Greetings, I wonder if anyone can offer any help or advice--even direction to an appropriate source of advice. I am trying to install rjags 1.0.1 on Mac OS X 10.5 (see http://www-fis.iarc.fr/~martyn/software/jags/). I have R.app 2.6.1 installed. JAGS 1.0.1 is apparently successfully installed. I (think I) know this because when I type 'jags' into Terminal, I get the following: Macintosh:Desktop ljs$ jags Welcome to JAGS 1.0.1 on Thu Dec 27 20:56:09 2007 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod Loading module: bugs . However, when I try to install rjags, I get the following problem. Macintosh:Desktop ljs$ sudo R CMD INSTALL rjags_1.0.1-1.tar.gz Password: * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'rjags' ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for JAGS... configure: error: Package requirements (jags = 1.0.1) were not met: No package 'jags' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. ERROR: configuration failed for package 'rjags' ** Removing '/Library/Frameworks/R.framework/Resources/library/rjags' I am really not sure what the problem is. I have (I think) set the proper environment variables correctly. See below: Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Macintosh:Desktop ljs$ echo $PKG_CONFIG_PATH /usr/local/bin I should say that I had many other problems along the way--gfortran not originally installed properly, R CMD INSTALL couldn't find pkg-config. However, the above description shows the problems remaining even after I have done a little homework. Best wishes, Lindsay Stirton
Trying to install rjags on Mac OS X 10.5
6 messages · Lindsay Stirton, Brian Ripley, Vincent Nijs +1 more
Macintosh:Desktop ljs$ echo $PKG_CONFIG_PATH /usr/local/bin
is unlikely to be correct. A typical Linux setting is PKG_CONFIG_PATH=/usr/local/lib64/pkgconfig:/usr/lib64/pkgconfig and on my Mac the pkg-config files are in /usr/local/lib/pkgconfig and /usr/lib/pkgconfig. Most likely it would work if PKG_CONFIG_PATH is not set, so try that first.
On Sun, 30 Dec 2007, Lindsay Stirton wrote:
Greetings, I wonder if anyone can offer any help or advice--even direction to an appropriate source of advice. I am trying to install rjags 1.0.1 on Mac OS X 10.5 (see http://www-fis.iarc.fr/~martyn/software/jags/). I have R.app 2.6.1 installed. JAGS 1.0.1 is apparently successfully installed. I (think I) know this because when I type 'jags' into Terminal, I get the following: Macintosh:Desktop ljs$ jags Welcome to JAGS 1.0.1 on Thu Dec 27 20:56:09 2007 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod Loading module: bugs . However, when I try to install rjags, I get the following problem. Macintosh:Desktop ljs$ sudo R CMD INSTALL rjags_1.0.1-1.tar.gz Password: * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'rjags' ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for JAGS... configure: error: Package requirements (jags = 1.0.1) were not met: No package 'jags' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. ERROR: configuration failed for package 'rjags' ** Removing '/Library/Frameworks/R.framework/Resources/library/rjags' I am really not sure what the problem is. I have (I think) set the proper environment variables correctly. See below: Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Macintosh:Desktop ljs$ echo $PKG_CONFIG_PATH /usr/local/bin I should say that I had many other problems along the way--gfortran not originally installed properly, R CMD INSTALL couldn't find pkg-config. However, the above description shows the problems remaining even after I have done a little homework. Best wishes, Lindsay Stirton
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Quoting Prof Brian Ripley <ripley at stats.ox.ac.uk>:
and on my Mac the pkg-config files are in /usr/local/lib/pkgconfig and /usr/lib/pkgconfig. Most likely it would work if PKG_CONFIG_PATH is not set, so try that first.
