Re: [R] rjags installation trouble
On 12-01-11 11:45 AM, Martyn Plummer wrote: > It looks like you are cross-linking to an earlier version of the JAGS > library at run time. Check > > /sbin/ldconfig -p | grep jags - > > When compiling rjags, you can hard-code the location of the jags library > using the [GNU-specific] configure option --enable-rpath. > > Martyn Thanks. I managed to sort it out by assiduously cleaning out all older versions of JAGS ... Ben Bolker > > On Tue, 2012-01-10 at 10:40 -0500, Ben Bolker wrote: >> Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0 >> installed on Ubuntu 10.04, with r-devel ... the bottom line is that it >> fails while loading with >> >> /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb >> >> Has anyone else seen this or is it a glitch somewhere in my system? >> >> thanks >> Ben Bolker >> >> == >> bolker@ubuntu-10-new:~/R/pkgs/rjags$ jags >> Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012 >> JAGS is free software and comes with ABSOLUTELY NO WARRANTY >> Loading module: basemod: ok >> Loading module: bugs: ok >> . >> >> === >> >> install.packages("rjags") starts out fine: >> >> Installing package(s) into >> ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’ >> (as ‘lib’ is unspecified) >> trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz' >> Content type 'application/x-gzip' length 66429 bytes (64 Kb) >> opened URL >> == >> downloaded 64 Kb >> >> * installing *source* package ‘rjags’ ... >> ** package ‘rjags’ successfully unpacked and MD5 sums checked >> checking for prefix by checking for jags... /usr/bin/jags >> >> [snip snip] >> >> ** libs >> g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS >> -I/usr/local/include-fpic -g -O2 -c jags.cc -o jags.o >> g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS >> -I/usr/local/include-fpic -g -O2 -c parallel.cc -o parallel.o >> g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags >> installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs >> ** R >> >> [snip snip] >> >> but fails at: >> >> ** building package indices >> Error : .onLoad failed in loadNamespace() for 'rjags', details: >> call: dyn.load(file, DLLpath = DLLpath, ...) >> error: unable to load shared object >> '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so': >> >> /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so: >> undefined symbol: _ZN7Console15checkAdaptationERb >> ERROR: installing package indices failed >> * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’ >> * restoring previous >> ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’ >> >> The downloaded source packages are in >> ‘/tmp/RtmpSKHIz5/downloaded_packages’ >> Warning message: >> In install.packages("rjags") : >> installation of package ‘rjags’ had non-zero exit status >>> sessionInfo() >> R Under development (unstable) (2012-01-01 r58032) >> Platform: i686-pc-linux-gnu (32-bit) >> >> locale: >> [1] LC_CTYPE=en_CA.utf8 LC_NUMERIC=C >> [3] LC_TIME=en_CA.utf8LC_COLLATE=en_CA.utf8 >> [5] LC_MONETARY=en_CA.utf8LC_MESSAGES=en_CA.utf8 >> [7] LC_PAPER=CLC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.0 > > > --- > This message and its attachments are strictly confiden...{{dropped:8}} __ R-help@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.
