Question: problems when trying to use biomaRt
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gravatar for Juan Pablo Fededa
9.8 years ago by
Juan Pablo Fededa50 wrote:
Dear bioconductor-help contributors, I'm trying to use biomaRt package in R, and when I run the last one of the next two lines, the R GUI crashes: library("biomaRt") ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") I'm using R 2.10.1 and the latest versions of biomaRt, XML ( downloaded from CRAN-extras) and RCurl. Do you have any idea of what can I change to make it work? Thanks in advance, Juan Pablo Fededa [[alternative HTML version deleted]]
gui biomart • 1.7k views
ADD COMMENTlink modified 9.8 years ago by Jenny Drnevich1.9k • written 9.8 years ago by Juan Pablo Fededa50
Answer: problems when trying to use biomaRt
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gravatar for Sean Davis
9.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, Mar 17, 2010 at 6:12 AM, Juan Pablo Fededa <jpfededa at="" gmail.com=""> wrote: > Dear bioconductor-help contributors, > > > I'm trying to use biomaRt package in R, and when I run the last one of the > next two lines, the R GUI crashes: > > library("biomaRt") > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > I'm using R 2.10.1 and the latest versions of biomaRt, XML ( downloaded from > CRAN-extras) and RCurl. > Do you have any idea of what can I change to make it work? Hi, Juan. There is not enough information here to help you. Please include the error message if you can and the output of sessionInfo() after loading biomaRt. Sean
ADD COMMENTlink written 9.8 years ago by Sean Davis21k
Answer: problems when trying to use biomaRt
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gravatar for Jenny Drnevich
9.8 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
Hi Juan, This won't be much help, other to say that I have the exact same problem on my machine, and I've never been able to figure out exactly what the problem is. I think it has something to do with our system's firewall or something, because once this happens, I can't even get biomart.org up on a browser!! It's like they are blocking the connection or something. Here's the start of the thread from before: https://stat.ethz.ch/pipermail/bioconductor/2009-November/030579.html. I confess I haven't spent much time since then trying to resolve the problem because I haven't really needed to use biomaRt. It is very inconvenient, and I'd like to figure it out at some point... Good luck, Jenny > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] biomaRt_2.2.0 limma_3.2.1 affyQCReport_1.24.0 [4] lattice_0.17-26 xtable_1.5-6 simpleaffy_2.22.0 [7] genefilter_1.28.2 made4_1.20.0 scatterplot3d_0.3-29 [10] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 [13] gdata_2.6.1 gtools_2.6.1 RColorBrewer_1.0-2 [16] ade4_1.4-14 affyPLM_1.22.0 preprocessCore_1.8.0 [19] gcrma_2.18.1 affycoretools_1.18.0 KEGG.db_2.3.5 [22] GO.db_2.3.5 RSQLite_0.8-0 DBI_0.2-5 [25] AnnotationDbi_1.8.1 affy_1.24.2 Biobase_2.6.1 [28] RWinEdt_1.8-2 loaded via a namespace (and not attached): [1] affyio_1.14.0 annaffy_1.18.0 annotate_1.24.0 Biostrings_2.14.10 [5] Category_2.12.0 GOstats_2.12.0 graph_1.24.1 GSEABase_1.8.0 [9] IRanges_1.4.9 RBGL_1.22.0 RCurl_1.2-1 splines_2.10.1 [13] survival_2.35-7 tools_2.10.1 XML_2.6-0 > At 06:00 AM 3/17/2010, Juan Pablo Fededa wrote: >Dear bioconductor-help contributors, > > >I'm trying to use biomaRt package in R, and when I run the next line, the R >GUI crashes: > >ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > >Theres is no error message at all, simply R is not responding anymore. >when loading library(biomaRt) the prompt sign appears again, and you can >already run basic things like: >listMarts() > >When I run sessionInfo() I get this: > >R version 2.10.1 (2009-12-14) >i386-pc-mingw32 > >locale: >[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >States.1252 >[3] LC_MONETARY=English_United States.1252 >LC_NUMERIC=C >[5] LC_TIME=English_United States.1252 > >attached base packages: >[1] stats graphics grDevices utils datasets methods base > >other attached packages: >[1] biomaRt_2.2.0 > >loaded via a namespace (and not attached): >[1] RCurl_1.3-1 XML_2.6-0 > >Do you have any idea of what can I change to make it work? >Thanks in advance, > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD COMMENTlink written 9.8 years ago by Jenny Drnevich1.9k
Answer: problems when trying to use biomaRt
0
gravatar for Jenny Drnevich
9.8 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
I did the debugging on useDataset, and it stopped here: Browse[2]> martAttributes(mart) <- bmAttrFilt("attributes", mart) I then started a fresh session and tried > debug(biomaRt:::bmAttrFilt) Within bmAttrFilt(), it stopped here: Browse[2]> attrfilt = bmRequest(request) bmRequest() is very simple: > biomaRt:::bmRequest function (request) { result = 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.") }) return(result) } <environment: namespace:biomart=""> So in another fresh R session, I tried debugging tryCatch, and it stopped here: Browse[2]> tryCatchList(expr, classes, parentenv, handlers) Interestingly, after ~1 min, the debugger did come back with the error message, and lot of other stuff and finally the prompt: Browse[2]> exiting from: 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.") }) debugging in: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error")) }) debug: { tryCatchList <- function(expr, names, parentenv, handlers) { nh <- length(names) if (nh > 1L) tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) else if (nh == 1L) tryCatchOne(expr, names, parentenv, handlers[[1L]]) else expr } tryCatchOne <- function(expr, name, parentenv, handler) { doTryCatch <- function(expr, name, parentenv, handler) { .Internal(.addCondHands(name, list(handler), parentenv, environment(), FALSE)) expr } value <- doTryCatch(return(expr), name, parentenv, handler) if (is.null(value[[1L]])) { msg <- .Internal(geterrmessage()) call <- value[[2L]] cond <- simpleError(msg, call) } else cond <- value[[1L]] value[[3L]](cond) } if (!missing(finally)) on.exit(finally) handlers <- list(...) classes <- names(handlers) parentenv <- parent.frame() if (length(classes) != length(handlers)) stop("bad handler specification") tryCatchList(expr, classes, parentenv, handlers) } Browse[2]> I think that's as far as I can go now. Any ideas? Thanks, Jenny > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.2-1 XML_2.6-0 > At 08:54 AM 3/17/2010, Juan Pablo Fededa wrote: >Thanks Martin, > >I get the next answer performing debug on useMart: > > > > library("biomaRt") > > debug(useMart) > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl") >debug: { > if (local || mysql || !missing(user) || !missing(password)) { > .Defunct(msg = "mysql access to Ensembl is no longer available >through this package the web service mode supports all queries. If mysql is >needed a separate package will become available with limited mysql query >support.") > } > if (missing(biomart)) > stop("No biomart databases specified. Specify a biomart database to >use using the biomart argument") > if (!