSTALL approach). Again, no errors reported.
However, when I fire up R, and try something simple like
library(R2jags)
I get a whole slew of error messages - following is reproducible on
Loading required package: rjags
Loading required package: coda
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
libjags.so.3: cannot open shared object file: No such file or directory
Error: package ‘rjags’ could not be loaded

Further puzzlement -- I uninstalled R2jags and rjags, with the idea that
re-installing them (ostensibly with the 'latest and greatest') would do
the trick. While the process went fine for R2jags, when I tried to
re-install rjags, got the following error messages:

checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking for jags_version in -ljags... yes
checking version of JAGS library... wrong version
configure: error: rjags requires JAGS version 4.x.y
ERROR: configuration failed for package ‘rjags’
* removing ‘/usr/lib64/R/library/rjags’
* restoring previous ‘/usr/lib64/R/library/rjags’

I'm confused as to how it is not finding JAGS 4.x.y, which is not only
most definitely on the system, but in the path:

[***@euler egc]# jags
Welcome to JAGS 4.0.1 on Wed Nov 4 15:35:12 2015
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok

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Rainer Hurling

2015-11-05 14:45:52 UTC

Permalink

Post by Evan Cooch

Further puzzlement -- I uninstalled R2jags and rjags, with the idea that
re-installing them (ostensibly with the 'latest and greatest') would do
the trick. While the process went fine for R2jags, when I tried to
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking for jags_version in -ljags... yes
checking version of JAGS library... wrong version
configure: error: rjags requires JAGS version 4.x.y
ERROR: configuration failed for package ‘rjags’
* removing ‘/usr/lib64/R/library/rjags’
* restoring previous ‘/usr/lib64/R/library/rjags’

Hmm, is it possible, that your JAGS 4.x.y installation is fine, but an
old libjags.so library is lying around from a not fully completed
deinstallation? Could you have a look for older libjags.so versions, please?

Just a thought.

Post by Evan Cooch
I'm confused as to how it is not finding JAGS 4.x.y, which is not only
Welcome to JAGS 4.0.1 on Wed Nov 4 15:35:12 2015
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok

Evan Cooch

2015-11-05 17:28:38 UTC

Permalink

Post by Rainer Hurling

Post by Evan Cooch

Further puzzlement -- I uninstalled R2jags and rjags, with the idea that
re-installing them (ostensibly with the 'latest and greatest') would do
the trick. While the process went fine for R2jags, when I tried to
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking for jags_version in -ljags... yes
checking version of JAGS library... wrong version
configure: error: rjags requires JAGS version 4.x.y
ERROR: configuration failed for package ‘rjags’
* removing ‘/usr/lib64/R/library/rjags’
* restoring previous ‘/usr/lib64/R/library/rjags’

I suppose thats possible -- I'll go through the sequence again at some
point, and report back.

______________________________________________
R-***@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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and provide commented, minimal,

Costantino Zazza

2015-11-19 13:36:13 UTC

Permalink

Hi R-users,

talking about the compilation of rjags (gnu 4.4.7 - blas and lapack
routines) package in R I have solved the issue in the thread as follows:

Before compiling JAGS I need to recompile BLAS and LAPACK libraries with
-fPIC instruction:

BLAS Makefile:
[***@n14 library]# cat /home/c.zazza/BLAS_pic/make.inc
####################################################################
# BLAS make include file. #
# March 2007 #
####################################################################
#
SHELL = /bin/sh
#
# The machine (platform) identifier to append to the library names
#
PLAT = _LINUX
#
# Modify the FORTRAN and OPTS definitions to refer to the
# compiler and desired compiler options for your machine. NOOPT
# refers to the compiler options desired when NO OPTIMIZATION is
# selected. Define LOADER and LOADOPTS to refer to the loader and
# desired load options for your machine.
#
FORTRAN = gfortran
*OPTS = -O3 -fPIC*
DRVOPTS = $(OPTS)
*NOOPT = -fPIC*
LOADER = gfortran
*LOADOPTS = -fPIC*
#
# The archiver and the flag(s) to use when building archive (library)
# If you system has no ranlib, set RANLIB = echo.
#
ARCH = ar
ARCHFLAGS= cr
RANLIB = ranlib
#
# The location and name of the Reference BLAS library.
#
BLASLIB = blas$(PLAT).a

