gmane.comp.lang.r.debian

How to set symbolic link correctly so that LaTeXfinds Sweave?

Marius Hofert — 2012-05-25T15:20:11

Hi,

I recently switched from Mac OS X (after 7 years) to Xubuntu 12.04 and I am
quite happy with it so far. I first installed R from source but I was somehow
missing certain things and I thus decided (after a new Xubuntu installation
which I had to make due to other reasons) to install R the "Ubuntu way":

,----[ R installation: ]
| 1) sudo emacs /etc/apt/sources.list
| 2) add:
|    deb http://stat.ethz.ch/CRAN/bin/linux/ubuntu precise/
| 3) in a terminal:
|    gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
|    gpg -a --export E084DAB9 | sudo apt-key add -
| 4) the "standard way":
|    sudo apt-get update
|    sudo apt-get install r-base
|    sudo apt-get install r-base-dev
|    sudo apt-get build-dep r-base-dev
`----

,----[ .libPaths() shows: ]
| "/usr/local/lib/R/site-library"
| "/usr/lib/R/site-library"
| "/usr/lib/R/library"
`----

I realized that the TeXLive Version which can be installed via the Ubuntu Software
Center is quite outdated (2009) for my needs. I therefore installed TeXLive 2011
like this:

,----[ TeXLive 2011 installation: ]
| 1) download install-tl-unx.tar.gz from http://www.tug.org/texlive/acquire-netinstall.html
| 2) tar -xzf install-tl-unx.tar.gz
| 3) sudo ./install-tl # see http://www.tug.org/texlive/quickinstall.html (hit "I")
| 4) add the newly installed version to PATH (in .profile):
|    PATH=/usr/local/texlive/2011/bin/x86_64-linux:$PATH
`----

So far, so good. I can easily work with R (and TeX) and I can also Sweave a .Rnw
file (and obtain the .tex). However, if I apply pdflatex to the .tex file (I
actually use latexmk for doing this but that doesn't matter), I obtain:

,----[ error on latexmk'ing the .tex file: ]
| ERROR: LaTeX Error: File `Sweave.sty' not found.
`----

Clearly, one has to tell LaTeX where Sweave can be found. I known that on the
Mac on could set a symbolic link to make LaTeX aware of Sweave. I tried the same
under Xubuntu:

,----[ set symbolic link: ]
| cd /usr/local/texlive/2011/texmf/tex/latex
| sudo ln -s /usr/share/R/share/texmf Sweave
`----

However, I still obtain the above error. 

Some thoughts:
1) Putting Sweave.sty in the same folder as the .tex file works (of course), but
I do not want to copy Sweave.sty all the time.
2) Setting the link in /usr/local/texlive/2011/bin/x86_64-linux also led to the
same error.

How can I set up the symbolic link so that latexmk/pdflatex finds Sweave?

Cheers,

Marius

MASS is blocked for R 2.15.0

Michael Friendly — 2012-05-14T13:16:52

I updated R to R 2.15.0 via apt-get and received the message that 
r-cran-mass was blocked.
I recently tried apt-get update/ apt-get safe-upgrade and received the 
same message, for
r-cran-mass-7.3.16-1lucid0

I currently have MASS 7.3-7 installed

How can I figure out what is wrong and correct it?

thx,

Installing LaTeX class files not available in Debianpackages

Douglas Bates — 2012-05-08T15:56:10

I apologize for abusing the list somewhat but there is some connection
to R.  Several of the example files in the knitr package for R use the
tufte-handout class, which, AFAICS, is not available in Ubuntu or
Debian packages (please correct me if I am wrong).

The source files are available at tufte-latex.googlecode.com (a.k.a.
code.google.com/p/tufte-latex) and I presume they should end up in a
subdirectory of /usr/local/share/texmf or something like that.  Is
there a standard approach to adding unpackaged class files?

A guide to R packages for Ubuntu

Michael Rutter — 2012-04-27T18:11:30

As per a request, here is a brief guide to what is available to R users 
as packages in Ubuntu.

Each release of Ubuntu includes the latest version of R and the 
recommended packages.  In addition, there are approximately 80 
additional r-cran packages available in the default repositories.  The 
limitation to these packages is that they are not updated and reflect 
the current version of the program or package when that version of 
Ubuntu was released.

