R and Microarray Analysis in R courses from Imperial College
1
0
Entering edit mode
@north-bernard-v-2082
Last seen 10.2 years ago
MICROARRAY AND R COURSES at Imperial College London, during June 2009 1) Introduction to R 17 June: 10 - 5pm Cost: £190 2) Statistical Microarray Analysis Using R 18 & 19 June: 10 - 5pm Cost: £350 Discount rate of £495.00 to take both courses The location for each course is: Imperial College London, South Kensington Campus: Room G28, Sir Alexander Fleming Building, South Kensington Campus, London SW7 2AZ. For further information please contact Richard Kells on 0207 594 3856 or stathelp@imperial.ac.uk **Please note that we also provide courses in Stata, Minitab, Matlab & SPSS. Alternatively an application form and accompanying course outline can be downloaded from our web-site: www.imperial.ac.uk/stathelp<http: www.imperial.ac.uk="" stathelp=""> Dr Bernard North Statistical Consultant Statistical Advisory Service Advice and Courses on Research Design and Methodology Imperial College South Kensington Campus Room 845, 4th Floor 8 Princes Gardens London SW7 1NA. Tel: 020 7594 2034 Fax: 020 7594 1489 Email: bnorth@imperial.ac.uk Web: www.ic.ac.uk/stathelp [[alternative HTML version deleted]]
Microarray Microarray • 1.5k views
ADD COMMENT •
0
Entering edit mode
@john-seers-ifr-1605
Last seen 10.2 years ago
Hello All Can anyone tell me why I get this error using Biomart? I am connected to the internet (as in I can install R packages). So is the Biomart website really down? I have been having this problem for at least 2 or 3 days. If I access http://www.biomart.org/ using a web browser it appears to be available. > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. If I access http://www.biomart.org/ using a web browser it appears to be available. Any suggestions as to what is going on or things to try are very welcome. Regards John Seers > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 RWinEdt_1.8-1 loaded via a namespace (and not attached): [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 tools_2.9.0 XML_2.3-0 >
ADD COMMENT •
0
Entering edit mode
Hi John, john seers (IFR) wrote: > Hello All > > Can anyone tell me why I get this error using Biomart? I am connected to > the internet (as in I can install R packages). So is the Biomart website > really down? I have been having this problem for at least 2 or 3 days. > > If I access http://www.biomart.org/ using a web browser it appears to be > available. > > >> listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. Works for me: > listMarts() biomart 1 ensembl 2 snp 3 vega 4 msd [snip] > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3 [4] XML_2.3-0 If you are still having problems, run traceback() after the error and post the output. Best, Jim > > If I access http://www.biomart.org/ using a web browser it appears to be > available. > > > Any suggestions as to what is going on or things to try are very > welcome. > > Regards > > John Seers > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 > RWinEdt_1.8-1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 > tools_2.9.0 XML_2.3-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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
ADD REPLY •
0
Entering edit mode
Hi James Thanks for the reply. That is useful to know it is probably not the biomart end. I have run a traceback() and results are below. I have also updated my sessionInfo() as that has changed. (I think I will also contact our IT department to see if something has changed). Regards John > > > listMarts() Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. > traceback() 7: stop("Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.") 6: value[[3L]](cond) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 3: tryCatch(getURL(request), error = function(e) { stop("Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.") }) 2: bmRequest(paste("http://", host, ":", port, path, "?type=registry&requestid=biomaRt", sep = "")) 1: listMarts() > > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.0.0 RWinEdt_1.8-1 loaded via a namespace (and not attached): [1] RCurl_0.97-3 XML_2.3-0 > -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: 04 June 2009 13:50 To: john seers (IFR) Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR) Subject: Re: [BioC] biomaRt not working? Hi John, john seers (IFR) wrote: > Hello All > > Can anyone tell me why I get this error using Biomart? I am connected to > the internet (as in I can install R packages). So is the Biomart website > really down? I have been having this problem for at least 2 or 3 days. > > If I access http://www.biomart.org/ using a web browser it appears to be > available. > > >> listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. Works for me: > listMarts() biomart 1 ensembl 2 snp 3 vega 4 msd [snip] > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3 [4] XML_2.3-0 If you are still having problems, run traceback() after the error and post the output. Best, Jim > > If I access http://www.biomart.org/ using a web browser it appears to be > available. > > > Any suggestions as to what is going on or things to try are very > welcome. > > Regards > > John Seers > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 > RWinEdt_1.8-1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 > tools_2.9.0 XML_2.3-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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
ADD REPLY •
0
Entering edit mode
