[Bio-Linux] Bio-Linux Digest, Vol 60, Issue 1

Tue Aug 27 12:45:34 EDT 2013

RStudio installed without error. 
Thanks!

 Tom
thokeller at gmail com

On Aug 16, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:

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> Today's Topics:
> 
>   1. Re: RStudio with Bio-Linux (Tom Keller)
>   2. Re: RStudio with Bio-Linux (Tim Booth)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 15 Aug 2013 10:27:13 -0700
> From: Tom Keller <kellert at ohsu.edu>
> Subject: Re: [Bio-Linux] RStudio with Bio-Linux
> To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> Message-ID: <E1685117-7357-4EC0-9A79-FD9D15859717 at ohsu.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Tim,
> Is there a way to use RStudio with R from Bio-Linux?
> 
> thanks for your help.
> Tom Keller
> Thomas J. Keller, Ph.D.; Director, DNA Services Core Facility ; Oregon Health & Science University;
> mailcode L220; 3181 SW Sam Jackson Park Rd; Portland, OR 97239; 503-494-2442
> 
> On Jul 23, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:
> 
>> Send Bio-Linux mailing list submissions to
>> 	bio-linux at nebclists.nerc.ac.uk
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>> or, via email, send a message with subject or body 'help' to
>> 	bio-linux-request at nebclists.nerc.ac.uk
>> 
>> You can reach the person managing the list at
>> 	bio-linux-owner at nebclists.nerc.ac.uk
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Bio-Linux digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Bio-Linux updated image and new packages (Tim Booth)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Mon, 22 Jul 2013 16:55:06 +0100
>> From: Tim Booth <tbooth at ceh.ac.uk>
>> Subject: [Bio-Linux] Bio-Linux updated image and new packages
>> To: Bio-Linux mailing list <bio-linux at nebclists.nerc.ac.uk>
>> Message-ID: <1374508506.10050.57.camel at balisaur>
>> Content-Type: text/plain; charset="UTF-8"
>> 
>> Hi All,
>> 
>> I've put a new Bio-Linux image update on the website today (7.0.7).
>> Existing users won't need to use this but I've added some new packages
>> which you might be interested in installing on your machines (sudo
>> apt-get install <packagename>):
>> 
>> abyss  (http://www.bcgsc.ca/platform/bioinfo/software/abyss)
>> ray    (http://denovoassembler.sourceforge.net/)
>> sickle (https://github.com/vsbuffalo/sickle)
>> scythe (https://github.com/vsbuffalo/scythe)
>> macs   (http://liulab.dfci.harvard.edu/MACS/)
>> 
>> The R environment has been upgraded to R3.0 and modules have been
>> recompiled to work on the new R.  If you have installed extra modules
>> and get an error about an incompatible R module you may need to run
>> "install.packages(<modulename>)" within R.
>> 
>> The new image has updated drivers from Ubuntu the 12.04.2 release and so
>> should work on some more modern computers.  I've not been able to test
>> UEFI booting so if you have a UEFI machine you may need to set it back
>> to BIOS boot for now.
>> 
>> The new STADEN Gap5 package and Taverna did not make this image release
>> but will be coming soon.
>> 
>> Cheers,
>> 
>> TIM
>> 
>> -- 
>> Tim Booth <tbooth at ceh.ac.uk>
>> NERC Environmental Bioinformatics Centre 
>> 
>> Centre for Ecology and Hydrology
>> Maclean Bldg, Benson Lane
>> Crowmarsh Gifford
>> Wallingford, England
>> OX10 8BB 
>> 
>> http://nebc.nerc.ac.uk
>> +44 1491 69 2705
>> 
>> 
>> 
>> 
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>> 
>> End of Bio-Linux Digest, Vol 59, Issue 4
>> ****************************************
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 15 Aug 2013 18:43:05 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> Subject: Re: [Bio-Linux] RStudio with Bio-Linux
> To: bio-linux at nebclists.nerc.ac.uk
> Message-ID: <1376588585.3416.211.camel at balisaur>
> Content-Type: text/plain; charset="UTF-8"
> 
> Hi Tom,
> 
> The RStudio website provides a .deb file which should work fine.  You
> can fetch and install it from the command line like so:
> 
> wget http://download1.rstudio.org/rstudio-0.97.551-amd64.deb
> sudo dpkg -i rstudio-0.97.551-amd64.deb
> sudo apt-get -f install
> 
> The second command may report an error, but the third command fixes it.
> 
> Then open the dash and start typing "rstudio" and you should see the
> icon, or just run "rstudio" on the command line.
> 
> Does that work for you?
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2013-08-15 at 18:27 +0100, Tom Keller wrote:
>> Hi Tim,
>> Is there a way to use RStudio with R from Bio-Linux?
>> 
> 
> 
> 
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> 
> End of Bio-Linux Digest, Vol 60, Issue 1
> ****************************************

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