If you want to have current versions of R and the recommended packages, 
there are two repositories to choose from:

CRAN: http://cran.r-project.org/bin/linux/ubuntu/
Launchpad PPA: https://launchpad.net/~marutter/+archive/rrutter

Both sites have the same packages (the PPA packages are mirrored on 
CRAN), but there may be a reason to use one over the other.

CRAN Advantages:
- A local mirror may be faster in terms of internet speed.
- Older versions of the packages are available, so if an update to R or 
a core package breaks your code, you can reinstall an older version via 
synaptic or apt.

PPA Advantages:
- Quickest way to get the updates (only by about 24 hours however)
- Easy to install (sudo add-apt-repository ppa:marutter/rrutter)

If you have been using CRAN, then there is no reason to change to the 
PPA, as the same packages is provided at both locations.  I will 
continue to maintain both sites, so no need to worry about one or the 
other going away.

If you want additional packages (over 1,100), you can check out my 
cran2deb4ubuntu PPA:

https://launchpad.net/~marutter/+archive/c2d4u

In theory, this PPA has all the packages listed in the CRAN Task Views 
and any dependencies.  In practice, is has about 98% of them, as some 
packages have issues.  These packages can be installed via synaptic or 
apt (sudo apt-get install r-cran-ggplot2, for example).  The main 
advantage of this approach is that tricky Ubuntu package requirements 
will automatically be installed when installing the package.  They will 
also be automatically updated during normal Ubuntu updates, which is 
another advantage.  These packages are NOT installed when a 
install.packages("foo") command is used from within R.

One of my plans this summer/sabbatical is create documentation for the 
cran2deb4ubuntu project and give more information about what is and what 
is not available.

If you have any further questions, please let me know.
Michael

R packages for Ubuntu 12.04 LTS Precise Pangolin nowavailable

Michael Rutter — 2012-04-26T13:19:28

Ubuntu users,

The latest version of Ubuntu (12.04 LTS: Precise Pangolin) has been 
released.  Current R packages are also available from the following 
locations:

The CRAN repository
http://cran.r-project.org/bin/linux/ubuntu/

My Launchpad PPA (feeds CRAN, has a few more packages)
https://launchpad.net/~marutter/+archive/rrutter

cran2deb4ubuntu (over 1000 packages found in CRAN Taskviews, not all 
uploaded yet)
https://launchpad.net/~marutter/+archive/c2d4u

If you have any questions, please let me know.
Michael

Error installing libraries (eg RODBC) on R-2.15.0 :cannot find 'config.log'

Wolfgang Raffelsberger — 2012-04-18T16:24:49

Dear list,

as I started installing R-2.15.0 on a Red Hat 4.5.1-4 as well a Ubuntu
10.04.3 systems.
While the basic installation went fine (like the previous R-2.14.2), now
I'm having trouble installing almost one third of the additional libraries
I want (which installed flawlessly with R-2.14.2), among them RODBC for
which I show the message below (obtained on Ubuntu) :

surf_forInstallation_> R  CMD INSTALL RODBC_1.3-5.tar.gz
* installing to library '/linux/biolo/R_surf/R-2.15.0/lib64/R/library'
* installing *source* package 'RODBC' ...
** package 'RODBC' successfully unpacked and MD5 sums checked
checking for gcc...
gcc -std=gnu99
checking for C compiler default output file name... configure: error: C
compiler cannot create executables
See `config.log' for more details.
ERROR: configuration failed for package 'RODBC'
* removing '/linux/biolo/R_surf/R-2.15.0/lib64/R/library/RODBC'


In fact, I get identical messages on our Red Hat 4.5.1-4 and the Ubuntu
10.04.3 systems mentioned above.
Obviously something with our C compiler(s) didn't work out.
In order to learn more about the problem I tried to look at config.log
mentioned in the installation-message above, however, I cannot find
the file, neither in my current path nor in
 /linux/biolo/R_surf/R-2.15.0/lib64/R/library .
Obviously the RODBC directory doesn't exist any more when the installation
attempt ends.

Any hints ?
I'm new to the Debian-list, but at least I haven't seen similar (recent)
posts on R-help or the bioconductor lists.