Re: [R] rjags installation trouble
It looks like you are cross-linking to an earlier version of the JAGS library at run time. Check /sbin/ldconfig -p | grep jags - When compiling rjags, you can hard-code the location of the jags library using the [GNU-specific] configure option --enable-rpath. Martyn On Tue, 2012-01-10 at 10:40 -0500, Ben Bolker wrote: > Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0 > installed on Ubuntu 10.04, with r-devel ... the bottom line is that it > fails while loading with > > /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb > > Has anyone else seen this or is it a glitch somewhere in my system? > > thanks > Ben Bolker > > == > bolker@ubuntu-10-new:~/R/pkgs/rjags$ jags > Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012 > JAGS is free software and comes with ABSOLUTELY NO WARRANTY > Loading module: basemod: ok > Loading module: bugs: ok > . > > === > > install.packages("rjags") starts out fine: > > Installing package(s) into > ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’ > (as ‘lib’ is unspecified) > trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz' > Content type 'application/x-gzip' length 66429 bytes (64 Kb) > opened URL > == > downloaded 64 Kb > > * installing *source* package ‘rjags’ ... > ** package ‘rjags’ successfully unpacked and MD5 sums checked > checking for prefix by checking for jags... /usr/bin/jags > > [snip snip] > > ** libs > g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS > -I/usr/local/include-fpic -g -O2 -c jags.cc -o jags.o > g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS > -I/usr/local/include-fpic -g -O2 -c parallel.cc -o parallel.o > g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags > installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs > ** R > > [snip snip] > > but fails at: > > ** building package indices > Error : .onLoad failed in loadNamespace() for 'rjags', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: unable to load shared object > '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so': > > /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so: > undefined symbol: _ZN7Console15checkAdaptationERb > ERROR: installing package indices failed > * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’ > * restoring previous > ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’ > > The downloaded source packages are in > ‘/tmp/RtmpSKHIz5/downloaded_packages’ > Warning message: > In install.packages("rjags") : > installation of package ‘rjags’ had non-zero exit status > > sessionInfo() > R Under development (unstable) (2012-01-01 r58032) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_CA.utf8 LC_NUMERIC=C > [3] LC_TIME=en_CA.utf8LC_COLLATE=en_CA.utf8 > [5] LC_MONETARY=en_CA.utf8LC_MESSAGES=en_CA.utf8 > [7] LC_PAPER=CLC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.15.0 --- This message and its attachments are strictly confidenti...{{dropped:8}} __ R-help@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.
[R] rjags installation trouble
Trying to install latest rjags (3-5) from CRAN with JAGS 3.2.0 installed on Ubuntu 10.04, with r-devel ... the bottom line is that it fails while loading with /libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb Has anyone else seen this or is it a glitch somewhere in my system? thanks Ben Bolker == bolker@ubuntu-10-new:~/R/pkgs/rjags$ jags Welcome to JAGS 3.2.0 on Tue Jan 10 10:38:31 2012 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod: ok Loading module: bugs: ok . === install.packages("rjags") starts out fine: Installing package(s) into ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library’ (as ‘lib’ is unspecified) trying URL 'http://probability.ca/cran/src/contrib/rjags_3-5.tar.gz' Content type 'application/x-gzip' length 66429 bytes (64 Kb) opened URL == downloaded 64 Kb * installing *source* package ‘rjags’ ... ** package ‘rjags’ successfully unpacked and MD5 sums checked checking for prefix by checking for jags... /usr/bin/jags [snip snip] ** libs g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS -I/usr/local/include-fpic -g -O2 -c jags.cc -o jags.o g++ -I/usr/local/lib/R/include -DNDEBUG -I/usr/include/JAGS -I/usr/local/include-fpic -g -O2 -c parallel.cc -o parallel.o g++ -shared -L/usr/local/lib -o rjags.so jags.o parallel.o -L/usr/lib -ljags installing to /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs ** R [snip snip] but fails at: ** building package indices Error : .onLoad failed in loadNamespace() for 'rjags', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so': /mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags/libs/rjags.so: undefined symbol: _ZN7Console15checkAdaptationERb ERROR: installing package indices failed * removing ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’ * restoring previous ‘/mnt/hgfs/bolker/Documents/LOCAL/lib/R/site-library/rjags’ The downloaded source packages are in ‘/tmp/RtmpSKHIz5/downloaded_packages’ Warning message: In install.packages("rjags") : installation of package ‘rjags’ had non-zero exit status > sessionInfo() R Under development (unstable) (2012-01-01 r58032) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_CA.utf8 LC_NUMERIC=C [3] LC_TIME=en_CA.utf8LC_COLLATE=en_CA.utf8 [5] LC_MONETARY=en_CA.utf8LC_MESSAGES=en_CA.utf8 [7] LC_PAPER=CLC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.15.0 __ R-help@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.