(is.character(biomart))) > stop("biomart argument is no string. The biomart argument should be >a single character string") > marts = NULL > marts = listMarts(host = host, path = path, port = port, > includeHosts = TRUE, archive = archive) > mindex = match(biomart, marts$biomart) > if is.na(mindex) || archive) { > mindex = match(biomart, marts$database) > } > if is.na(mindex)) > stop("Incorrect BioMart name, use the listMarts function to see >which BioMart databases are available") > if is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) || > is.na(marts$host[mindex]) || is.na(marts$port[mindex]) || > is.na(marts$path[mindex])) > stop("The selected biomart databases is not available due to error >in the BioMart central registry, please report so the BioMart registry file >can be fixed.") > if (marts$path[mindex] == "") > marts$path[mindex] = "/biomart/martservice" > if (archive) > biomart = marts$biomart[mindex] > biomart = sub(" ", "%20", biomart) > mart <- new("Mart", biomart = biomart, vschema = marts$vschema[mindex], > host = paste("http://", marts$host[mindex], ":", marts$port[mindex], > > marts$path[mindex], sep = ""), archive = archive) > if (!missing(dataset)) { > mart = useDataset(mart = mart, dataset = dataset) > } > return(mart) >} >Browse[2]> > > >In the step-by-step execution of the above function, R GUI starts not >responding after: > >mart = useDataset(mart = mart, dataset = dataset) > >Any clue about what is going on? >Thanks again, > > >Juan > > > > > >On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > > On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: > > > Dear bioconductor-help contributors, > > > > > > > > > I'm trying to use biomaRt package in R, and when I run the next line, the > > R > > > GUI crashes: > > > > > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > > > > > Theres is no error message at all, simply R is not responding anymore. > > > when loading library(biomaRt) the prompt sign appears again, and you can > > > already run basic things like: > > > listMarts() > > > > This is unusual, because the only part of useMart that might end up with > > real trouble is a call to listMarts() ! Start R with the --vanilla > > argument, e.g., from the DOS shell > > > > Rgui --vanilla > > > > try to place a debugger on useMart, and step through until R stops > > responding. Restart R, get to a similar place, and look at the arguments > > to the function that causes problems. Any hints? > > > > > debug(useMart) > > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > Browser[2]> n > > > > ('n' is for 'next', see ?browser) > > > > Martin > > > > > > > > When I run sessionInfo() I get this: > > > > > > R version 2.10.1 (2009-12-14) > > > i386-pc-mingw32 > > > > > > locale: > > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > > States.1252 > > > [3] LC_MONETARY=English_United States.1252 > > > LC_NUMERIC=C > > > [5] LC_TIME=English_United States.1252 > > > > > > attached base packages: > > > [1] stats graphics grDevices utils datasets methods base > > > > > > other attached packages: > > > [1] biomaRt_2.2.0 > > > > > > loaded via a namespace (and not attached): > > > [1] RCurl_1.3-1 XML_2.6-0 > > > > > > Do you have any idea of what can I change to make it work? > > > Thanks in advance, > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > 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 > > > > > > -- > > Martin Morgan > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 > > > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD COMMENTlink written 9.8 years ago by Jenny Drnevich1.9k
Answer: problems when trying to use biomaRt
0
gravatar for Juan Pablo Fededa
9.8 years ago by
Juan Pablo Fededa50 wrote:
Dear bioconductor-help contributors, I'm trying to use biomaRt package in R, and when I run the next line, the R GUI crashes: ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") Theres is no error message at all, simply R is not responding anymore. when loading library(biomaRt) the prompt sign appears again, and you can already run basic things like: listMarts() When I run sessionInfo() I get this: R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] RCurl_1.3-1 XML_2.6-0 Do you have any idea of what can I change to make it work? Thanks in advance, [[alternative HTML version deleted]]
ADD COMMENTlink written 9.8 years ago by Juan Pablo Fededa50
On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: > Dear bioconductor-help contributors, > > > I'm trying to use biomaRt package in R, and when I run the next line, the R > GUI crashes: > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > Theres is no error message at all, simply R is not responding anymore. > when loading library(biomaRt) the prompt sign appears again, and you can > already run basic things like: > listMarts() This is unusual, because the only part of useMart that might end up with real trouble is a call to listMarts() ! Start R with the --vanilla argument, e.g., from the DOS shell Rgui --vanilla try to place a debugger on useMart, and step through until R stops responding. Restart R, get to a similar place, and look at the arguments to the function that causes problems. Any hints? > debug(useMart) > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") Browser[2]> n ('n' is for 'next', see ?browser) Martin > > When I run sessionInfo() I get this: > > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-1 XML_2.6-0 > > Do you have any idea of what can I change to make it work? > Thanks in advance, > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 9.8 years ago by Martin Morgan ♦♦ 24k
Thanks Martin, I get the next answer performing debug on useMart: > library("biomaRt") > debug(useMart) > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl") debug: { if (local || mysql || !missing(user) || !missing(password)) { .Defunct(msg = "mysql access to Ensembl is no longer available through this package the web service mode supports all queries. If mysql is needed a separate package will become available with limited mysql query support.") } if (missing(biomart)) stop("No biomart databases specified. Specify a biomart database to use using the biomart argument") if (!(is.character(biomart))) stop("biomart argument is no string. The biomart argument should be a single character string") marts = NULL marts = listMarts(host = host, path = path, port = port, includeHosts = TRUE, archive = archive) mindex = match(biomart, marts$biomart) if is.na(mindex) || archive) { mindex = match(biomart, marts$database) } if is.na(mindex)) stop("Incorrect BioMart name, use the listMarts function to see which BioMart databases are available") if is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) || is.na(marts$host[mindex]) || is.na(marts$port[mindex]) || is.na(marts$path[mindex])) stop("The selected biomart databases is not available due to error in the BioMart central registry, please report so the BioMart registry file can be fixed.") if (marts$path[mindex] == "") marts$path[mindex] = "/biomart/martservice" if (archive) biomart = marts$biomart[mindex] biomart = sub(" ", "%20", biomart) mart <- new("Mart", biomart = biomart, vschema = marts$vschema[mindex], host = paste("http://", marts$host[mindex], ":", marts$port[mindex], marts$path[mindex], sep = ""), archive = archive) if (!missing(dataset)) { mart = useDataset(mart = mart, dataset = dataset) } return(mart) } Browse[2]> In the step-by-step execution of the above function, R GUI starts not responding after: mart = useDataset(mart = mart, dataset = dataset) Any clue about what is going on? Thanks again, Juan On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: > > Dear bioconductor-help contributors, > > > > > > I'm trying to use biomaRt package in R, and when I run the next line, the > R > > GUI crashes: > > > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > > > Theres