For completeness :
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


Many thanks in advance,
Wolfgang

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
IGBMC,
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
wolfgang.raffelsberger at igbmc.fr

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Dependency problem bug with r-cran-vr

Jaisen Nedumpala — 2012-04-11T16:18:54

Hi,

I was trying to connect GRASS with R, following the guidelines described here:

http://grass.osgeo.org/wiki/R_statistics

The line in my /etc/apt/sources.list is like:

deb http://ftp.iitm.ac.in/cran/bin/linux/debian squeeze-cran/

But when I tried to install r-cran-vr, I got an unmet dependency
problem with r-cran-mass and r-cran-class.
But these two packages were already installed. Then why it happen?
--------------------------------------------------------------
jaisen< at >debian:~$ sudo apt-get install r-cran-vr
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-cran-vr : Depends: r-cran-mass but it is not going to be installed
             Depends: r-cran-class but it is not going to be installed
E: Broken packages
jaisen< at >debian:~$
--------------------------------------------------------------
Everything was nice and fine, except this one. How to fix this
problem? Please help me.

Regards,

symbol lookup error

Andreas Leha — 2012-04-06T22:56:39

Hi all,

I am on debian testing with pre-packaged R (2.14.1) installed.  I started
getting weird crashes.  Now I have a reproducible example:

# R
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

# 


Right after entering 'save(' I pressed TAB.

Any help on this would be highly appreciated.

Regards,
Andreas

Ubuntu Lucid, R 2.14.2, and ggplot2

Scott Smith — 2012-03-22T19:02:03

I've just updated to the latest R (2.14.2) on my Ubuntu Lucid box, and now the ggplot2 installed as a .deb package fails to work.

$ R -e 'library(ggplot2)'
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : 
  package ‘proto’ does not have a NAMESPACE and should be re-installed
Calls: library -> .getRequiredPackages2 -> library
Execution halted

Here is what I did to ensure the packages were up-to-date:

$ sudo apt-get update
$ sudo apt-get install r-base r-base-core r-cran-ggplot2 r-cran-proto

Here is what my sources list and dpkg list looks like:

$ cat /etc/apt/sources.list.d/r-cran.list 
deb http://cran.wustl.edu/bin/linux/ubuntu lucid/

$ dpkg -l r-base r-base-core r-cran-ggplot2 r-cran-proto
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name                      Version                   Description
+++-=========================-=========================-==================================================================
ii  r-base                    2.14.2-3lucid0            GNU R statistical computation and graphics system
ii  r-base-core               2.14.2-3lucid0            GNU R core of statistical computation and graphics system
ii  r-cran-ggplot2            0.8.9-1cran1              GNU R package "An implementation of the Grammar of
ii  r-cran-proto              0.3-9-1cran1              GNU R package "Prototype object-based programming"

Secure apt

Scott Raynaud — 2012-03-18T13:25:29

I am trying to add Michael Rutter's ppa to my
repository.  I cannot do this from the command
line.  I think I may be behind a firewall so copying
the key to a text file is my best option.  When I
search for the key at 

http://keyserver.ubuntu.com:11371/

the search fails.  Tried typing and 
cutting and pasting E084DAB9 into 
the search box without success.  How 
can I get the key?

Upgrade from 2.11.1 to 2.14.2 options?

Jim Armstrong — 2012-03-13T21:57:43

Linux kernel 2.6.18-2-pve Proxmox vm.
debian_version 6.0.4 Squeeze
sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu
locale:
C

New to R, new to Debian.

I'm trying to upgrade from 2.11.1 to 2.14 following the steps outlined in
the doc below that I found on the link.

http://www.r-project.org/ -

DEBIAN PACKAGES OF R SOFTWARE

I added this line to the sources.list file it's my closest mirror.
deb-src http://cran.wustl.edu/bin/linux/debian squeeze-cran/

Ran apt-get update and then apt-get install r-base r-base-dev
No errors returned seemed to run clean.
Ran sessionInfo() from within R and it returns 2.11.1

Am I doing something wrong?
Do I need to take a different approach?

I have this link but I'm not sure of what I need off of it. If I do need to
pull something from it.