Thanks--but this still doesn't seem to get me anywhere (see below). Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Macintosh:Desktop ljs$ whereis jags Macintosh:Desktop ljs$ Last login: Sun Dec 30 17:40:41 on ttys001 Macintosh:~ ljs$ echo $PKG_CONFIG_PATH Macintosh:~ ljs$ cd Desktop/ Macintosh:Desktop ljs$ sudo R CMD INSTALL rjags_1.0.1-1.tar.gz * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'rjags' ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for JAGS... configure: error: Package requirements (jags = 1.0.1) were not met: No package 'jags' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. ERROR: configuration failed for package 'rjags' ** Removing '/Library/Frameworks/R.framework/Resources/library/rjags' Macintosh:Desktop ljs$ Would I be right in thinking that the problem is not in fiding the path to pkg-config but in finding JAGS? I have Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Best wishes, Lindsay Stirton
I had the same issue on my Mac. After install pkg-config from MacPorts Martyn suggested to add the following 2 lines to my .bashrc file: export LD_LIBRARY_PATH="/usr/local/lib" export PKG_CONFIG_PATH="/usr/local/lib/pkgconfig" Everything worked after that. Best, Vincent On Dec 30, 11:56 am, Lindsay Stirton
<Lindsay.Stir... at manchester.ac.uk> wrote:
Quoting Prof Brian Ripley <rip... at stats.ox.ac.uk>:
and on my Mac the pkg-config files are in /usr/local/lib/pkgconfig and /usr/lib/pkgconfig. Most likely it would work if PKG_CONFIG_PATH is not set, so try that first.
Thanks--but this still doesn't seem to get me anywhere (see below). Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Macintosh:Desktop ljs$ whereis jags Macintosh:Desktop ljs$ Last login: Sun Dec 30 17:40:41 on ttys001 Macintosh:~ ljs$ echo $PKG_CONFIG_PATH Macintosh:~ ljs$ cd Desktop/ Macintosh:Desktop ljs$ sudo R CMD INSTALL rjags_1.0.1-1.tar.gz * Installing to library '/Library/Frameworks/R.framework/Resources/library' * Installing *source* package 'rjags' ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for JAGS... configure: error: Package requirements (jags = 1.0.1) were not met: No package 'jags' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. ERROR: configuration failed for package 'rjags' ** Removing '/Library/Frameworks/R.framework/Resources/library/rjags' Macintosh:Desktop ljs$ Would I be right in thinking that the problem is not in fiding the path to pkg-config but in finding JAGS? I have Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Best wishes, Lindsay Stirton
______________________________________________ R-h... at r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hi Lindsay, Did have some difficulties as well, but got it to work using Xcode3.0, Apple's gcc4.2preview release and gfortran 4.2.1 from Simon's web site. This was on R-devel though, on a Mac Intel. Can it find the jags executable say from your home directory? Have you tried 'make check' in the classic-bugs/vol1 or vol2 example dirs (in the Terminal)? That would indeed confirm jags is running fine. For rjags, I am a bit worried about the /opt/... . Did you at some point install software from Fink or Darwin ports? Until I installed the above newer toolset, I had never been able to get rjags to work. Of course you don't really need rjags, only coda. I have also installed the package 'arm' and the packages arm depends on (Matrix, lattice, lme4, R2WinBugs). If it would help I can send you a 'template' dir for the line example that does not use rjags. A dependency I ran into was coda v 13.1, as of a couple of days ago not available as a binary package, but available as a source package on CRAN. Rob
On Dec 30, 2007, at 8:27 AM, Lindsay Stirton wrote:
Greetings, I wonder if anyone can offer any help or advice--even direction to an appropriate source of advice. I am trying to install rjags 1.0.1 on Mac OS X 10.5 (see http://www-fis.iarc.fr/~martyn/software/jags/). I have R.app 2.6.1 installed. JAGS 1.0.1 is apparently successfully installed. I (think I) know this because when I type 'jags' into Terminal, I get the following: Macintosh:Desktop ljs$ jags Welcome to JAGS 1.0.1 on Thu Dec 27 20:56:09 2007 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod Loading module: bugs . However, when I try to install rjags, I get the following problem. Macintosh:Desktop ljs$ sudo R CMD INSTALL rjags_1.0.1-1.tar.gz Password: * Installing to library '/Library/Frameworks/R.framework/Resources/ library' * Installing *source* package 'rjags' ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for JAGS... configure: error: Package requirements (jags = 1.0.1) were not met: No package 'jags' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. ERROR: configuration failed for package 'rjags' ** Removing '/Library/Frameworks/R.framework/Resources/library/rjags' I am really not sure what the problem is. I have (I think) set the proper environment variables correctly. See below: Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Macintosh:Desktop ljs$ echo $PKG_CONFIG_PATH /usr/local/bin I should say that I had many other problems along the way--gfortran not originally installed properly, R CMD INSTALL couldn't find pkg-config. However, the above description shows the problems remaining even after I have done a little homework. Best wishes, Lindsay Stirton
______________________________________________ R-help at r-project.org 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.
