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
