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

[Henri Losoi]

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.
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?