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.
Am 04.11.2015 um 20:08 schrieb 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 > 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)On FreeBSD, I get the following, when I try to load package R2jags: library(R2jags) Lade n?tiges Paket: rjags Lade n?tiges 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> > 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.
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
On 11/4/2015 2:08 PM, Evan Cooch wrote:> 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 > >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: [root at 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
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.
Am 04.11.2015 um 21:36 schrieb Evan Cooch:> > > On 11/4/2015 2:08 PM, Evan Cooch wrote: >> 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 >> >> > > 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?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.> > > 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: > > [root at 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