Thanks Rob, Since I already had Xcode 3.0, I re-installed gfortran (from the R website, not from the .dmg) and gcc4.2.1 preview. I am afraid the outcome was the same, i.e. jags 1.0.1 not found. Yes I do use Macports (and formery used Fink, which is still installed). What issues does this raise? On your suggestion, I made sure that both were up to date--still no success. Your offer to send me a template directory to figure things out from is very much appreciated. Yes please! Lindsay Quoting Rob Goedman <goedman at mac.com>:
Hi Lindsay, Did have some difficulties as well, but got it to work using Xcode3.0, Apple's gcc4.2preview release and gfortran 4.2.1 from Simon's web site. This was on R-devel though, on a Mac Intel. Can it find the jags executable say from your home directory? Have you tried 'make check' in the classic-bugs/vol1 or vol2 example dirs (in the Terminal)? That would indeed confirm jags is running fine. For rjags, I am a bit worried about the /opt/... . Did you at some point install software from Fink or Darwin ports? Until I installed the above newer toolset, I had never been able to get rjags to work. Of course you don't really need rjags, only coda. I have also installed the package 'arm' and the packages arm depends on (Matrix, lattice, lme4, R2WinBugs). If it would help I can send you a 'template' dir for the line example that does not use rjags. A dependency I ran into was coda v 13.1, as of a couple of days ago not available as a binary package, but available as a source package on CRAN. Rob On Dec 30, 2007, at 8:27 AM, Lindsay Stirton wrote:
Greetings, I wonder if anyone can offer any help or advice--even direction to an appropriate source of advice. I am trying to install rjags 1.0.1 on Mac OS X 10.5 (see http://www-fis.iarc.fr/~martyn/software/jags/). I have R.app 2.6.1 installed. JAGS 1.0.1 is apparently successfully installed. I (think I) know this because when I type 'jags' into Terminal, I get the following: Macintosh:Desktop ljs$ jags Welcome to JAGS 1.0.1 on Thu Dec 27 20:56:09 2007 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod Loading module: bugs . However, when I try to install rjags, I get the following problem. Macintosh:Desktop ljs$ sudo R CMD INSTALL rjags_1.0.1-1.tar.gz Password: * Installing to library '/Library/Frameworks/R.framework/Resources/ library' * Installing *source* package 'rjags' ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for JAGS... configure: error: Package requirements (jags = 1.0.1) were not met: No package 'jags' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. ERROR: configuration failed for package 'rjags' ** Removing '/Library/Frameworks/R.framework/Resources/library/rjags' I am really not sure what the problem is. I have (I think) set the proper environment variables correctly. See below: Macintosh:Desktop ljs$ which jags /usr/local/bin/jags Macintosh:Desktop ljs$ echo $PKG_CONFIG_PATH /usr/local/bin I should say that I had many other problems along the way--gfortran not originally installed properly, R CMD INSTALL couldn't find pkg-config. However, the above description shows the problems remaining even after I have done a little homework. Best wishes, Lindsay Stirton
______________________________________________ R-help at r-project.org 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.