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Question: Kegg Profile package problem
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5.5 years ago by
gregory voisin430 wrote:
modified 5.5 years ago • written 5.5 years ago by gregory voisin430
0
5.5 years ago by
gregory voisin430 wrote:
For your information, 3 weeks ago, I subscribed to Amazon web services to use R studio and bioconductor. Here, I highlight a problem about the weird bill associated to the Amazon web services: When you create a stack , a stockage volume is created and normally when you delete a stack,the stockage volume is deleted too. But, in my case, the deletion of volume was problematic and after, 3 weeks of usage, I had 40 stockage volume ( 40 gig by volume)associated to my Amazon account and I have paid for that ( the first 40 gig is free). The charge for that is not important ( 20 $CA for 3 weeks) but could be more important if you don't check. It's not very clear if it's a lack of understanding of me or if it's a technical problem associated to web service when you delete your instance, check your stockage volume: 1.http://aws.amazon.com/fr/console/ 2. connect to AWS console 3. click on EC2 ( virtual servers in the cloud) 4. In part " My services" : check EBS volume(normally :0) Greg Montreal ________________________________ De : Dan Tenenbaum <dtenenba@fhcrc.org> Cc : "bioconductor@r-project.org" <bioconductor@r-project.org> Envoyé le : Jeudi 27 décembre 2012 2h35 Objet : Re: [BioC] Kegg Profile package problem > > > > Hi, > I use KeggProfile in my pipeline analysis and it's efficient, but I have problem with one pathway_ID. > > Exemple ( copy and paste): > > require(KEGGprofile) > download_KEGGfile(pathway_id="04110",specis='hsa') > > #In this case , not problem > > download_KEGGfile(pathway_id="00910",specis='hsa') I think perhaps there is no such pathway. Here's a list of all human pathways: http://rest.kegg.jp/list/pathway/hsa 04110 is included but 00910 is not. Dan > > #this pahway exits in KEGG, but the download is impossible > #[1] "Downloading files: 1/1" > #essai de l'URL 'http://www.genome.jp/kegg- bin/download?entry=hsa00910&format=kgml' > #Content type 'text/plain' length unknown > #URL ouverte > #downloaded 1 bytes > > #essai de l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png' > #Erreur dans download.file(paste("http://www.genome.jp/kegg/pathway/", specis, : > # impossible d'ouvrir l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png' > #De plus : Message d'avis : > #In download.file(paste("http://www.genome.jp/kegg/pathway/", specis, : > # ouverture impossible : le statut HTTP était '404 Not Found' > > > My solution : omit this pathway in my analysis: ponctual, fast but [[elided Yahoo spam]] > > If someone has a suggestion , comments or solution, let's go , > > Thanks > > Greg > Montréal > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] ADD REPLYlink written 5.5 years ago by gregory voisin430 Hi Greg, On Thu, Dec 27, 2012 at 7:04 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: > For your information, > 3 weeks ago, I subscribed to Amazon web services to use R studio and > bioconductor. > Here, I highlight a problem about the weird bill associated to the Amazon > web services: > > When you create a stack , a stockage volume is created and normally when you > delete a stack,the stockage volume is deleted too. > > But, in my case, the deletion of volume was problematic and after, 3 weeks > of usage, I had 40 stockage volume ( 40 gig by volume)associated to my > Amazon account and I have paid for that ( the first 40 gig is free). The > charge for that is not important ( 20$CA for 3 weeks) but could be more > important if you don't check. > > It's not very clear if it's a lack of understanding of me or if it's a > technical problem associated to web service > > when you delete your instance, check your stockage volume: > 1.http://aws.amazon.com/fr/console/ > 2. connect to AWS console > 3. click on EC2 ( virtual servers in the cloud) > 4. In part " My services" : check EBS volume(normally :0) > I've changed our public AMIs so that EBS volumes that are created when instances are launched, are now deleted when the instances are terminated. So this problem will no longer occur. Thanks, Dan > Greg > Montreal > > > > > > ________________________________ > De : Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > ? : gregory voisin <voisingreg at="" yahoo.fr=""> > Cc : "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Envoy? le : Jeudi 27 d?cembre 2012 2h35 > Objet : Re: [BioC] Kegg Profile package problem > > On Wed, Dec 26, 2012 at 6:54 AM, gregory voisin <voisingreg at="" yahoo.fr=""> wrote: >> >> >> >> Hi, >> I use KeggProfile in my pipeline analysis and it's efficient, but I have >> problem with one pathway_ID. >> >> Exemple ( copy and paste): >> >> require(KEGGprofile) >> download_KEGGfile(pathway_id="04110",specis='hsa') >> >> #In this case , not problem >> >> download_KEGGfile(pathway_id="00910",specis='hsa') > > > I think perhaps there is no such pathway. Here's a list of all human > pathways: > http://rest.kegg.jp/list/pathway/hsa > > 04110 is included but 00910 is not. > > Dan > > >> >> #this pahway exits in KEGG, but the download is impossible >> #[1] "Downloading files: 1/1" >> #essai de l'URL >> 'http://www.genome.jp/kegg-bin/download?entry=hsa00910&format=kgml' >> #Content type 'text/plain' length unknown >> #URL ouverte >> #downloaded 1 bytes >> >> #essai de l'URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png' >> #Erreur dans download.file(paste("http://www.genome.jp/kegg/pathway/", >> specis, : >> # impossible d'ouvrir l'URL >> 'http://www.genome.jp/kegg/pathway/hsa/hsa00910.png' >> #De plus : Message d'avis : >> #In download.file(paste("http://www.genome.jp/kegg/pathway/", specis, : >> # ouverture impossible : le statut HTTP ?tait '404 Not Found' >> >> >> My solution : omit this pathway in my analysis: ponctual, fast but not >> very elegant and not professional !! >> >> If someone has a suggestion , comments or solution, let's go , >> >> Thanks >> >> Greg >> Montr?al >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> 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 > >