Also lapack makefile needs for -fPIC:
[***@n14 library]# cat /home/c.zazza/lapack-3.5.0_pic/make.inc
####################################################################
# LAPACK make include file. #
# LAPACK, Version 3.5.0 #
# November 2013 #
####################################################################
#
SHELL = /bin/sh
#
# Modify the FORTRAN and OPTS definitions to refer to the
# compiler and desired compiler options for your machine. NOOPT
# refers to the compiler options desired when NO OPTIMIZATION is
# selected. Define LOADER and LOADOPTS to refer to the loader and
# desired load options for your machine.
#
FORTRAN = gfortran
OPTS = -O2 -frecursive -fPIC
DRVOPTS = $(OPTS)
NOOPT = -O0 -frecursive -fPIC
LOADER = gfortran
LOADOPTS = -fPIC
#
# Timer for the SECOND and DSECND routines
#
# Default : SECOND and DSECND will use a call to the EXTERNAL FUNCTION ETIME
#TIMER = EXT_ETIME
# For RS6K : SECOND and DSECND will use a call to the EXTERNAL FUNCTION
ETIME_
# TIMER = EXT_ETIME_
# For gfortran compiler: SECOND and DSECND will use a call to the INTERNAL
FUNCTION ETIME
TIMER = INT_ETIME
# If your Fortran compiler does not provide etime (like Nag Fortran
Compiler, etc...)
# SECOND and DSECND will use a call to the INTERNAL FUNCTION CPU_TIME
# TIMER = INT_CPU_TIME
# If neither of this works...you can use the NONE value... In that case,
SECOND and DSECND will always return 0
# TIMER = NONE
#
# Configuration LAPACKE: Native C interface to LAPACK
# To generate LAPACKE library: type 'make lapackelib'
# Configuration file: turned off (default)
# Complex types: C99 (default)
# Name pattern: mixed case (default)
# (64-bit) Data model: LP64 (default)
#
# CC is the C compiler, normally invoked with options CFLAGS.
#
CC = gcc
CFLAGS = -O3 -fPIC
#
# The archiver and the flag(s) to use when building archive (library)
# If you system has no ranlib, set RANLIB = echo.
#
ARCH = ar
ARCHFLAGS= cr
RANLIB = ranlib
#
# Location of the extended-precision BLAS (XBLAS) Fortran library
# used for building and testing extended-precision routines. The
# relevant routines will be compiled and XBLAS will be linked only if
# USEXBLAS is defined.
#
# USEXBLAS = Yes
XBLASLIB =
# XBLASLIB = -lxblas
#
# The location of the libraries to which you will link. (The
# machine-specific, optimized BLAS library should be used whenever
# possible.)
#
#BLASLIB = ../../librefblas.a
BLASLIB = /home/c.zazza/BLAS/blas_LINUX.a
LAPACKLIB = liblapack.a
TMGLIB = libtmglib.a
LAPACKELIB = liblapacke.a

Next, we compile JAGS as follows:

*1032 wget
http://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.0.0.tar.gz
<http://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.0.0.tar.gz>*
* 1034 tar -zxvf JAGS-4.0.0.tar.gz*
* 1035 cd /share/apps/JAGS-4.0.0*
*1038 ./configure F77="gfortran"
--with-blas="/apps/BLAS_pic/blas_LINUX.a" --with-lapack="-ltmglib -llapack"
LDFLAGS="-L/apps/lapack-3.5.0_pic" --prefix="/apps/jags"
--libdir="/apps/jags/lib64"*
*1039 make -j4 >& make.log &*
* 1040 tail -f make.log*
* 1041 make install*

afterwards, before running R we need to set this:* (otherwise you obtain
the error you posted like: libjargs.x.y.z etc etc):*
*1027 export LD_LIBRARY_PATH=$RDIR/lib64/R/lib:${LD_LIBRARY_PATH}*

Finally, within the R-environment we install rjags as follows:

*install.packages("rjags", configure.args = "--with-jags-prefix=/apps/jags
--with-jags-include=/apps/jags/include/JAGS
--with-jags-lib=/apps/jags/lib64
--with-jags-modules=/apps/jags/lib/JAGS/modules-4")*