Hi John, I had some similar trouble with RCurl_0.95-1, but everything worked fine again when I rolled back to RCurl_0.94-1. The command listMarts() would work, but getBM() gave me a similar error. Hope that's vaguely useful, Steve john seers (IFR) wrote: > > Hi James > > Thanks for the reply. That is useful to know it is probably not the > biomart end. I have run a traceback() and results are below. I have also > updated my sessionInfo() as that has changed. > > (I think I will also contact our IT department to see if something has > changed). > > Regards > > John > >> >> listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. >> traceback() > 7: stop("Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down.") > 6: value[[3L]](cond) > 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 4: tryCatchList(expr, classes, parentenv, handlers) > 3: tryCatch(getURL(request), error = function(e) { > stop("Request to BioMart web service failed. Verify if you are > still connected to the internet. Alternatively the BioMart web service > is temporarily down.") > }) > 2: bmRequest(paste("http://", host, ":", port, path, > "?type=registry&requestid=biomaRt", > sep = "")) > 1: listMarts() > > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.0.0 RWinEdt_1.8-1 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-3 XML_2.3-0 > > > > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 04 June 2009 13:50 > To: john seers (IFR) > Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR) > Subject: Re: [BioC] biomaRt not working? > > Hi John, > > > > john seers (IFR) wrote: >> Hello All >> >> Can anyone tell me why I get this error using Biomart? I am connected > to >> the internet (as in I can install R packages). So is the Biomart > website >> really down? I have been having this problem for at least 2 or 3 days. >> >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >>> listMarts() >> Error in value[[3L]](cond) : >> Request to BioMart web service failed. Verify if you are still >> connected to the internet. Alternatively the BioMart web service is >> temporarily down. > > Works for me: > > > listMarts() > biomart > 1 ensembl > 2 snp > 3 vega > 4 msd > [snip] > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3 > [4] XML_2.3-0 > > > If you are still having problems, run traceback() after the error and > post the output. > > Best, > > Jim > > >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >> Any suggestions as to what is going on or things to try are very >> welcome. >> >> Regards >> >> John Seers >> >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> >> other attached packages: >> [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 >> RWinEdt_1.8-1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 >> tools_2.9.0 XML_2.3-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY •
0
Entering edit mode
Hi Steve All useful information. I notice there were some messages in the forum about problems with biomaRT/RCurl in the development version but I assumed that was not much to do with my problem. I have gone in the other direction with RCurl_0.97-3 in the hope it would fix it. Obviously the wrong direction! I am not sure how to get hold of an older version of a package - RCurl_0.94-1. I'll go and have an explore. Do you build it from source? Regards John -----Original Message----- From: Steve Pederson [mailto:stephen.pederson@adelaide.edu.au] Sent: 05 June 2009 02:45 To: john seers (IFR) Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt not working? Hi John, I had some similar trouble with RCurl_0.95-1, but everything worked fine again when I rolled back to RCurl_0.94-1. The command listMarts() would work, but getBM() gave me a similar error. Hope that's vaguely useful, Steve john seers (IFR) wrote: > > Hi James > > Thanks for the reply. That is useful to know it is probably not the > biomart end. I have run a traceback() and results are below. I have also > updated my sessionInfo() as that has changed. > > (I think I will also contact our IT department to see if something has > changed). > > Regards > > John > >> >> listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. >> traceback() > 7: stop("Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down.") > 6: value[[3L]](cond) > 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 4: tryCatchList(expr, classes, parentenv, handlers) > 3: tryCatch(getURL(request), error = function(e) { > stop("Request to BioMart web service failed. Verify if you are > still connected to the internet. Alternatively the BioMart web service > is temporarily down.") > }) > 2: bmRequest(paste("http://", host, ":", port, path, > "?type=registry&requestid=biomaRt", > sep = "")) > 1: listMarts() > > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.0.0 RWinEdt_1.8-1 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-3 XML_2.3-0 > > > > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 04 June 2009 13:50 > To: john seers (IFR) > Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR) > Subject: Re: [BioC] biomaRt not working? > > Hi John, > > > > john seers (IFR) wrote: >> Hello All >> >> Can anyone tell me why I get this error using Biomart? I am connected > to >> the internet (as in I can install R packages). So is the Biomart > website >> really down? I have been having this problem for at least 2 or 3 days. >> >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >>> listMarts() >> Error in value[[3L]](cond) : >> Request to BioMart web service failed. Verify if you are still >> connected to the internet. Alternatively the BioMart web service is >> temporarily down. > > Works for me: > > > listMarts() > biomart > 1 ensembl > 2 snp > 3 vega > 4 msd > [snip] > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3 > [4] XML_2.3-0 > > > If you are still having problems, run traceback() after the error and > post the output. > > Best, > > Jim > > >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >> Any suggestions as to what is going on or things to try are very >> welcome. >> >> Regards >> >> John Seers >> >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> >> other attached packages: >> [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 >> RWinEdt_1.8-1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 >> tools_2.9.0 XML_2.3-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY •
