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problem with rjags installation in ubuntu 14.04

2 messages · kenrichardson, Michael Rutter

#
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
#
On 09/29/2017 04:54 PM, kenrichardson wrote:
Ken,

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