[***@n14 bin]# export
LD_LIBRARY_PATH="/home/apps/jags/lib64:${LD_LIBRARY_PATH}"
[***@n14 bin]# echo $LD_LIBRARY_PATH
/home/apps/jags/lib64:/home/apps/R-3.2.1/lib64/R/lib:/opt/torque/lib:/home/apps/R/3.1.0/lib64:/opt/openmpi/gnu4.4.7/lib:/home/apps/gromacs-4.6.5/build_intel.13.1.1/lib:/usr/local/cuda/lib64:/opt/intel/composer_xe_2013.3.163/compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/mpirt/lib/intel64:/opt/intel/composer_xe_2013.3.163/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/ipp/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/opt/intel/composer_xe_2013.3.163/compiler/lib/intel64:/opt/intel/composer_xe_2013.3.163/mkl/lib/intel64:/opt/intel/composer_xe_2013.3.163/tbb/lib/intel64/gcc4.4
[***@n14 bin]# R
R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

install.packages("rjags", configure.args =

"--with-jags-prefix=/home/apps/jags
--with-jags-include=/home/apps/jags/include/JAGS
--with-jags-lib=/home/apps/jags/lib64
--with-jags-modules=/home/apps/jags/lib/JAGS/modules-4")
--- Please select a CRAN mirror for use in this session ---
CRAN mirror
1: 0-Cloud [https] 2: 0-Cloud
3: Algeria 4: Argentina (La Plata)
5: Australia (Canberra) 6: Australia (Melbourne)
7: Austria [https] 8: Austria
9: Belgium (Antwerp) 10: Belgium (Ghent)
11: Brazil (BA) 12: Brazil (PR)
13: Brazil (RJ) 14: Brazil (SP 1)
15: Brazil (SP 2) 16: Canada (BC)
17: Canada (NS) 18: Canada (ON)
19: Chile [https] 20: Chile
21: China (Beijing 2) 22: China (Beijing 3)
23: China (Beijing 4) [https] 24: China (Beijing 4)
25: China (Xiamen) 26: Colombia (Cali) [https]
27: Colombia (Cali) 28: Czech Republic
29: Denmark 30: Ecuador
31: El Salvador 32: Estonia
33: France (Lyon 1) 34: France (Lyon 2) [https]
35: France (Lyon 2) 36: France (Marseille)
37: France (Montpellier) 38: France (Paris 1)
39: France (Paris 2) [https] 40: France (Paris 2)
41: Germany (Berlin) 42: Germany (Göttingen)
43: Germany (Münster) [https] 44: Germany (Münster)
45: Greece 46: Hungary
47: Iceland [https] 48: Iceland
49: India 50: Indonesia (Jakarta)
51: Iran 52: Ireland
53: Italy (Milano) 54: Italy (Padua) [https]
55: Italy (Padua) 56: Italy (Palermo)
57: Japan (Tokyo) 58: Japan (Yamagata)
59: Korea (Seoul 1) 60: Korea (Seoul 2)
61: Korea (Ulsan) 62: Lebanon
63: Mexico (Mexico City) [https] 64: Mexico (Mexico City)
65: Mexico (Texcoco) 66: Mexico (Queretaro)
67: Netherlands (Amsterdam) 68: Netherlands (Utrecht)
69: New Zealand 70: Norway
71: Philippines 72: Poland
73: Portugal (Lisbon) 74: Russia (Moscow) [https]
75: Russia (Moscow) 76: Singapore
77: Slovakia 78: South Africa (Cape Town)
79: South Africa (Johannesburg) 80: Spain (A Coruña) [https]
81: Spain (A Coruña) 82: Spain (Madrid)
83: Sweden 84: Switzerland [https]
85: Switzerland 86: Taiwan (Chungli)
87: Taiwan (Taipei) 88: Thailand
89: Turkey (Denizli) 90: Turkey (Mersin)
91: UK (Bristol) [https] 92: UK (Bristol)
93: UK (Cambridge) [https] 94: UK (Cambridge)
95: UK (London 1) 96: UK (London 2)
97: UK (St Andrews) 98: USA (CA 1) [https]
99: USA (CA 1) 100: USA (CA 2)
101: USA (CO) 102: USA (IA)
103: USA (IN) 104: USA (KS) [https]
105: USA (KS) 106: USA (MD) [https]
107: USA (MD) 108: USA (MI 1) [https]
109: USA (MI 1) 110: USA (MI 2)
111: USA (MO) 112: USA (NC)
113: USA (OH 1) 114: USA (OH 2)
115: USA (OR) 116: USA (PA 1)
117: USA (PA 2) 118: USA (TN) [https]
119: USA (TN) 120: USA (TX) [https]
121: USA (TX) 122: USA (WA) [https]
123: USA (WA) 124: Venezuela