is no error message at all, simply R is not responding anymore. > > when loading library(biomaRt) the prompt sign appears again, and you can > > already run basic things like: > > listMarts() > > This is unusual, because the only part of useMart that might end up with > real trouble is a call to listMarts() ! Start R with the --vanilla > argument, e.g., from the DOS shell > > Rgui --vanilla > > try to place a debugger on useMart, and step through until R stops > responding. Restart R, get to a similar place, and look at the arguments > to the function that causes problems. Any hints? > > > debug(useMart) > > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > Browser[2]> n > > ('n' is for 'next', see ?browser) > > Martin > > > > > When I run sessionInfo() I get this: > > > > R version 2.10.1 (2009-12-14) > > i386-pc-mingw32 > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > States.1252 > > [3] LC_MONETARY=English_United States.1252 > > LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] biomaRt_2.2.0 > > > > loaded via a namespace (and not attached): > > [1] RCurl_1.3-1 XML_2.6-0 > > > > Do you have any idea of what can I change to make it work? > > Thanks in advance, > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
ADD REPLYlink written 9.8 years ago by Juan Pablo Fededa50
On 03/17/2010 06:54 AM, Juan Pablo Fededa wrote: > Thanks Martin, > > I get the next answer performing debug on useMart: > > >> library("biomaRt") >> debug(useMart) >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl") > debug: { > if (local || mysql || !missing(user) || !missing(password)) { > .Defunct(msg = "mysql access to Ensembl is no longer available > through this package the web service mode supports all queries. If mysql is > needed a separate package will become available with limited mysql query > support.") > } > if (missing(biomart)) > stop("No biomart databases specified. Specify a biomart database to > use using the biomart argument") > if (!(is.character(biomart))) > stop("biomart argument is no string. The biomart argument should be > a single character string") > marts = NULL > marts = listMarts(host = host, path = path, port = port, > includeHosts = TRUE, archive = archive) > mindex = match(biomart, marts$biomart) > if is.na(mindex) || archive) { > mindex = match(biomart, marts$database) > } > if is.na(mindex)) > stop("Incorrect BioMart name, use the listMarts function to see > which BioMart databases are available") > if is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) || > is.na(marts$host[mindex]) || is.na(marts$port[mindex]) || > is.na(marts$path[mindex])) > stop("The selected biomart databases is not available due to error > in the BioMart central registry, please report so the BioMart registry file > can be fixed.") > if (marts$path[mindex] == "") > marts$path[mindex] = "/biomart/martservice" > if (archive) > biomart = marts$biomart[mindex] > biomart = sub(" ", "%20", biomart) > mart <- new("Mart", biomart = biomart, vschema = marts$vschema[mindex], > host = paste("http://", marts$host[mindex], ":", marts$port[mindex], > > marts$path[mindex], sep = ""), archive = archive) > if (!missing(dataset)) { > mart = useDataset(mart = mart, dataset = dataset) > } > return(mart) > } > Browse[2]> > > > In the step-by-step execution of the above function, R GUI starts not > responding after: > > mart = useDataset(mart = mart, dataset = dataset) > > Any clue about what is going on? now try debug(useDataset), and so on. Some functions might not be exported from biomaRt's name space, and then you will need to debug(biomaRt:::bmAttrFilter), for instance. When you do get to the 'bottom' of the problem, it would be good to know what the variable values are, e.g., some biomaRt functions seem to compose a variable named 'request' that contains the string to be sent to biomaRt. >From Jenny's post, I'm not sure how successful this will be in the long run, but it would be helpful to have a precise location of the problem. Martin > Thanks again, > > > Juan > > > > > > On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > >> On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: >>> Dear bioconductor-help contributors, >>> >>> >>> I'm trying to use biomaRt package in R, and when I run the next line, the >> R >>> GUI crashes: >>> >>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >>> >>> Theres is no error message at all, simply R is not responding anymore. >>> when loading library(biomaRt) the prompt sign appears again, and you can >>> already run basic things like: >>> listMarts() >> >> This is unusual, because the only part of useMart that might end up with >> real trouble is a call to listMarts() ! Start R with the --vanilla >> argument, e.g., from the DOS shell >> >> Rgui --vanilla >> >> try to place a debugger on useMart, and step through until R stops >> responding. Restart R, get to a similar place, and look at the arguments >> to the function that causes problems. Any hints? >> >> > debug(useMart) >> > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> Browser[2]> n >> >> ('n' is for 'next', see ?browser) >> >> Martin >> >>> >>> When I run sessionInfo() I get this: >>> >>> R version 2.10.1 (2009-12-14) >>> i386-pc-mingw32 >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>> States.1252 >>> [3] LC_MONETARY=English_United States.1252 >>> LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] biomaRt_2.2.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.3-1 XML_2.6-0 >>> >>> Do you have any idea of what can I change to make it work? >>> Thanks in advance, >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> Martin Morgan >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 9.8 years ago by Martin Morgan ♦♦ 24k
Hi Martin, >now try debug(useDataset), and so on. Some functions might not be >exported from biomaRt's name space, and then you will need to >debug(biomaRt:::bmAttrFilter), for instance. When you do get to the >'bottom' of the problem, it would be good to know what the variable >values are, e.g., some biomaRt functions seem to compose a variable >named 'request' that contains the string to be sent to biomaRt. > > >From Jenny's post, I'm not sure how successful this will be in the long >run, but it would be helpful to have a precise location of the problem. Here are my variable values: debug: tryCatchList(expr, classes, parentenv, handlers) Browse[2]> expr [1] "\n<martregistry>\n <marturllocation database="\" ensembl_mart_57\""="" default="\" 1\""="" displayname="\" ENSEMBL"="" genes="" 57="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" ensembl\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" snp_mart_57\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" variation="" 57="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" snp\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" functional_genomics_mart_57\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" functional="" genomics="" 57="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" functional_genomics\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" vega_mart_57\""="" default="\" 0\""="" displayname="\" VEGA"="" 37="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" vega\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" genomic_features_mart_57\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" genomic="" features="" 