Index of /bin/linux/debian/squeeze-cran

Thanks


    For a backport of the latest R release to squeeze, simply add something
like

     deb http://<favorite-cran-mirror>/
   bin/linux/debian squeeze-cran/

   to the file /etc/apt/sources.list on your computer and install as
   usual. Note that you need to substitute <favorite-cran-mirror> by one of
the
   mirror URLs listed in

     http://cran.r-project.org/mirrors.html

   There are binaries for the i386 and amd64 architectures. You
   can use the source packages from

     deb-src http://<favorite-cran-mirror>/bin/linux/debian squeeze-cran/

   to compile binaries for other platforms.

   With an appropriate entry in /etc/apt/sources.list, the newest R release
   can be
   installed using a command sequence like

     apt-get update
     apt-get install r-base r-base-dev

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Problem installing gWidgetsRGtk2 on Ubuntu 10.04

Karin Eitel — 2012-03-13T10:52:07

dear all,
I'm totally new to R and want to install the RQDA package.
It fails because of a dependency with gWidgetsRGtk2, which doesn't 
install because of the following:

** R
** inst
** preparing package for lazy loading
Error in eval(expr, envir, enclos) :
konnte Funktion "setRefClass" nicht finden (=could not find function 
"setRefClass")
Error : unable to load R code in package 'gWidgetsRGtk2'
ERROR: lazy loading failed for package ‘gWidgetsRGtk2’
* removing ‘/home/k/R/i486-pc-linux-gnu-library/2.10/gWidgetsRGtk2’

I have no idea what this could mean.
I tried it with R-Commander and RKWard with the same result (which is 
not surprising)
My system ist Ubuntu 10.04 (lucid) and R 2.10.1-2 which I installed with 
synaptic.

Does anyone have any suggestions?

Kind regards
karin

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ROracle package

jose luis cañadas — 2012-03-06T21:22:43

Hello everybody.

I'm a newbie in R in a debian and linux in general

I'm trying install roracle in my debian 64 bit system. I've read the
http://cran.r-project.org/web/packages/ROracle/INSTALL and I've
installed Oracel Instant Client by rpm package (using alien to deb convert).

When I try to install I write

  export LD_LIBRARY_PATH=/usr/lib/oracle/11.2/client64/lib:$LD_LIBRARY_PATH


in terminal and then I download ROracle_1.1-1.tar.gz from cran and I
type sudo R CMD INSTALL ROracle_1.1-1.tar.gz where I've downloaded the
tar.gz file.

I always get the same error
jose< at >jose-laptop:~/Descargas$ sudo R CMD INSTALL ROracle_1.1-1.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘ROracle’ ...
** package ‘ROracle’ successfully unpacked and MD5 sums checked
configure: error: OCI libraries not found
ERROR: configuration failed for package ‘ROracle’
* removing ‘/usr/local/lib/R/site-library/ROracle’

and I don't understand why. any idea?

Thanks.

PD: Really I need install ROracle for my job. please help me ;)

Time Series statistical modeling: about time lab

于涛 — 2012-03-01T09:37:24

Dear R users:

    My data sets contain response variables and state variables.But unfortunately, my state variables are not correspond one-to-one with 
the response variables，we call it time lag effects.

    How can I make the data correspond? Please give some advice! 

    Thanks!

Robin

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Broken R

Ed Siefker — 2012-02-29T18:33:25

Hi, I am running Debian Sid. I am having
trouble with the R packages.

Executing 'help()' or 'demo()' launches 'most' with no text.
'help.start()' works properly.

When I try to install a package, I get the following problem:

*********************************************************************
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning: unable to access index for repository
http://cran.cnr.Berkeley.edu/src/contrib
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘ctv’ is not available (for R version 2.14.2)
*********************************************************************

The system in question has a direct connection to the internet.
I can browse to the repository and find the ctv package.
The user has read and write permissions on '/usr/local/lib/R/site-library'

I don't know what to do here.  Can someone advise?

readVECT6 and readRAST6 fails with R and GRASS 7 ???

Eric Momsen — 2012-02-20T17:28:00

Hello all,

I'm having troubles getting R to load data from GRASS 7.  I suspect I have
installed something wrong, but can't figure out what.  Any suggestions for
what I could look for or how to trouble shoot this?  Thanks in advance for
any help!

After having other issues last week, we have upgraded Debian to the testing
version.  The other problems are solved, but now I can't get readVECT6 and
readRAST6 to work.

