Installing rjags on a Mac

rjags_mac.md

To install

1. Install jags: in the terminal using homebrew brew install jags
2. Install rjags: in R

install.packages("rjags")
library(rjags)

Potential issues

Compiler issues

If you run into a problem like:

configure: error: C++ compiler cannot create executables

It's probably because R is not finding the right compiler, therefore you need to create or modify the file ~/.R/Makevars

Setting the correct CC and CXX, in my case:

CC=clang
CXX=clang++

Do this and then retry install.packages("rjags") or devtools::install_url.

Non-default jags installation

The problem

I installed jags via homebrew. However, my homebrew is setup on my home directory (/Users/casallas/homebrew) rather than the default, /usr/local.

When I do

install.packages("rjags")

everything works fine, except that loading the library doesn't work:

library(rjags)
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/casallas/Library/R/3.0/library/rjags/libs/rjags.so':
  dlopen(/Users/casallas/Library/R/3.0/library/rjags/libs/rjags.so, 10): Library not loaded: /usr/local/lib/libjags.3.dylib
  Referenced from: /Users/casallas/Library/R/3.0/library/rjags/libs/rjags.so
  Reason: image not found
Error: package or namespace load failed for ‘rjags’

As you can see, rjags is expecting jags to be in /usr/local.

The solution

The easiest solution is to install rjags from source, using devtools::install_url with the following configure.args, as specified in rjags README:

devtools::install_url("http://sourceforge.net/projects/mcmc-jags/files/rjags/3/rjags_3-2.tar.gz",
                      args="--configure-args='--with-jags-include=/Users/casallas/homebrew/opt/jags/include/JAGS        
                                              --with-jags-lib=/Users/casallas/homebrew/opt/jags/lib'
                            "
                      )

Cannot install rjags either. Solutions above do not work:

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rjags’:
.onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/svacchanda/Library/R/powerpc/4.1/library/00LOCK-rjags/00new/rjags/libs/rjags.so':
dlopen(/Users/svacchanda/Library/R/powerpc/4.1/library/00LOCK-rjags/00new/rjags/libs/rjags.so, 10): Symbol not found: __ZN4jags5Model12rngFactoriesB5cxx11Ev
Referenced from: /Users/svacchanda/Library/R/powerpc/4.1/library/00LOCK-rjags/00new/rjags/libs/rjags.so
Expected in: dynamic lookup

Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘/Users/svacchanda/Library/R/powerpc/4.1/library/rjags’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/rD/rDeCM6SDHv8daLCecrRmrU+++TI/-Tmp-//RtmpgawayR/file130455010bb8a/rjags_4-4.tar.gz’ had non-zero exit status

MAC with M1 用不了，不用试了，建议换成window

Easiest way to install native arm64 jags:

brew install pkg-config jags
/Applications/RStudio.app/Contents/MacOS/RStudio
install.packages("rjags", type="source")

It is important to launch RStudio from a terminal and not the app directly, because otherwise the homebrew bin path will not be added to your PATH, and installation of rjags will fail.

Thanks a lot. This works on my computer.

Unfortunately, I am having an issue with installing RJAGS on Mac OS Big Sur, 2018 Mac Pro, Intel I9.
Running R 4.1.1. I have installed JAGS and I am able to run that program independently.

I also worked through the devtools include option mentioned above but still no luck. Any thoughts?

Approach 1

>install.packages("rjags")
* installing *source* package ‘rjags’ ...
** package ‘rjags’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
configure: Setting compile and link flags according to pkg-config
configure: Compile flags are -I/usr/local/include/JAGS
configure: Link flags are -L/usr/local/lib -ljags
checking for gcc... /usr/local/bin/gcc-11
checking whether we are using the GNU C compiler... no
checking whether /usr/local/bin/gcc-11 accepts -g... no
checking for /usr/local/bin/gcc-11 option to accept ISO C89... unsupported
checking for jags_version in -ljags... yes
checking version of JAGS library... OK
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/unix/zzz.R
** libs
/usr/local/bin/gcc-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
/usr/local/bin/g++-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS   -I/usr/local/include   -fPIC  -Wall -g -O2  -c jags.cc -o jags.o
/usr/local/bin/g++-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS   -I/usr/local/include   -fPIC  -Wall -g -O2  -c parallel.cc -o parallel.o
/usr/local/bin/g++-11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rjags.so init.o jags.o parallel.o -L/usr/local/lib -ljags -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rjags’:
 .onLoad failed in loadNamespace() for 'rjags', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so, 10): Symbol not found: __ZN4jags11SimpleRangeC1ERKSt6vectorIiSaIiEES5_
  Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjags’

The downloaded source packages are in
	‘/private/var/folders/_3/8v09s_c91fs5myl646c2_ts80000gp/T/Rtmp0930vW/downloaded_packages’
Warning message:
In install.packages("rjags") :
  installation of package ‘rjags’ had non-zero exit status