Selection: 53
trying URL
'http://cran.mirror.garr.it/mirrors/CRAN/src/contrib/rjags_4-4.tar.gz'
Content type 'text/plain' length 72125 bytes (70 KB)
==================================================
downloaded 70 KB
* installing *source* package ‘rjags’ ...
** package ‘rjags’ successfully unpacked and MD5 sums checked
configure: WARNING: unrecognized options: --with-jags-include,
--with-jags-lib, --with-jags-modules
checking for pkg-config... /usr/bin/pkg-config
configure: WARNING: pkg-config file for jags 4 unavailable
configure: WARNING: Consider adding the directory containing `jags.pc`
configure: WARNING: to the PKG_CONFIG_PATH environment variable
configure: Attempting legacy configuration of rjags
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking Console.h usability... yes
checking Console.h presence... yes
checking for Console.h... yes
configure: Compile flags are -I/home/apps/jags/include/JAGS
configure: Link flags are -L/home/apps/jags/lib64 -ljags
checking for gcc... gcc -std=gnu99
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for jags_version in -ljags... yes
checking version of JAGS library... OK
configure: creating ./config.status
config.status: creating src/Makevars
configure: WARNING: unrecognized options: --with-jags-include,
--with-jags-lib, --with-jags-modules
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/unix/zzz.R
configure: WARNING: unrecognized options: --with-jags-include,
--with-jags-lib, --with-jags-modules
** libs
g++ -I/home/apps/R-3.2.1/lib64/R/include -DNDEBUG
-I/home/apps/jags/include/JAGS -I/usr/local/include -fpic -g -O2 -c
jags.cc -o jags.o
g++ -I/home/apps/R-3.2.1/lib64/R/include -DNDEBUG
-I/home/apps/jags/include/JAGS -I/usr/local/include -fpic -g -O2 -c
parallel.cc -o parallel.o
g++ -shared -L/usr/local/lib64 -o rjags.so jags.o parallel.o
-L/home/apps/jags/lib64 -ljags
installing to /home/apps/R-3.2.1/lib64/R/library/rjags/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rjags)
The downloaded source packages are in
‘/tmp/Rtmpd2BSpp/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

All the best,
Costantino

Post by Rainer Hurling

Post by Evan Cooch

Further puzzlement -- I uninstalled R2jags and rjags, with the idea that
re-installing them (ostensibly with the 'latest and greatest') would do
the trick. While the process went fine for R2jags, when I tried to
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking for jags_version in -ljags... yes
checking version of JAGS library... wrong version
configure: error: rjags requires JAGS version 4.x.y
ERROR: configuration failed for package ‘rjags’
* removing ‘/usr/lib64/R/library/rjags’
* restoring previous ‘/usr/lib64/R/library/rjags’

I suppose thats possible -- I'll go through the sequence again at some
point, and report back.
______________________________________________
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.

Evan Cooch

2015-11-05 14:44:00 UTC

Permalink

Well, sort of. I got sufficiently frustrated that I completely
uninstalled R, jags, and everything related. Did a re-install using only
versions of R nd JAGS found in the epel repo. No muss, no muss -- all
works.

Out of curiosity, uninstalled again, and tried my usual sequence of
manually compile R from source, same with JAGS. R works, JAGS works, but
can't get any R package linking the two (say, rjags, R2jags), to
recognize that JAGS is installed.

Ah well, at least the 'install from repos' approach works. I'll have to
make do with that.

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Rainer Hurling

2015-11-05 17:25:19 UTC

Permalink

Post by Evan Cooch
Well, sort of. I got sufficiently frustrated that I completely
uninstalled R, jags, and everything related. Did a re-install using only
versions of R nd JAGS found in the epel repo. No muss, no muss -- all
works.
Out of curiosity, uninstalled again, and tried my usual sequence of
manually compile R from source, same with JAGS. R works, JAGS works, but
can't get any R package linking the two (say, rjags, R2jags), to
recognize that JAGS is installed.
Ah well, at least the 'install from repos' approach works. I'll have to
make do with that.

Just took another look in my installation call, I made some time ago.
What I did to get it work on FreeBSD was:

R CMD INSTALL rjags_4-4.tar.gz --configure-args='CPPFLAGS="-fPIC"
LDFLAGS="-L/usr/local/lib -ljags"
--with-jags-include=/usr/local/include/JAGS --with-jags-lib=/usr/local/lib'

So I used --configure-args, LDFLAGS, --with-jags-inlcue and
--with-jags-lib in my installation procedure. Perhaps it is worth
another try?

______________________________________________
R-***@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.