I have followed the instructions at http://grass.osgeo.org/wiki/R_statistics -
first under the Debian instructions to use apt-get to install some of the
packages and  others via R.  After that didn't work, I tried the ctv
package to install the Spatial view (Core only).  The results are the same.
 I can execute GRASS commands, but the readVECT6 crashes R, and readRAST6
gives an error.  (I believe there are probably two separate causes.)

-Eric

(I've left the version numbers here but deleted much of the output
data...spearfish70 is simply spearfish60 after running v.build.all)

Welcome to GRASS 7.0.svn
GRASS 7.0.svn (spearfish70):~ > R
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Loading required package: sp
Loading required package: XML
GRASS GIS interface loaded with GRASS version: GRASS 7.0.svn50847M (2012)
and location: spearfish70
gisdbase    /home/shared/research/GRASSDATA
location    spearfish70
...etc...
----------------------------------------------

vector files available in mapset <PERMANENT>:
archsites       roads           t_9961_200      t_9961_500
 t_roads_prime
bugsites        roads_net       t_9961_200_all  t_9961_500_all
 t_roads_second
...etc...


= FALSE)
Loading required package: rgdal
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.7.3, released 2010/11/10
Path to GDAL shared files: /usr/share/gdal/1.7
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
Path to PROJ.4 shared files: (autodetected)
GRASS 7.0.svn (spearfish70):~ >


Started up R again...and tried readRAST6

Loading required package: rgdal
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 1.7.3, released 2010/11/10
Path to GDAL shared files: /usr/share/gdal/1.7
Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
Path to PROJ.4 shared files: (autodetected)
Command: r.info
Description: Outputs basic information about a raster map.
Keywords: raster, metadata, history
Parameters:
  name: map, type: string, required: yes, multiple: no
  keydesc: name, keydesc_count: 1
[Name of raster map]
Flags:
  name: g [Print raster array information only] {FALSE}
  name: r [Print range only] {FALSE}
  name: e [Print extended metadata information only] {FALSE}
  name: h [Print raster history instead of info] {FALSE}
  name: verbose [Verbose module output] {FALSE}
  name: quiet [Quiet module output] {FALSE}
Error in doGRASS(cmd, flags = flags, ..., parameters = parameters, echoCmd
= echoCmd) :
  Invalid flag value: t

....so I tried running r.info which runs fine....

 +----------------------------------------------------------------------------+
 | Layer:    elevation.dem< at >PERMANENT        Date: Tue Mar 14 07:15:44 1989
   |
 | Mapset:   PERMANENT                      Login of Creator: grass
  |
 | Location: spearfish70
   |
 | DataBase: /home/shared/research/GRASSDATA
   |
 | Title:    DEM (7.5 minute) ( elevation )
  |
....etc....

[[alternative HTML version deleted]]

Accessto OpenBLAS

Scott Raynaud — 2012-02-14T21:56:44

My IT people have set up R on a a Kubuntu box with an RWkard 
front end.  I have OpenBLAS set up as a shared BLAS but I'm not
sure how to get R to see it.  A.3.1 of the installation docs talks
about it but I'm not clear if I need a option on my startup line or
if I need to find a config file.  The BLAS is is in:
 
/usr/lib/openblas-base
 
on my machine. I'm not sure how to confirm that R is seeing 
the BLAS.
 
Recommendations?

php and RMySQL produces R crash

Christoph Knapp — 2012-01-27T00:21:31

Hi all,
I have a very strange problem with the RMySql package. I'm running linux ubuntu 64 bit and R 2.14. I'm trying to solve this now for a week and could not find anything helpful on the net.

Now the problem

If I start my R script from php (script attached) the output is as followed

Start R Script from php

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[1] "Error in library(RMySQL) : there is no package called 'RMySQL'\n"
attr(,"class")
[1] "try-error"
attr(,"condition")

running R script

It fails to load the library RMySQL.

if I start my R script from terminal with the same command used in php

christoph< at >dell-desktop:~/Desktop$ R -f "reproduceProblem.R"

R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Loading required package: DBI
[1] "RMySQL"    "DBI"       "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"
running R script

it works

If I use require instead of library it returns FALSE and R crashes when the database connection is made and the code also loads the DBI package. I assume this is because RMySQL is never loaded but DBI.

