ubuntu install woes

[Keith Bierman]

Having given up on a native Mac/Mavericks install, I fired up virtualbox and ubuntu 13 (saucy) 64bit. Following the directions at: http://rattle.togaware.com/rattle-install-ubuntu.html. During the step where we enable ppa.launchpad I received an error condition:

Reading package lists... Done
W: GPG error: http://ppa.launchpad.net saucy Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 5E25F516B04C661B
This is 1984 up on the previous count with 1984 new packages.
There are 0 new upgrades

Going forward, I continued as per instructions, ultimately ran R. The colorspaces package autoinstalled, But the XML package failed as noted below:

* installing *source* package ‘colorspace’ ...

** package ‘colorspace’ successfully unpacked and MD5 sums checked

** libs

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c colorspace.c -o colorspace.o

gcc -std=gnu99 -shared -o colorspace.so colorspace.o -L/usr/lib/R/lib -lR

installing to /home/khb/R/x86_64-pc-linux-gnu-library/3.0/colorspace/libs

** R

** data

*** moving datasets to lazyload DB

** inst

** preparing package for lazy loading

Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘colorspace’

** help

*** installing help indices

** building package indices

** installing vignettes

** testing if installed package can be loaded

* DONE (colorspace)

The downloaded source packages are in

‘/tmp/Rtmprlyrjt/downloaded_packages’

Installing package into ‘/home/khb/R/x86_64-pc-linux-gnu-library/3.0’

(as ‘lib’ is unspecified)

trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/XML_3.98-1.1.tar.gz'

Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb)

opened URL

==================================================

downloaded 1.5 Mb

* installing *source* package ‘XML’ ...

** package ‘XML’ successfully unpacked and MD5 sums checked

checking for gcc... gcc

checking for C compiler default output file name... rm: cannot remove 'a.out.dSYM': Is a directory

a.out

checking whether the C compiler works... yes

checking whether we are cross compiling... no

checking for suffix of executables... 

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking how to run the C preprocessor... gcc -E

checking for sed... /bin/sed

checking for pkg-config... /usr/bin/pkg-config

checking for xml2-config... no

Cannot find xml2-config

ERROR: configuration failed for package ‘XML’

* removing ‘/home/khb/R/x86_64-pc-linux-gnu-library/3.0/XML’

The downloaded source packages are in

‘/tmp/Rtmprlyrjt/downloaded_packages’

Error in loadTooltips() : could not find function "xmlTreeParse"

In addition: Warning messages:

1: In install.packages(pkg) :

  installation of package ‘XML’ had non-zero exit status

2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :

  there is no package called ‘XML’

> 

Hints, RTFM pointers,  etc. all greatly appreciated.

Keith Bierman
khb...@gmail.com
kbiermank AIM
303 997 2749

[Graham Williams]

Best to install from the c2d4u repository as in steps 2 and 3 on http://rattle.togaware.com/rattle-install-ubuntu.html

Add:

deb http://ppa.launchpad.net/marutter/c2d4u/ubuntu saucy main

to /etc/apt/sources.list and then

$ sudo apt-get update

$ sudo apt-get install r-cran-xml

In fact, best to install all the listed r-cran packages.

Graham Williams

http://togaware.com

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[Keith Bierman]

Thanks, with enough repetition I found my typos. For everyone else, a few suggestions:

1) Make sure to enable the VirtualBox guest additions, and bidirectional cut/paste first

The rest of this could/should be scripted for 1 line sh ./install-rattle

2) I suggest a modest reorganization to the instructions. Edit the sudo vi /etc/apt/sources.list once with the two lines that need to be added.

3) group the two repository keep updates together

4) There's a typo in the final wajig install ... \     r-cran-vcd -rcran-waveslim

 

I'd rather use the Mac native version; but I've never gotten that to work. The Linux install does have the advantage of being easier to explain to my Windows friends how to deploy (viz. install virtualbox, etc. ;>)

I've never spotted a good supported rattle "appliance" VM. Has anyone made one? 

Keith Bierman
khb...@gmail.com
kbiermank AIM
303 997 2749