57="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" genomic_features\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" ontology_mart_57\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" ontology="" 57="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" ontology\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" sequence_mart_57\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" sequence="" 57="" (sanger="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" sequence\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" bacterial_mart_4\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" bacteria="" 4="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" bacterial_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" bacterial_sequence_mart_4\""="" default="\" 0\""="" displayname="\" \""="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" bacterial_sequence_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" fungal_mart_4\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" fungal="" 4="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" fungal_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" fungal_sequence_mart_4\""="" default="\" 0\""="" displayname="\" \""="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" fungal_sequence_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" metazoa_genomic_features_mart_4\""="" default="\" 0\""="" displayname="\" \""="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" metazoa_genomic_features_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" metazoa_mart_4\""="" default="\" 1\""="" displayname="\" ENSEMBL"="" metazoa="" 4="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" metazoa_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" metazoa_sequence_mart_4\""="" default="\" 0\""="" displayname="\" \""="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" metazoa_sequence_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" plant_mart_4\""="" default="\" 0\""="" displayname="\" ENSEMBL"="" plant="" 4="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" plant_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" plant_sequence_mart_4\""="" default="\" 0\""="" displayname="\" \""="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" plant_sequence_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" protist_mart_4\""="" default="\" 1\""="" displayname="\" ENSEMBL"="" protists="" 4="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" protist_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" protist_sequence_mart_4\""="" default="\" 0\""="" displayname="\" \""="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" protist_sequence_mart_4\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 0\""=""/>\n <marturllocation database="\" msd_mart_4\""="" default="\" 0\""="" displayname="\" MSD"="" prototype="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" msd\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" utlp\""="" default="\" \""="" displayname="\" HIGH"="" throughput="" gene="" targeting="" and="" trapping="" (sanger="" uk)\"="" host="\" www.sanger.ac.uk\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" htgt\""="" path="\" htgt="" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" test_reactome_mart\""="" default="\" 1\""="" displayname="\" REACTOME"="" (cshl="" us)\"="" host="\" banon.cshl.edu\""="" includedatasets="\" complex,pathway,reaction,interaction\""="" martuser="\" \""="" name="\" REACTOME\""="" path="\" biomart="" martservice\""="" port="\" 5555\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" wormmart\""="" default="\" 1\""="" displayname="\" WORMBASE"="" (cshl="" us)\"="" host="\" www.wormbase.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" wormbase_current\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation default="\" 0\""="" displayname="\" DICTYBASE"="" (northwestern="" us)\"="" host="\" www.dictybase.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" dicty\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" dictyMart\""="" visible="\" 1\""=""/>\n <marturllocation database="\" biomart\""="" default="\" 1\""="" displayname="\" MGI"="" (jackson="" laboratory="" us)\"="" host="\" biomart.informatics.jax.org\""="" includedatasets="\" markers\""="" name="\" biomart\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" rgd__mart\""="" default="\" \""="" displayname="\" RGD"="" genes="" (mcw="" us)\"="" host="\" rote.hmgc.mcw.edu\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" rgd__mart\""="" path="\" biomart="" martservice\""="" port="\" 9999\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" ipi_rat__mart\""="" default="\" \""="" displayname="\" RGD"="" ipi="" mart="" (mcw="" us)\"="" host="\" rote.hmgc.mcw.edu\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" ipi_rat__mart\""="" path="\" biomart="" martservice\""="" port="\" 9999\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" SSLP__mart\""="" default="\" \""="" displayname="\" RGD"="" microsatellite="" markers="" (mcw="" us)\"="" host="\" rote.hmgc.mcw.edu\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" SSLP__mart\""="" path="\" biomart="" martservice\""="" port="\" 9999\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" g4public\""="" default="\" \""="" displayname="\" HGNC"="" (ebi="" uk)\"="" host="\" www.genenames.org\""="" includedatasets="\" \""="" name="\" g4public\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" pride_mart_1\""="" default="\" 1\""="" displayname="\" PRIDE"="" (ebi="" uk)\"="" host="\" www.ebi.ac.uk\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" pride\""="" path="\" pride="" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" intermart_2\""="" default="\" 1\""="" displayname="\" INTERPRO"="" (ebi="" uk)\"="" host="\" www.biomart.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" prod-intermart_2\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" SPMART\""="" default="\" \""="" displayname="\" UNIPROT"="" (ebi="" uk)\"="" host="\" www.ebi.ac.uk\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" uniprot_mart\""="" path="\" uniprot="" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" ensembl_expressionmart_48\""="" default="\" 1\""="" displayname="\" EURATMART"="" (ebi="" uk)\"="" host="\" www.ebi.ac.uk\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" ensembl_expressionmart_48\""="" path="\" euratools="" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" biomartDB\""="" default="\" \""="" displayname="\" PARAMECIUM"="" genome="" (cnrs="" france)\"="" host="\" paramecium.cgm.cnrs-gif.fr\""="" includedatasets="\" macronuclear\""="" martuser="\" \""="" name="\" biomartDB\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" tdb_biomart_new\""="" default="\" \""="" displayname="\" EUREXPRESS"="" (mrc="" edinburgh="" uk)\"="" host="\" biomart.eurexpress.org\""="" includedatasets="\" template\""="" martuser="\" \""="" name="\" Eurexpress"="" biomart\"="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" pepseekerGOLD_mart06\""="" default="\" 0\""="" displayname="\" PEPSEEKER"="" (university="" of="" manchester="" uk)\"="" host="\" www.ispider.manchester.ac.uk\""="" includedatasets="\" peptide\""="" martuser="\" \""="" name="\" pepseekerGOLD_mart06\""="" path="\" pepseeker="" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" pepseekerGOLD\""="" visible="\" 1\""=""/>\n <marturllocation database="\" datacippotato_martpot_001\""="" default="\" \""="" displayname="\" DB_POTATO"="" (international="" potato="" center-cip)\"="" host="\" germplasmdb.cip.cgiar.