Any ideas why R can not load RMySQL when started from a php script but otherwise there is no problem?

I attached two small scripts which reproduce the problem for me.

Any help is much appreciated.

Christoph
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R-scripts as executables for debian

Michel Kuhlmann — 2012-01-19T14:39:43

Hi,
I'm looking for a way to make executable R-scripts -- which are bound to
a certain package -- available to the operating system's search path.
The executable R-scripts I put in the package's 'exec' directory. 

Different solutions have come to my mind: 
    o 'configure'-script copies the files to /usr/local/bin
    o make a 'require'-shell function which adds 
      '/usr/local/lib/R/site-library/<pkg>/exec' dynamically to $PATH
    o generate a debian-package which contains separately the
      executables. 

Thank you for any suggestions or pointers,
Michel

R2jags update, jags.parallel

Elizabeth Tighe — 2012-01-13T16:29:17

Anyone used jags.parallel in latest version of R2jags?

Ubuntu Oneiric, just ran updates in R to get latest R2jags package which 
supposedly has added jags.parallel command to send chains to multiple 
cores ... but when I submit, I get:

test <- jags.parallel(d, inits, param, model.file="rats.bug",
                      n.chains=3, n.iter=2000)

Error: could not find function "jags.parallel"

checked sessionInfo() to be sure I did actually have the udpated version:

R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] R2jags_0.03-02   rjags_3-5        arm_1.4-14       abind_1.4-0
  [5] R2WinBUGS_2.1-18 coda_0.14-6      lme4_0.999375-42 Matrix_1.0-2
  [9] lattice_0.20-0   MASS_7.3-16

loaded via a namespace (and not attached):
[1] grid_2.14.1   nlme_3.1-102  stats4_2.14.1

And then checked the library information and see that the jags.parallel 
command doesn't actually appear:

 > library(help=R2jags)

                 Information on package âR2jagsâ

Description:

Package:              R2jags
Version:              0.03-02
Date:                 2012-1-12
Title:                A Package for Running jags from R
Author:               Yu-Sung Su <suyusung< at >tsinghua.edu.cn>, Masanao
                       Yajima <yajima< at >stat.columbia.edu>,
Maintainer:           Yu-Sung Su <suyusung< at >tsinghua.edu.cn>
Depends:              methods, R (>= 2.14.0), coda (>= 0.13),
                       R2WinBUGS, rjags (>= 3-3), parallel
SystemRequirements:   jags (>= 3.3.0)
Description:          Using this package to call jags from R.
License:              GPL (>= 2)
Packaged:             2012-01-12 07:54:55 UTC; yusung
Repository:           CRAN
Date/Publication:     2012-01-12 09:39:14
Built:                R 2.14.1; ; 2012-01-13 15:09:30 UTC; unix

Index:

attach.jags             Attach/detach elements of jags objects to
                         search path
autojags                Function for auto-updating jags until the model
                         converges
jags                    Run jags from R
jags2bugs               Read jags output files in CODA format
recompile               Function for recompiling rjags object
traceplot               Trace plot of bugs object

-------------------------

any tips would be much appreciated!

Thanks,
Liz Tighe

cannot find -lquadmath

Peter Muhlberger — 2012-01-13T02:30:14

Apologies if this has been posted about recently, but I haven't been
on this listserve for a while.

I ran into a problem trying to compile Hmisc (required package for
rms) and have found a solution that I'd like to share.  The compile
fails with the message:

/usr/bin/ld: cannot find -lquadmath

libquadmath exists on my Debian Squeeze system (up-to-date, recently installed):

ldconfig -p | grep libquad*
       libquadmath.so.0 (libc6,x86-64) =>
/usr/lib/x86_64-linux-gnu/libquadmath.so.0

The problem appears to be that libquadmath.so.0 is buried in the
directory x86_64-linux-gnu where the compiler apparently can't see it.

The fix is:

cd /usr/lib
sudo ln -s /usr/lib/x86_64-linux-gnu/libquadmath.so.0 /usr/lib/libquadmath.so

Now, the compile works.

Whoever is setting up R or R packages for Debian should try to insure
that users don't have to apply fixes like the one above.

Cheers,
Peter