[BioC] I AM NEW USER TO XCMS AND REALLY NEED HELP!

Wed Jan 18 15:14:24 CET 2012

Hi Habib,

On 1/17/2012 2:57 PM, HABIBALLAH HAMZEHZARGHANI wrote:
>   
> I AM A NEW USED OF XCMS WHO DOES NOT KNOW HOW TO WORK WITH R BUT VERY INTERESTED TO TRY XCMS FOR DECONVOLUTION, BASE NOOISE CORRECTION AND PEAK ALIGNMENT OF MY NETCDF GCMS FILES.
> I FOLLOWED THE INSTRUCTIONS GIVEN ON YOUR WEBSITE @ http://www.bioconductor.org/packages/release/bioc/html/xcms.html
> TO INSTALL XCMS ON MY COMPOUTER. APPEARENTLY TO INSTALL XCMS Release (2.9), ONE SHOULD COPY AND PAST THE FOLLOWING SCRIPT INTO R:
> To install this package, start R and enter:
>      source("http://www.bioconductor.org/biocLite.R")
>      biocLite("xcms")
>   
> I DID EXACTLY THE SAME THING AND WHAT I GOT WAS THE MESSAGE SHOWING IN THE R CONSOLE AS SHOWN IN THE PICTURED INSERTED IN THE ATTACHED FILE.

The list servers will not pass picture files. A better option is to cut 
and paste the output from your R console.

> I DO NOT KNOW WHAT I DID WRONG OR IF I NEEDED TO DO SOME PRELIMINARY PREPARATION I DID NOT DO?
> I TRIED FINDING OTHER WAYS AND WENT THROUGH Installation Instructions for xcms ON YOUR WEBSITE (@http://www.bioconductor.org/packages/release/bioc/html/xcms.html). I DOWNLOADED zipfiles of multtest, xcms and faahKO AND INSTALLED THEM USING INSTALL PACKAGES AND GOT THEM INSTALLED AND UNPACKED SUCCESSFULLY, HOWEVER WHEN I TRY USING IT, IT DOES NOT WORK. I AM JUST FRUSTRATED, SOMEBODY PLEASE HELP.

Installing packages by hand like that will often not work. Many 
Bioconductor packages are tightly linked to both the version of R they 
are designed for, as well as the version of dependent packages. The 
biocLite() function automatically ensures that you get the correct 
version of packages for your version of R, so you should always install 
using that function.

You should always run sessionInfo(), and paste the output from that 
function into your email as well. Unless we know what version of 
packages you are using, it is not likely that we will be able to help.

Now for some etiquette. An email that is in ALL CAPS is not only hard to 
read, but is considered rude (it's like yelling at someone), so please 
use regular capitalization rules.

In addition, if you have a new question, please start with a new email, 
rather than taking an existing thread and changing the Subject line. 
Many people use thread-aware email clients, and this email would have 
been attached to the thread about the Bioconductor AMI not being found, 
so it would be much less likely that you would get a response.

Best,

Jim

> BEST REGARDS
> HABIB
>   
>   It is not the strongest of the species that survive, nor the most intelligent, but the one most responsive to change. -Charles Darwin
>   
> --------------------------------------------------
> H.Hamzehzarghani,
> Ph.D, Assistant Professor
> Department of Plant Protection
> College of Agriculture, Badjgah
> Shiraz University, Shiraz,
> Postal Code: 71444-65186  IRAN
> Phone: +1198-711-613-8322
> Fax: +1198-711-228-6087
> ---------------------------------------------------
>   
>      
>
>
> ________________________________
> From: Dan Tenenbaum<dtenenba at fhcrc.org>
> To: Glynn Dennis<glynnsc at gmail.com>
> Cc: bioconductor at r-project.org
> Sent: Tuesday, January 17, 2012 9:48 PM
> Subject: Re: [BioC] Bioconductor AMI NOT FOUND
>
> On Tue, Jan 17, 2012 at 10:15 AM, Glynn Dennis<glynnsc at gmail.com>  wrote:
>> that's it!
> Glad it helped.
> Dan
>
>
>> Thanks,
>> glynn
>>
>>
>> On Tue, Jan 17, 2012 at 10:10 AM, Dan Tenenbaum<dtenenba at fhcrc.org>  wrote:
>>> On Tue, Jan 17, 2012 at 10:09 AM, Glynn Dennis<glynnsc at gmail.com>  wrote:
>>>> Hi Dan, thanks much for the reply.
>>>>
>>>> I'm not getting any error messages, but here are some screen-shots of
>>>> what
>>>> is going on.
>>>>
>>>> Screen-shots of:
>>>> Dashboard:
>>>> Launch wizard
>>>> Community AMI tab
>>>> not found ami-9de037f4
>>>>
>>>> Is there a regional requirment? -- notice I'm in the US-west
>>>> N.California
>>>> region.
>>>
>>> Yes, please see my previous email:
>>>
>>> http://permalink.gmane.org/gmane.science.biology.informatics.conductor/38491
>>> Dan
>>>
>>>> Thanks,
>>>> glynn
>>>>
>>>>
>>>> On Tue, Jan 17, 2012 at 9:18 AM, Dan Tenenbaum<dtenenba at fhcrc.org>
>>>> wrote:
>>>>> On Tue, Jan 17, 2012 at 9:08 AM, Dan Tenenbaum<dtenenba at fhcrc.org>
>>>>> wrote:
>>>>>> On Tue, Jan 17, 2012 at 8:57 AM, glynn [guest]
>>>>>> <guest at bioconductor.org>
>>>>>> wrote:
>>>>>>> Hello, I'm trying to start an EC2 instance of R/bioconductor.
>>>>>>>
>>>>>>> I have an account with AWS.
>>>>>>> I have set up other EC2 instances.
>>>>>>>
>>>>>>> Following the instructions here:
>>>>>>> http://bioconductor.org/help/bioconductor-cloud-ami/
>>>>>>>
>>>>>>> In the Launching the AMI section, neither ami id shown below is
>>>>>>> found.
>>>>>>>
>>>>>>> Is there an up-to-date ami id someone can provide.
>>>>>> I am able to launch both AMIs from a personal account. Can you
>>>>>> explain
>>>>>> exactly what steps you are doing and what error messages you see?
>>>>>>
>>>>> Note that the AMIs are in the us-east-1 region, so if you are using
>>>>> the AWS console, you should be using a URL like this:
>>>>>
>>>>> https://console.aws.amazon.com/ec2/home?region=us-east-1
>>>>>
>>>>> The web page has been updated to make this explicit.
>>>>> Dan
>>>>>
>>>>>
>>>>>> Dan
>>>>>>
>>>>>>
>>>>>>> Thanks in advance,
>>>>>>> glynn
>>>>>>>
>>>>>>> Bioconductor Version
>>>>>>> R Version       AMI ID
>>>>>>> 2.9     2.14    ami-9de037f4
>>>>>>> 2.8     2.13    ami-4b2fee22
>>>>>>>
>>>>>>>
>>>>>>>   -- output of sessionInfo():
>>>>>>>
>>>>>>> EC2 question
>>>>>>>
>>>>>>> --
>>>>>>> Sent via the guest posting facility at bioconductor.org.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
>>>>>>> Bioconductor at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives:
>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 