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" Potato_01\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" datacipsweet_martsweet_001\""="" default="\" \""="" displayname="\" DB_SWEETPOTATO"="" (international="" potato="" center-cip)\"="" host="\" germplasmdb.cip.cgiar.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" Sweetpotato_01\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" phytozome_mart_v5\""="" default="\" \""="" displayname="\" PHYTOZOME"="" (jgi="" cig="" us)\"="" host="\" www.phytozome.net\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" phytozome_mart\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" zome_mart\""="" visible="\" 1\""=""/>\n <marturllocation database="\" sequence_mart_v5\""="" default="\" \""="" displayname="\" Sequences\""="" host="\" www.phytozome.net\""="" includedatasets="\" sequence_phytozome\""="" martuser="\" \""="" name="\" sequence_mart\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" zome_mart\""="" visible="\" 0\""=""/>\n <marturllocation database="\" mart_cyanobase_1\""="" default="\" 1\""="" displayname="\" CYANOBASE"="" 1="" (kazusa="" japan)\"="" host="\" mart.kazusa.or.jp\""="" includedatasets="\" \""="" martuser="\" default\""="" name="\" cyanobase_1\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" hapmart_27_36\""="" default="\" 1\""="" displayname="\" HAPMAP"="" 27="" (ncbi="" us)\"="" host="\" hapmap.ncbi.nlm.nih.gov\""="" includedatasets="\" \""="" name="\" HapMap_rel27\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" rel27_NCBI_Build36\""="" visible="\" 1\""=""/>\n <marturllocation database="\" cosp\""="" default="\" 1\""="" displayname="\" COSMIC"="" (sanger="" uk)\"="" host="\" www.sanger.ac.uk\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" CosmicMart\""="" path="\" genetics="" CGP="" cosmic="" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" cosmic\""="" visible="\" 1\""=""/>\n <marturllocation database="\" ciliumDBall\""="" default="\" \""="" displayname="\" CILDB"="" inparanoid="" and="" filtered="" best="" hit="" (cnrs="" france)\"="" host="\" cildb.cgm.cnrs-gif.fr\""="" includedatasets="\" \""="" name="\" ciliumDBall\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" ciliumDBinp\""="" default="\" \""="" displayname="\" CILDB"="" inparanoid="" (cnrs="" france)\"="" host="\" cildb.cgm.cnrs-gif.fr\""="" includedatasets="\" \""="" name="\" ciliumDBinp\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" ciliumDBcutoff\""="" default="\" \""="" displayname="\" CILDB"="" filtered="" blastp="" (cnrs="" france)\"="" host="\" cildb.cgm.cnrs-gif.fr\""="" includedatasets="\" \""="" name="\" ciliumDBcutoff\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n <marturllocation database="\" ensembl_latest\""="" default="\" \""="" displayname="\" PANCREATIC"="" expression="" database="" (institute="" of="" cancer="" uk)\"="" host="\" www.pancreasexpression.org\""="" includedatasets="\" \""="" martuser="\" \""="" name="\" Ensembl56\""="" path="\" biomart="" martservice\""="" port="\" 80\""="" redirect="\" 1\""="" servervirtualschema="\" default\""="" visible="\" 1\""=""/>\n</martregistry>\n" Browse[2]> classes [1] "error" Browse[2]> parentenv <environment: 0x023bb8e8=""> Browse[2]> handlers $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.") } <environment: 0x023bb8e8=""> Browse[2]> Thanks, Jenny >Martin > > > Thanks again, > > > > > > Juan > > > > > > > > > > > > On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > > >> On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: > >>> Dear bioconductor-help contributors, > >>> > >>> > >>> I'm trying to use biomaRt package in R, and when I run the next line, the > >> R > >>> GUI crashes: > >>> > >>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > >>> > >>> Theres is no error message at all, simply R is not responding anymore. > >>> when loading library(biomaRt) the prompt sign appears again, and you can > >>> already run basic things like: > >>> listMarts() > >> > >> This is unusual, because the only part of useMart that might end up with > >> real trouble is a call to listMarts() ! Start R with the --vanilla > >> argument, e.g., from the DOS shell > >> > >> Rgui --vanilla > >> > >> try to place a debugger on useMart, and step through until R stops > >> responding. Restart R, get to a similar place, and look at the arguments > >> to the function that causes problems. Any hints? > >> > >> > debug(useMart) > >> > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > >> Browser[2]> n > >> > >> ('n' is for 'next', see ?browser) > >> > >> Martin > >> > >>> > >>> When I run sessionInfo() I get this: > >>> > >>> R version 2.10.1 (2009-12-14) > >>> i386-pc-mingw32 > >>> > >>> locale: > >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > >>> States.1252 > >>> [3] LC_MONETARY=English_United States.1252 > >>> LC_NUMERIC=C > >>> [5] LC_TIME=English_United States.1252 > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] biomaRt_2.2.0 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] RCurl_1.3-1 XML_2.6-0 > >>> > >>> Do you have any idea of what can I change to make it work? > >>> Thanks in advance, > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> 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 > >> > >> > >> -- > >> Martin Morgan > >> Computational Biology / Fred Hutchinson Cancer Research Center > >> 1100 Fairview Ave. N. > >> PO Box 19024 Seattle, WA 98109 > >> > >> Location: Arnold Building M1 B861 > >> Phone: (206) 667-2793 > >> > > > > >-- >Martin Morgan >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M1 B861 >Phone: (206) 667-2793 > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD REPLYlink written 9.8 years ago by Jenny Drnevich1.9k
Hi Jenny -- On 03/17/2010 08:13 AM, Jenny Drnevich wrote: > Hi Martin, > >> now try debug(useDataset), and so on. Some functions might not be >> exported from biomaRt's name space, and then you will need to >> debug(biomaRt:::bmAttrFilter), for instance. When you do get to the >> 'bottom' of the problem, it would be good to know what the variable >> values are, e.g., some biomaRt functions seem to compose a variable >> named 'request' that contains the string to be sent to biomaRt. >> >> >From Jenny's post, I'm not sure how successful this will be in the long >> run, but it would be helpful to have a precise location of the problem. > > Here are my variable values: > > debug: tryCatchList(expr, classes, parentenv, handlers) > Browse[2]> expr > [1] "\n<martregistry>\n <marturllocation database="\" ensembl_mart_57\""=""> default=\"1\" displayName=\"ENSEMBL GENES 57 (SANGER UK)\" hmm, a little too deep. Let's try trace(biomaRt:::bmRequest, quote(print(request)), quote(print("done"))) useMart("ensembl", dataset="hsapiens_gene_ensembl") My output is below, what does yours look like? Each of those http://... should be executable in a web browser (watch for line endings -- these should just be one line long). If the url doesn't load in the browser, then it seems very likely that it is a BioMart issue (e.g., blocked ports) and not an R issue, which is where your previous thread ended up. If it does load in the browser, it might be interesting to try the troublesome (i.e., last reported) url in a new R session with RCurl directly library(RCurl) getURL("http://...", ssl.verifypeer=TRUE) perhaps one or several times Martin > trace(biomaRt:::bmRequest, quote(print(request)), quote(print("done"))) Tracing function "bmRequest" in package "biomaRt (not-exported)" [1] "bmRequest" > useMart("ensembl", dataset="hsapiens_gene_ensembl") Tracing bmRequest(paste("http://", host, ":", port, path, "?type=registry&requestid=biomaRt", .... on entry [1] "http://www.biomart.org:80/biomart/martservice?type=registry&requestid =biomaRt" Tracing bmRequest(paste("http://", host, ":", port, path, "?type=registry&requestid=biomaRt", .... on exit [1] "done" Checking attributes ...Tracing bmRequest(request) on entry [1] "http://www.biomart.org:80/biomart/martservice?type=attributes&dataset =hsapiens_gene_ensembl&requestid=biomaRt&mart=ensembl&virtualSchema=de fault" Tracing bmRequest(request) on exit [1] "done" ok Checking filters ...Tracing bmRequest(request) on entry [1] "http://www.biomart.org:80/biomart/martservice?type=filters&dataset=hs apiens_gene_ensembl&requestid=biomaRt&mart=ensembl&virtualSchema=defau lt" Tracing bmRequest(request) on exit [1] "done" ok -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 9.8 years ago by Martin Morgan ♦♦ 24k