Approach 2: Devtools

>devtools::install_url("http://sourceforge.net/projects/mcmc-jags/files/rjags/4/rjags_4-4.tar.gz",
                      args="--configure-args='--with-jags-include=/usr/local/include/JAGS 
                                                                 --with-jags-lib=/usr/local/opt/jags/lib'
                            ")

Downloading package from url: http://sourceforge.net/projects/mcmc-jags/files/rjags/4/rjags_4-4.tar.gz
✓  checking for file ‘/private/var/folders/_3/8v09s_c91fs5myl646c2_ts80000gp/T/Rtmpark1rv/remotes3785557112a/rjags/DESCRIPTION’ ...
─  preparing ‘rjags’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘rjags_4-4.tar.gz’
   
* installing *source* package ‘rjags’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
configure: Setting compile and link flags according to pkg-config
configure: Compile flags are -I/usr/local/include/JAGS
configure: Link flags are -L/usr/local/lib -ljags
checking for gcc... /usr/local/bin/gcc-11
checking whether we are using the GNU C compiler... no
checking whether /usr/local/bin/gcc-11 accepts -g... no
checking for /usr/local/bin/gcc-11 option to accept ISO C89... unsupported
checking for jags_version in -ljags... yes
checking version of JAGS library... OK
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/unix/zzz.R
** libs
/usr/local/bin/g++-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS   -I/usr/local/include   -fPIC  -Wall -g -O2  -c jags.cc -o jags.o
jags.cc: In function 'jags::SimpleRange makeRange(SEXP, SEXP)':
jags.cc:213:29: warning: catching polymorphic type 'class std::logic_error' by value [-Wcatch-value=]
  213 |     catch (std::logic_error except) {
      |                             ^~~~~~
/usr/local/bin/g++-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS   -I/usr/local/include   -fPIC  -Wall -g -O2  -c parallel.cc -o parallel.o
/usr/local/bin/g++-11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/local/lib -ljags -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rjags’:
 .onLoad failed in loadNamespace() for 'rjags', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so, 10): Symbol not found: __ZN4jags11SimpleRangeC1ERKSt6vectorIiSaIiEES5_
  Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjags’
Warning messages:
1: In i.p(...) :
  installation of package ‘/var/folders/_3/8v09s_c91fs5myl646c2_ts80000gp/T//Rtmpark1rv/file3781530638c/rjags_4-4.tar.gz’ had non-zero exit status
2: 1 components of `...` were not used.

We detected these problematic arguments:
* `args`

Did you misspecify an argument? 

use the R vision of intel ，just this way 发自我的iPhone

…

------------------ Original ------------------ From: Kumar MS ***@***.***> Date: Fri,Apr 22,2022 9:23 PM To: casallas ***@***.***> Cc: peijianying ***@***.***>, Comment ***@***.***> Subject: Re: casallas/rjags_mac.md @mskb01 commented on this gist. Unfortunately, I am having an issue with installing RJAGS on Mac OS Big Sur, 2018 Mac Pro, Intel I9. Running R 4.1.1 * installing *source* package ‘rjags’ ... ** package ‘rjags’ successfully unpacked and MD5 sums checked ** using staged installation checking for pkg-config... /usr/local/bin/pkg-config configure: Setting compile and link flags according to pkg-config configure: Compile flags are -I/usr/local/include/JAGS configure: Link flags are -L/usr/local/lib -ljags checking for gcc... /usr/local/bin/gcc-11 checking whether we are using the GNU C compiler... no checking whether /usr/local/bin/gcc-11 accepts -g... no checking for /usr/local/bin/gcc-11 option to accept ISO C89... unsupported checking for jags_version in -ljags... yes checking version of JAGS library... OK configure: creating ./config.status config.status: creating src/Makevars configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/unix/zzz.R ** libs /usr/local/bin/gcc-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o /usr/local/bin/g++-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS -I/usr/local/include -fPIC -Wall -g -O2 -c jags.cc -o jags.o /usr/local/bin/g++-11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include/JAGS -I/usr/local/include -fPIC -Wall -g -O2 -c parallel.cc -o parallel.o /usr/local/bin/g++-11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rjags.so init.o jags.o parallel.o -L/usr/local/lib -ljags -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘rjags’: .onLoad failed in loadNamespace() for 'rjags', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so': dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so, 10): Symbol not found: __ZN4jags11SimpleRangeC1ERKSt6vectorIiSaIiEES5_ Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-rjags/00new/rjags/libs/rjags.so Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rjags’ The downloaded source packages are in ‘/private/var/folders/_3/8v09s_c91fs5myl646c2_ts80000gp/T/Rtmp0930vW/downloaded_packages’ Warning message: In install.packages("rjags") : installation of package ‘rjags’ had non-zero exit status — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[Kumailwasif] your solution worked for me thank you!

I was able to get around the load library error after installing jags with home-brew by installing rjags from source like so:

install.packages("rjags",type = "source")