Bioconductor AMI NOT FOUND
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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. 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.
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Dan Tenenbaum ★ 8.2k
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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? 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
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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
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Dan Tenenbaum ★ 8.2k
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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.conduc tor/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 >> > >> > > >
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? 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. 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. ? 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@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.conduc tor/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
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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.condu ctor/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
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