I found out that is Windows specific, all the functions work fine in Mac I just found out. I also try different version of R on Win and none worked with biomaRt. Any clue from this facts? TNX, Juan On Wed, Mar 17, 2010 at 3:29 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 03/17/2010 06:54 AM, Juan Pablo Fededa wrote: > > Thanks Martin, > > > > I get the next answer performing debug on useMart: > > > > > >> library("biomaRt") > >> debug(useMart) > >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > debug: { > > if (local || mysql || !missing(user) || !missing(password)) { > > .Defunct(msg = "mysql access to Ensembl is no longer available > > through this package the web service mode supports all queries. If mysql > is > > needed a separate package will become available with limited mysql query > > support.") > > } > > if (missing(biomart)) > > stop("No biomart databases specified. Specify a biomart database > to > > use using the biomart argument") > > if (!(is.character(biomart))) > > stop("biomart argument is no string. The biomart argument should > be > > a single character string") > > marts = NULL > > marts = listMarts(host = host, path = path, port = port, > > includeHosts = TRUE, archive = archive) > > mindex = match(biomart, marts$biomart) > > if is.na(mindex) || archive) { > > mindex = match(biomart, marts$database) > > } > > if is.na(mindex)) > > stop("Incorrect BioMart name, use the listMarts function to see > > which BioMart databases are available") > > if is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) || > > is.na(marts$host[mindex]) || is.na(marts$port[mindex]) || > > is.na(marts$path[mindex])) > > stop("The selected biomart databases is not available due to > error > > in the BioMart central registry, please report so the BioMart registry > file > > can be fixed.") > > if (marts$path[mindex] == "") > > marts$path[mindex] = "/biomart/martservice" > > if (archive) > > biomart = marts$biomart[mindex] > > biomart = sub(" ", "%20", biomart) > > mart <- new("Mart", biomart = biomart, vschema = > marts$vschema[mindex], > > host = paste("http://", marts$host[mindex], ":", > marts$port[mindex], > > > > marts$path[mindex], sep = ""), archive = archive) > > if (!missing(dataset)) { > > mart = useDataset(mart = mart, dataset = dataset) > > } > > return(mart) > > } > > Browse[2]> > > > > > > In the step-by-step execution of the above function, R GUI starts not > > responding after: > > > > mart = useDataset(mart = mart, dataset = dataset) > > > > Any clue about what is going on? > > now try debug(useDataset), and so on. Some functions might not be > exported from biomaRt's name space, and then you will need to > debug(biomaRt:::bmAttrFilter), for instance. When you do get to the > 'bottom' of the problem, it would be good to know what the variable > values are, e.g., some biomaRt functions seem to compose a variable > named 'request' that contains the string to be sent to biomaRt. > > From Jenny's post, I'm not sure how successful this will be in the long > run, but it would be helpful to have a precise location of the problem. > > Martin > > > Thanks again, > > > > > > Juan > > > > > > > > > > > > On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan@fhcrc.org> > wrote: > > > >> On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: > >>> Dear bioconductor-help contributors, > >>> > >>> > >>> I'm trying to use biomaRt package in R, and when I run the next line, > the > >> R > >>> GUI crashes: > >>> > >>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > >>> > >>> Theres is no error message at all, simply R is not responding anymore. > >>> when loading library(biomaRt) the prompt sign appears again, and you > can > >>> already run basic things like: > >>> listMarts() > >> > >> This is unusual, because the only part of useMart that might end up with > >> real trouble is a call to listMarts() ! Start R with the --vanilla > >> argument, e.g., from the DOS shell > >> > >> Rgui --vanilla > >> > >> try to place a debugger on useMart, and step through until R stops > >> responding. Restart R, get to a similar place, and look at the arguments > >> to the function that causes problems. Any hints? > >> > >> > debug(useMart) > >> > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > >> Browser[2]> n > >> > >> ('n' is for 'next', see ?browser) > >> > >> Martin > >> > >>> > >>> When I run sessionInfo() I get this: > >>> > >>> R version 2.10.1 (2009-12-14) > >>> i386-pc-mingw32 > >>> > >>> locale: > >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > >>> States.1252 > >>> [3] LC_MONETARY=English_United States.1252 > >>> LC_NUMERIC=C > >>> [5] LC_TIME=English_United States.1252 > >>> > >>> attached base packages: > >>> [1] stats graphics grDevices utils datasets methods base > >>> > >>> other attached packages: > >>> [1] biomaRt_2.2.0 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] RCurl_1.3-1 XML_2.6-0 > >>> > >>> Do you have any idea of what can I change to make it work? > >>> Thanks in advance, > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > >> -- > >> Martin Morgan > >> Computational Biology / Fred Hutchinson Cancer Research Center > >> 1100 Fairview Ave. N. > >> PO Box 19024 Seattle, WA 98109 > >> > >> Location: Arnold Building M1 B861 > >> Phone: (206) 667-2793 > >> > > > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
ADD REPLYlink written 9.8 years ago by Juan Pablo Fededa50
Answer: problems when trying to use biomaRt
0
gravatar for Jenny Drnevich
9.8 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