0
Entering edit mode
In case this helps : These 2 combinations of biomart and Rcurl work fine for me : > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.97-3 XML_1.95-3 > ################## developement version > sessionInfo() R version 2.10.0 Under development (unstable) (2009-06-02 r48703) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Mmusculus.UCSC.mm9_1.3.11 BSgenome_1.13.6 [3] Biostrings_2.13.11 IRanges_1.3.21 [5] biomaRt_2.1.0 loaded via a namespace (and not attached): [1] Biobase_2.5.2 RCurl_0.97-3 XML_2.5-0 - Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- ---------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au -----Original Message----- From: john seers (IFR) <john.seers@bbsrc.ac.uk> To: Steve Pederson <stephen.pederson at="" adelaide.edu.au=""> Cc: James W. MacDonald <jmacdon at="" med.umich.edu="">, bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt not working? Date: Fri, 5 Jun 2009 08:23:56 +0100 Hi Steve All useful information. I notice there were some messages in the forum about problems with biomaRT/RCurl in the development version but I assumed that was not much to do with my problem. I have gone in the other direction with RCurl_0.97-3 in the hope it would fix it. Obviously the wrong direction! I am not sure how to get hold of an older version of a package - RCurl_0.94-1. I'll go and have an explore. Do you build it from source? Regards John -----Original Message----- From: Steve Pederson [mailto:stephen.pederson@adelaide.edu.au] Sent: 05 June 2009 02:45 To: john seers (IFR) Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt not working? Hi John, I had some similar trouble with RCurl_0.95-1, but everything worked fine again when I rolled back to RCurl_0.94-1. The command listMarts() would work, but getBM() gave me a similar error. Hope that's vaguely useful, Steve john seers (IFR) wrote: > > Hi James > > Thanks for the reply. That is useful to know it is probably not the > biomart end. I have run a traceback() and results are below. I have also > updated my sessionInfo() as that has changed. > > (I think I will also contact our IT department to see if something has > changed). > > Regards > > John > >> >> listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. >> traceback() > 7: stop("Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down.") > 6: value[[3L]](cond) > 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 4: tryCatchList(expr, classes, parentenv, handlers) > 3: tryCatch(getURL(request), error = function(e) { > stop("Request to BioMart web service failed. Verify if you are > still connected to the internet. Alternatively the BioMart web service > is temporarily down.") > }) > 2: bmRequest(paste("http://", host, ":", port, path, > "?type=registry&requestid=biomaRt", > sep = "")) > 1: listMarts() > > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.0.0 RWinEdt_1.8-1 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-3 XML_2.3-0 > > > > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 04 June 2009 13:50 > To: john seers (IFR) > Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR) > Subject: Re: [BioC] biomaRt not working? > > Hi John, > > > > john seers (IFR) wrote: >> Hello All >> >> Can anyone tell me why I get this error using Biomart? I am connected > to >> the internet (as in I can install R packages). So is the Biomart > website >> really down? I have been having this problem for at least 2 or 3 days. >> >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >>> listMarts() >> Error in value[[3L]](cond) : >> Request to BioMart web service failed. Verify if you are still >> connected to the internet. Alternatively the BioMart web service is >> temporarily down. > > Works for me: > > > listMarts() > biomart > 1 ensembl > 2 snp > 3 vega > 4 msd > [snip] > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3 > [4] XML_2.3-0 > > > If you are still having problems, run traceback() after the error and > post the output. > > Best, > > Jim > > >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >> Any suggestions as to what is going on or things to try are very >> welcome. >> >> Regards >> >> John Seers >> >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> >> other attached packages: >> [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 >> RWinEdt_1.8-1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 >> tools_2.9.0 XML_2.3-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY •
0
Entering edit mode
