Hi All I think we have found the problem and a workaround. Thanks to all who offered help and advice. Using the "--internet2" option to specify the proxy appears to not be good enough any more. Using the "http_proxy" option to specify the proxy server directly worked. I think "--internet2" says use the Explorer/browser options. Why this does not work any more I do not know. It could be a fix/change to Windows at my end that does not pass back the information as it used to? Or perhaps biomart/RCurl does not handle it well any more? Anyway, we are up and running again. Regards John -----Original Message----- From: john seers (IFR) Sent: 05 June 2009 09:23 To: 'Paul Leo' Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] biomaRt not working? Hi Paul That does not sound very hopeful. :( I am not sure I know how to go figure that. Perhaps the time has nearly come to approach the package owner for a suggestion. Perhaps I will try a bit more digging first. Perhaps see if I can trace the problem a bit deeper. Regards John -----Original Message----- From: Paul Leo [mailto:p.leo@uq.edu.au] Sent: 05 June 2009 09:08 To: john seers (IFR) Subject: RE: [BioC] biomaRt not working? I had something vaguely similar happen to me this week, using update.packages() I had the correct versions of BioMart and RCurl but it kept failing. I reinstalled R and BioC and all of a sudden it was fine ... go figure.... But that was on R.10 for linux.... - 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: Paul Leo <p.leo at="" uq.edu.au=""> Cc: Steve Pederson <stephen.pederson at="" adelaide.edu.au="">, 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 08:53:07 +0100 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

Hi All Having thought this was fixed we found that it was still not enough. To get all the code to work (i.e. biomart/listMart/useMart and downloading packages) we have to specify access to our proxy using the "--internet2" and the "http_proxy_user" options. So it looks like some code uses one option to obtain proxy information and another bit of code uses the other option. Up to now I thought these were exclusive options. At least, I am fairly certain I did not have to do this before and it does not feel correct to have to specify the proxy options twice. Can the developers of biomaRt/RCurl have a look? Or someone tell me what I have missed? Regards John Seers -----Original Message----- From: john seers (IFR) Sent: 05 June 2009 13:34 To: bioconductor at stat.math.ethz.ch Subject: FW: [BioC] biomaRt not working? Hi All I think we have found the problem and a workaround. Thanks to all who offered help and advice. Using the "--internet2" option to specify the proxy appears to not be good enough any more. Using the "http_proxy" option to specify the proxy server directly worked. I think "--internet2" says use the Explorer/browser options. Why this does not work any more I do not know. It could be a fix/change to Windows at my end that does not pass back the information as it used to? Or perhaps biomart/RCurl does not handle it well any more? Anyway, we are up and running again. Regards John -----Original Message----- From: john seers (IFR) Sent: 05 June 2009 09:23 To: 'Paul Leo' Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] biomaRt not working? Hi Paul That does not sound very hopeful. :( I am not sure I know how to go figure that. Perhaps the time has nearly come to approach the package owner for a suggestion. Perhaps I will try a bit more digging first. Perhaps see if I can trace the problem a bit deeper. Regards John -----Original Message----- From: Paul Leo [mailto:p.leo@uq.edu.au] Sent: 05 June 2009 09:08 To: john seers (IFR) Subject: RE: [BioC] biomaRt not working? I had something vaguely similar happen to me this week, using update.packages() I had the correct versions of BioMart and RCurl but it kept failing. I reinstalled R and BioC and all of a sudden it was fine ... go figure.... But that was on R.10 for linux.... - 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: Paul Leo <p.leo at="" uq.edu.au=""> Cc: Steve Pederson <stephen.pederson at="" adelaide.edu.au="">, 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 08:53:07 +0100 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