[R-sig-Debian] Problems in installing R -packages

[Dirk Eddelbuettel]

On 27 August 2012 at 15:20, Henri Losoi wrote:
| Hallo!
| 
| @Johannes: Nein, ich habe das nicht gemacht [1]. Jakson Aquino, der Autor
| des Vimcom, hat Ubuntu 12.04 mit R 12.15 benutzt, kein Problem mit noexec.
| 
| @ALL: The author of Vimcom was unable to comment about the problem
| with R 2.11. He has only tested R 2.15, not 2.11 that I am running.

Why would you want to run R 2.11 which is two years out of date?  

Why do you expect us to support an outdated version?

Dirk

| I consulted some people in Freenode's channels such as R and Vim where we
| spotted some errors with built-vars [2]. For example, the "-lpthreads"
| -flag missing on the line 15 of the latter example and some err dumps
| [3], also some in my twitter -account close to the tweets.
| 
| We are now stuck to the last err-dump [3], apparently a problem with
| linking and gcc. If you know the solution to the problem, please, send
| the patches to Jakson [4][5] because the problem is still with the
| Vim-R-plugin, thank you.
| 
| -- 
| M.f.G.
| Henri Losoi
| 
| References
| [1] https://twitter.com/heoaLov/status/240054739402891264
| [2] https://twitter.com/heoaLov/status/238923344550981633
| [3] http://koti.kapsi.fi/~he/SO/err_vimcom
| [4] http://www.vim.org/scripts/script.php?script_id=2628
| [5] http://www.vim.org/scripts/script.php?script_id=2628
| 
| On Mon, Aug 27, 2012 at 11:00:33AM +0200, Johannes Ranke wrote:
| > Henry,
| > 
| > On my end (Debian squeeze), vimcom installs fine (see below).
| > 
| > However, if I remount my /home directory using the "noexec" option and set the 
| > lib argument in install.packages to a place on /home, I get a similar error 
| > message (in German...), about R not being able to load the shared object.
| > 
| > So my question would be, did you mount your /home drive using the noexec 
| > option?
| > 
| > Kind regards,
| > 
| > Johannes
| > 
| > 
| > ranke at time:~$ R
| > 
| > R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
| > Copyright (C) 2012 The R Foundation for Statistical Computing
| > ISBN 3-900051-07-0
| > Platform: x86_64-pc-linux-gnu (64-bit)
| > 
| > R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
| > Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
| > Tippen Sie 'license()' or 'licence()' für Details dazu.
| > 
| > R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
| > Tippen Sie 'contributors()' für mehr Information und 'citation()',
| > um zu erfahren, wie R oder R packages in Publikationen zitiert werden können.
| > 
| > Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
| > 'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
| > Tippen Sie 'q()', um R zu verlassen.
| > 
| > > install.packages("vimcom")
| > Installiere Paket(e) nach ‘/usr/local/lib/R/site-library’
| > (da ‘lib’ nicht spezifiziert)
| > versuche URL 'http://cran.r-project.org/src/contrib/vimcom_0.9-2.tar.gz'
| > Content type 'application/x-gzip' length 16039 bytes (15 Kb)
| > URL geöffnet
| > ==================================================
| > downloaded 15 Kb
| > 
| > * installing *source* package ‘vimcom’ ...
| > ** Paket ‘vimcom’ erfolgreich entpackt und MD5 Summen überprüft
| > ** libs
| > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c 
| > vimcom.c -o vimcom.o
| > gcc -std=gnu99 -shared -o vimcom.so vimcom.o -L/usr/lib64/R/lib -lR
| > installiert nach /usr/local/lib/R/site-library/vimcom/libs
| > ** R
| > ** preparing package for lazy loading
| > ** help
| > *** installing help indices
| > ** building package indices
| > ** testing if installed package can be loaded
| > 
| > * DONE (vimcom)
| > 
| > Die heruntergeladenen Quellpakete sind in 
| >         ‘/tmp/RtmpReyLfN/downloaded_packages’
| > 
| > 
| > On Friday 24 August 2012 01:58:41 Henri Losoi wrote:
| > > Hello,
| > > err dump [1], perhaps related [2]. Also
| > > 
| > > 	$ sudo chown -R xyz:staff ~/R
| > > 	# sudo su; su xyz; groups
| > > 	web-content staff
| > > 
| > > Not just vim-R-plugin -problem anymore, more pkg -installation -prob,
| > > doubting perms/group -issue but fixed them in accordance by Dirk's hints.
| > > 
| > > What is the problem in installing packages?
| 
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com