Hi Juan, Was your Mac on the same internet connection as your PC? I have trouble with my PC in my office, but other PC's at the University (but not our network) don't have this problem. I think one of my co-workers has a Mac - if I have time tomorrow, I'll see if he'll let me test it out on his machine through our network. Jenny At 09:47 AM 3/17/2010, Juan Pablo Fededa wrote: >I found out that is Windows specific, all the functions work fine in Mac I >just found out. >I also try different version of R on Win and none worked with biomaRt. >Any clue from this facts? >TNX, > > >Juan > >On Wed, Mar 17, 2010 at 3:29 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > > On 03/17/2010 06:54 AM, Juan Pablo Fededa wrote: > > > Thanks Martin, > > > > > > I get the next answer performing debug on useMart: > > > > > > > > >> library("biomaRt") > > >> debug(useMart) > > >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > > debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > > debug: { > > > if (local || mysql || !missing(user) || !missing(password)) { > > > .Defunct(msg = "mysql access to Ensembl is no longer available > > > through this package the web service mode supports all queries. If mysql > > is > > > needed a separate package will become available with limited mysql query > > > support.") > > > } > > > if (missing(biomart)) > > > stop("No biomart databases specified. Specify a biomart database > > to > > > use using the biomart argument") > > > if (!(is.character(biomart))) > > > stop("biomart argument is no string. The biomart argument should > > be > > > a single character string") > > > marts = NULL > > > marts = listMarts(host = host, path = path, port = port, > > > includeHosts = TRUE, archive = archive) > > > mindex = match(biomart, marts$biomart) > > > if is.na(mindex) || archive) { > > > mindex = match(biomart, marts$database) > > > } > > > if is.na(mindex)) > > > stop("Incorrect BioMart name, use the listMarts function to see > > > which BioMart databases are available") > > > if is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) || > > > is.na(marts$host[mindex]) || is.na(marts$port[mindex]) || > > > is.na(marts$path[mindex])) > > > stop("The selected biomart databases is not available due to > > error > > > in the BioMart central registry, please report so the BioMart registry > > file > > > can be fixed.") > > > if (marts$path[mindex] == "") > > > marts$path[mindex] = "/biomart/martservice" > > > if (archive) > > > biomart = marts$biomart[mindex] > > > biomart = sub(" ", "%20", biomart) > > > mart <- new("Mart", biomart = biomart, vschema = > > marts$vschema[mindex], > > > host = paste("http://", marts$host[mindex], ":", > > marts$port[mindex], > > > > > > marts$path[mindex], sep = ""), archive = archive) > > > if (!missing(dataset)) { > > > mart = useDataset(mart = mart, dataset = dataset) > > > } > > > return(mart) > > > } > > > Browse[2]> > > > > > > > > > In the step-by-step execution of the above function, R GUI starts not > > > responding after: > > > > > > mart = useDataset(mart = mart, dataset = dataset) > > > > > > Any clue about what is going on? > > > > now try debug(useDataset), and so on. Some functions might not be > > exported from biomaRt's name space, and then you will need to > > debug(biomaRt:::bmAttrFilter), for instance. When you do get to the > > 'bottom' of the problem, it would be good to know what the variable > > values are, e.g., some biomaRt functions seem to compose a variable > > named 'request' that contains the string to be sent to biomaRt. > > > > From Jenny's post, I'm not sure how successful this will be in the long > > run, but it would be helpful to have a precise location of the problem. > > > > Martin > > > > > Thanks again, > > > > > > > > > Juan > > > > > > > > > > > > > > > > > > On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> > > wrote: > > > > > >> On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: > > >>> Dear bioconductor-help contributors, > > >>> > > >>> > > >>> I'm trying to use biomaRt package in R, and when I run the next line, > > the > > >> R > > >>> GUI crashes: > > >>> > > >>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > >>> > > >>> Theres is no error message at all, simply R is not responding anymore. > > >>> when loading library(biomaRt) the prompt sign appears again, and you > > can > > >>> already run basic things like: > > >>> listMarts() > > >> > > >> This is unusual, because the only part of useMart that might end up with > > >> real trouble is a call to listMarts() ! Start R with the --vanilla > > >> argument, e.g., from the DOS shell > > >> > > >> Rgui --vanilla > > >> > > >> try to place a debugger on useMart, and step through until R stops > > >> responding. Restart R, get to a similar place, and look at the arguments > > >> to the function that causes problems. Any hints? > > >> > > >> > debug(useMart) > > >> > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > >> Browser[2]> n > > >> > > >> ('n' is for 'next', see ?browser) > > >> > > >> Martin > > >> > > >>> > > >>> When I run sessionInfo() I get this: > > >>> > > >>> R version 2.10.1 (2009-12-14) > > >>> i386-pc-mingw32 > > >>> > > >>> locale: > > >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > >>> States.1252 > > >>> [3] LC_MONETARY=English_United States.1252 > > >>> LC_NUMERIC=C > > >>> [5] LC_TIME=English_United States.1252 > > >>> > > >>> attached base packages: > > >>> [1] stats graphics grDevices utils datasets methods base > > >>> > > >>> other attached packages: > > >>> [1] biomaRt_2.2.0 > > >>> > > >>> loaded via a namespace (and not attached): > > >>> [1] RCurl_1.3-1 XML_2.6-0 > > >>> > > >>> Do you have any idea of what can I change to make it work? > > >>> Thanks in advance, > > >>> > > >>> [[alternative HTML version deleted]] > > >>> > > >>> _______________________________________________ > > >>> 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 > > >> > > >> > > >> -- > > >> Martin Morgan > > >> Computational Biology / Fred Hutchinson Cancer Research Center > > >> 1100 Fairview Ave. N. > > >> PO Box 19024 Seattle, WA 98109 > > >> > > >> Location: Arnold Building M1 B861 > > >> Phone: (206) 667-2793 > > >> > > > > > > > > > -- > > Martin Morgan > > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > > PO Box 19024 Seattle, WA 98109 > > > > Location: Arnold Building M1 B861 > > Phone: (206) 667-2793 > > > > [[alternative HTML version deleted]] > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD COMMENTlink written 9.8 years ago by Jenny Drnevich1.9k
Hi Jenny & Martin, To Jenny,yes, my MAC was in the same internet connection. To Martin, when I try to debug useDataset I get this: > library("biomaRt") > debug(useDataset) > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") debugging in: useDataset(mart = mart, dataset = dataset) debug: { if (missing(mart) || class(mart) != "Mart") stop("No valid Mart object given, specify a Mart object with the attribute mart") if (missing(dataset)) stop("No dataset given. Please use the dataset argument to specify which dataset you want to use. Correct dataset names can be obtained with the listDatasets function.") validDatasets = listDatasets(mart) if is.na(match(dataset, validDatasets$dataset))) stop(paste("The given dataset: ", dataset, ", is not valid. Correct dataset names can be obtained with the listDatasets function.")) martDataset(mart) = dataset messageToUser("Checking attributes ...") martAttributes(mart) <- bmAttrFilt("attributes", mart) messageToUser(" ok\n") messageToUser("Checking filters ...") martFilters(mart) <- bmAttrFilt("filters", mart) messageToUser(" ok\n") return(mart) } Browse[2]> n debug: if (missing(mart) || class(mart) != "Mart") stop("No valid Mart object given, specify a Mart object with the attribute mart") Browse[2]> debug: NULL Browse[2]> debug: if (missing(dataset)) stop("No dataset given. Please use the dataset argument to specify which dataset you want to use. Correct dataset names can be obtained with the listDatasets function.") Browse[2]> debug: NULL Browse[2]> debug: validDatasets = listDatasets(mart) Browse[2]> debug: if is.na(match(dataset, validDatasets$dataset))) stop(paste("The given dataset: ", dataset, ", is not valid. Correct dataset names can be obtained with the listDatasets function.")) Browse[2]> debug: NULL Browse[2]> debug: martDataset(mart) = dataset Browse[2]> debug: messageToUser("Checking attributes ...") Browse[2]> Checking