kenrichardson
2017-Sep-29 20:54 UTC
[R-sig-Debian] problem with rjags installation in ubuntu 14.04
Hello folks Earlier versions of jags and rjags installed on my system without any difficulty, but I'm having trouble with jags version 4.3.0-1ubuntu2~ubuntu14.04.1~ppa1 (from Michael Rutter's R ppa) and rjags version 4.6. The call to install.packages() I always used successfully now produces the error "cannot link to JAGS library in /usr/lib/x86_64-linux-gnu."? shown below I wondered if the location of jags headers, libraries, and modules om my system might be in non-standard places, so after locating them (with dpkg -L jags and /sbin/ldconfig -p | grep jags - ) I tried install.packages("rjags", configure.args="--with-jags-include=/usr/include/JAGS --with-jags-lib=/usr/lib/x86_64-linux-gnu --with-jags-modules=/usr/lib/x86_64-linux-gnu/JAGS/modules-4") which unfortunately produced the same result. Any advice on how to sort this out would be appreciated. For example I could always try compiling both jags and/or rjags and hardcoding the location of jags libraries, but maybe there's a simpler way. sessioninfo() and library() output are also shown below, but if other information is required please let me know Regards Ken ----------------------------------------------- install.packages("rjags") Installing package into ?/home/krichardson/R/x86_64-pc-linux-gnu-library/3.4? (as ?lib? is unspecified) Warning: unable to access index for repository //http://cran.stat.auckland.ac.nz/src/contrib: ? cannot open URL '//http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES' trying URL 'http://cran.r-project.org/src/contrib/rjags_4-6.tar.gz' Content type 'application/x-gzip' length 71719 bytes (70 KB) =================================================downloaded 70 KB Loading required package: grDevices Loading required package: graphics Loading required package: stats Loading required package: utils Loading required package: nlme This is mgcv 1.8-22. For overview type 'help("mgcv-package")'. * installing *source* package ?rjags? ... ** package ?rjags? successfully unpacked and MD5 sums checked checking for pkg-config... /usr/bin/pkg-config configure: Setting compile and link flags according to pkg-config configure: Compile flags are -I/usr/include/JAGS configure: Link flags are -ljags checking for gcc... gcc -std=gnu99 checking whether we are using the GNU C compiler... no checking whether gcc -std=gnu99 accepts -g... no checking for gcc -std=gnu99 option to accept ISO C89... unsupported checking for jags_version in -ljags... no configure: error: "cannot link to JAGS library in /usr/lib/x86_64-linux-gnu." ERROR: configuration failed for package ?rjags? <snip> In install.packages("rjags") : ?installation of package ?rjags? had non-zero exit status ----------------------------------- sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.0 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale: ?[1] LC_CTYPE=en_NZ.UTF-8?????? LC_NUMERIC=C LC_TIME=en_NZ.UTF-8??????? LC_COLLATE=en_NZ.UTF-8 LC_MONETARY=en_NZ.UTF-8 ?[6] LC_MESSAGES=en_NZ.UTF-8??? LC_PAPER=en_NZ.UTF-8 LC_NAME=C????????????????? LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] datasets? splines?? utils???? stats???? graphics? grDevices methods?? base other attached packages: [1] xtable_1.7-1 mgcv_1.8-22? nlme_3.1-131 MASS_7.3-47 loaded via a namespace (and not attached): [1] compiler_3.4.1? Matrix_1.2-11?? grid_3.4.1 lattice_0.20-35 ------ library(help="rjags") Description: Package:????????????? rjags Version:????????????? 4-6 Date:???????????????? 2016-02-19 Title:??????????????? Bayesian Graphical Models using MCMC Authors at R:??????????? c(person("Martyn", "Plummer", role=c("aut","cre"), email="plummerm at iarc.fr"), person("Alexey", "Stukalov", role="ctb"), ????????????????????? person("Matt", "Denwood", role="ctb")) Depends:????????????? R (>= 2.14.0), coda (>= 0.13) SystemRequirements:?? JAGS 4.x.y URL:????????????????? http://mcmc-jags.sourceforge.net Suggests:???????????? tcltk Description:????????? Interface to the JAGS MCMC library. License:????????????? GPL (== 2) NeedsCompilation:???? yes Packaged:???????????? 2016-02-19 13:31:22 UTC; martyn Author:?????????????? Martyn Plummer [aut, cre], Alexey Stukalov [ctb], Matt Denwood [ctb] Maintainer:?????????? Martyn Plummer <plummerm at iarc.fr> Repository:?????????? CRAN Date/Publication:???? 2016-02-19 23:59:59 Built:??????????????? R 3.2.5; x86_64-pc-linux-gnu; "Sun, 01 May 2016 18:23:42 +0000"; unix Index: LINE??????????????????? Linear regression example adapt?????????????????? Adaptive phase for JAGS models coda.samples??????????? Generate posterior samples in mcmc.list format dic.samples???????????? Generate penalized deviance samples diffdic???????????????? Differences in penalized deviance jags.model????????????? Create a JAGS model object jags.samples??????????? Generate posterior samples list.factories????????? Advanced control over JAGS load.module???????????? Dynamically load JAGS modules mcarray.object????????? Objects for representing MCMC output parallel.seeds????????? Get initial values for parallel RNGs read.jagsdata?????????? Read data files for jags models rjags-deprecated??????? Deprecated Functions in the rjags package rjags-package?????????? Bayesian graphical models using MCMC update.jags???????????? Update jags models variable.names.jags???? Functions for manipulating jags model objects
Michael Rutter
2017-Sep-30 20:13 UTC
[R-sig-Debian] problem with rjags installation in ubuntu 14.04
On 09/29/2017 04:54 PM, kenrichardson wrote:> Hello folks > > Earlier versions of jags and rjags installed on my system without any > difficulty, but I'm having trouble with jags version > 4.3.0-1ubuntu2~ubuntu14.04.1~ppa1 (from Michael Rutter's R ppa) and > rjags version 4.6. > > The call to install.packages() I always used successfully now produces > the error "cannot link to JAGS library in /usr/lib/x86_64-linux-gnu." > shown below > > I wondered if the location of jags headers, libraries, and modules om my > system might be in non-standard places, so after locating them (with > dpkg -L jags and /sbin/ldconfig -p | grep jags - ) I tried > > install.packages("rjags", > configure.args="--with-jags-include=/usr/include/JAGS > --with-jags-lib=/usr/lib/x86_64-linux-gnu > --with-jags-modules=/usr/lib/x86_64-linux-gnu/JAGS/modules-4") > > which unfortunately produced the same result. > > Any advice on how to sort this out would be appreciated. For example I > could always try compiling both jags and/or rjags and hardcoding the > location of jags libraries, but maybe there's a simpler way. > > sessioninfo() and library() output are also shown below, but if other > information is required please let me know > > Regards KenKen, I experienced something similar in the past couple of days, so I recompiled rjags against all the current versions of the other packages. I was able to successfully install r-cran-rjags and use it from the PPA. Please try installing with apt-get again and let me know if you have any issues. Michael