Hi Paul The same combination as me - the major difference is I am on Windows and you are on Linux. But James below was running from Windows with the same versions. Thanks for the information. Does anybody know how I can get an earlier version of RCurl? I have had a look around but cannot find any. (Not even source code.) Regards John -----Original Message----- From: Paul Leo [mailto:p.leo@uq.edu.au] Sent: 05 June 2009 08:35 To: john seers (IFR) Cc: Steve Pederson; James W. MacDonald; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt not working? In case this helps : These 2 combinations of biomart and Rcurl work fine for me : > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .U TF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAM E= C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICA TI ON=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.97-3 XML_1.95-3 > ################## developement version > sessionInfo() R version 2.10.0 Under development (unstable) (2009-06-02 r48703) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Mmusculus.UCSC.mm9_1.3.11 BSgenome_1.13.6 [3] Biostrings_2.13.11 IRanges_1.3.21 [5] biomaRt_2.1.0 loaded via a namespace (and not attached): [1] Biobase_2.5.2 RCurl_0.97-3 XML_2.5-0 - Dr Paul Leo Bioinformatician Diamantina Institute for Cancer, Immunology and Metabolic Medicine University of Queensland ---------------------------------------------------------------------- -- -------------- Research Wing, Bldg 1 Princess Alexandria Hospital Woolloongabba, QLD, 4102 Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946 Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au -----Original Message----- From: john seers (IFR) <john.seers@bbsrc.ac.uk> To: Steve Pederson <stephen.pederson at="" adelaide.edu.au=""> Cc: James W. MacDonald <jmacdon at="" med.umich.edu="">, bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt not working? Date: Fri, 5 Jun 2009 08:23:56 +0100 Hi Steve All useful information. I notice there were some messages in the forum about problems with biomaRT/RCurl in the development version but I assumed that was not much to do with my problem. I have gone in the other direction with RCurl_0.97-3 in the hope it would fix it. Obviously the wrong direction! I am not sure how to get hold of an older version of a package - RCurl_0.94-1. I'll go and have an explore. Do you build it from source? Regards John -----Original Message----- From: Steve Pederson [mailto:stephen.pederson@adelaide.edu.au] Sent: 05 June 2009 02:45 To: john seers (IFR) Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] biomaRt not working? Hi John, I had some similar trouble with RCurl_0.95-1, but everything worked fine again when I rolled back to RCurl_0.94-1. The command listMarts() would work, but getBM() gave me a similar error. Hope that's vaguely useful, Steve john seers (IFR) wrote: > > Hi James > > Thanks for the reply. That is useful to know it is probably not the > biomart end. I have run a traceback() and results are below. I have also > updated my sessionInfo() as that has changed. > > (I think I will also contact our IT department to see if something has > changed). > > Regards > > John > >> >> listMarts() > Error in value[[3L]](cond) : > Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down. >> traceback() > 7: stop("Request to BioMart web service failed. Verify if you are still > connected to the internet. Alternatively the BioMart web service is > temporarily down.") > 6: value[[3L]](cond) > 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 4: tryCatchList(expr, classes, parentenv, handlers) > 3: tryCatch(getURL(request), error = function(e) { > stop("Request to BioMart web service failed. Verify if you are > still connected to the internet. Alternatively the BioMart web service > is temporarily down.") > }) > 2: bmRequest(paste("http://", host, ":", port, path, > "?type=registry&requestid=biomaRt", > sep = "")) > 1: listMarts() > > > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_2.0.0 RWinEdt_1.8-1 > > loaded via a namespace (and not attached): > [1] RCurl_0.97-3 XML_2.3-0 > > > > > > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 04 June 2009 13:50 > To: john seers (IFR) > Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR) > Subject: Re: [BioC] biomaRt not working? > > Hi John, > > > > john seers (IFR) wrote: >> Hello All >> >> Can anyone tell me why I get this error using Biomart? I am connected > to >> the internet (as in I can install R packages). So is the Biomart > website >> really down? I have been having this problem for at least 2 or 3 days. >> >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >>> listMarts() >> Error in value[[3L]](cond) : >> Request to BioMart web service failed. Verify if you are still >> connected to the internet. Alternatively the BioMart web service is >> temporarily down. > > Works for me: > > > listMarts() > biomart > 1 ensembl > 2 snp > 3 vega > 4 msd > [snip] > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3 > [4] XML_2.3-0 > > > If you are still having problems, run traceback() after the error and > post the output. > > Best, > > Jim > > >> If I access http://www.biomart.org/ using a web browser it appears to > be >> available. >> >> >> Any suggestions as to what is going on or things to try are very >> welcome. >> >> Regards >> >> John Seers >> >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >> Kingdom.1252;LC_MONETARY=English_United >> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> >> other attached packages: >> [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1 >> RWinEdt_1.8-1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1 >> tools_2.9.0 XML_2.3-0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 529 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6