attributes ...debug: martAttributes(mart) <- bmAttrFilt("attributes", mart) Browse[2]> R CRASH ( not responding any more) Then, I opened again R and tryed to debug bmAttrFilt, but I get this message when trying to do so: > library("biomaRt") > debug(bmAttrFilt) Error in debug(bmAttrFilt) : object 'bmAttrFilt' not found > Do you have any idea how to follow debugging? Thanks to both, Juan On Wed, Mar 17, 2010 at 11:05 PM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Juan, > > Was your Mac on the same internet connection as your PC? I have trouble > with my PC in my office, but other PC's at the University (but not our > network) don't have this problem. I think one of my co-workers has a Mac - > if I have time tomorrow, I'll see if he'll let me test it out on his machine > through our network. > > Jenny > > > At 09:47 AM 3/17/2010, Juan Pablo Fededa wrote: > >> I found out that is Windows specific, all the functions work fine in Mac I >> just found out. >> I also try different version of R on Win and none worked with biomaRt. >> Any clue from this facts? >> TNX, >> >> >> Juan >> >> On Wed, Mar 17, 2010 at 3:29 PM, Martin Morgan <mtmorgan@fhcrc.org> >> wrote: >> >> > On 03/17/2010 06:54 AM, Juan Pablo Fededa wrote: >> > > Thanks Martin, >> > > >> > > I get the next answer performing debug on useMart: >> > > >> > > >> > >> library("biomaRt") >> > >> debug(useMart) >> > >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > > debugging in: useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > > debug: { >> > > if (local || mysql || !missing(user) || !missing(password)) { >> > > .Defunct(msg = "mysql access to Ensembl is no longer available >> > > through this package the web service mode supports all queries. If >> mysql >> > is >> > > needed a separate package will become available with limited mysql >> query >> > > support.") >> > > } >> > > if (missing(biomart)) >> > > stop("No biomart databases specified. Specify a biomart >> database >> > to >> > > use using the biomart argument") >> > > if (!(is.character(biomart))) >> > > stop("biomart argument is no string. The biomart argument >> should >> > be >> > > a single character string") >> > > marts = NULL >> > > marts = listMarts(host = host, path = path, port = port, >> > > includeHosts = TRUE, archive = archive) >> > > mindex = match(biomart, marts$biomart) >> > > if is.na(mindex) || archive) { >> > > mindex = match(biomart, marts$database) >> > > } >> > > if is.na(mindex)) >> > > stop("Incorrect BioMart name, use the listMarts function to >> see >> > > which BioMart databases are available") >> > > if is.na(marts$path[mindex]) || is.na(marts$vschema[mindex]) || >> > > is.na(marts$host[mindex]) || is.na(marts$port[mindex]) || >> > > is.na(marts$path[mindex])) >> > > stop("The selected biomart databases is not available due to >> > error >> > > in the BioMart central registry, please report so the BioMart registry >> > file >> > > can be fixed.") >> > > if (marts$path[mindex] == "") >> > > marts$path[mindex] = "/biomart/martservice" >> > > if (archive) >> > > biomart = marts$biomart[mindex] >> > > biomart = sub(" ", "%20", biomart) >> > > mart <- new("Mart", biomart = biomart, vschema = >> > marts$vschema[mindex], >> > > host = paste("http://", marts$host[mindex], ":", >> > marts$port[mindex], >> > > >> > > marts$path[mindex], sep = ""), archive = archive) >> > > if (!missing(dataset)) { >> > > mart = useDataset(mart = mart, dataset = dataset) >> > > } >> > > return(mart) >> > > } >> > > Browse[2]> >> > > >> > > >> > > In the step-by-step execution of the above function, R GUI starts not >> > > responding after: >> > > >> > > mart = useDataset(mart = mart, dataset = dataset) >> > > >> > > Any clue about what is going on? >> > >> > now try debug(useDataset), and so on. Some functions might not be >> > exported from biomaRt's name space, and then you will need to >> > debug(biomaRt:::bmAttrFilter), for instance. When you do get to the >> > 'bottom' of the problem, it would be good to know what the variable >> > values are, e.g., some biomaRt functions seem to compose a variable >> > named 'request' that contains the string to be sent to biomaRt. >> > >> > From Jenny's post, I'm not sure how successful this will be in the long >> > run, but it would be helpful to have a precise location of the problem. >> > >> > Martin >> > >> > > Thanks again, >> > > >> > > >> > > Juan >> > > >> > > >> > > >> > > >> > > >> > > On Wed, Mar 17, 2010 at 2:39 PM, Martin Morgan <mtmorgan@fhcrc.org> >> > wrote: >> > > >> > >> On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote: >> > >>> Dear bioconductor-help contributors, >> > >>> >> > >>> >> > >>> I'm trying to use biomaRt package in R, and when I run the next >> line, >> > the >> > >> R >> > >>> GUI crashes: >> > >>> >> > >>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > >>> >> > >>> Theres is no error message at all, simply R is not responding >> anymore. >> > >>> when loading library(biomaRt) the prompt sign appears again, and you >> > can >> > >>> already run basic things like: >> > >>> listMarts() >> > >> >> > >> This is unusual, because the only part of useMart that might end up >> with >> > >> real trouble is a call to listMarts() ! Start R with the --vanilla >> > >> argument, e.g., from the DOS shell >> > >> >> > >> Rgui --vanilla >> > >> >> > >> try to place a debugger on useMart, and step through until R stops >> > >> responding. Restart R, get to a similar place, and look at the >> arguments >> > >> to the function that causes problems. Any hints? >> > >> >> > >> > debug(useMart) >> > >> > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > >> Browser[2]> n >> > >> >> > >> ('n' is for 'next', see ?browser) >> > >> >> > >> Martin >> > >> >> > >>> >> > >>> When I run sessionInfo() I get this: >> > >>> >> > >>> R version 2.10.1 (2009-12-14) >> > >>> i386-pc-mingw32 >> > >>> >> > >>> locale: >> > >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> > >>> States.1252 >> > >>> [3] LC_MONETARY=English_United States.1252 >> > >>> LC_NUMERIC=C >> > >>> [5] LC_TIME=English_United States.1252 >> > >>> >> > >>> attached base packages: >> > >>> [1] stats graphics grDevices utils datasets methods base >> > >>> >> > >>> other attached packages: >> > >>> [1] biomaRt_2.2.0 >> > >>> >> > >>> loaded via a namespace (and not attached): >> > >>> [1] RCurl_1.3-1 XML_2.6-0 >> > >>> >> > >>> Do you have any idea of what can I change to make it work? >> > >>> Thanks in advance, >> > >>> >> > >>> [[alternative HTML version deleted]] >> > >>> >> > >>> _______________________________________________ >> > >>> Bioconductor mailing list >> > >>> Bioconductor@stat.math.ethz.ch >> > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >>> Search the archives: >> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> > >> >> > >> -- >> > >> Martin Morgan >> > >> Computational Biology / Fred Hutchinson Cancer Research Center >> > >> 1100 Fairview Ave. N. >> > >> PO Box 19024 Seattle, WA 98109 >> > >> >> > >> Location: Arnold Building M1 B861 >> > >> Phone: (206) 667-2793 >> > >> >> > > >> > >> > >> > -- >> > Martin Morgan >> > Computational Biology / Fred Hutchinson Cancer Research Center >> > 1100 Fairview Ave. N. >> > PO Box 19024 Seattle, WA 98109 >> > >> > Location: Arnold Building M1 B861 >> > Phone: (206) 667-2793 >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]
ADD REPLYlink written 9.7 years ago by Juan Pablo Fededa50
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