[BioC] bug report in pathview (XML?)
Luo Weijun
luo_weijun at yahoo.com
Sat Sep 7 02:21:34 CEST 2013
Hi Martin,
I actually communicated offline with Shang yesterday. I couldn’t not reproduce the error/crash running his code with his data on both Linux and Mac machine. Shang mentioned their Windows version worked just fine. A similar example on metagenomic data mapped to KEGG ortholog pathways works fine in pathview vignette too. This crash problem hasn’t been reported by any other users. I believe it is because of the specially setting of their 64-bit redhat system.
Very likely XML package has some problem in their machine based on the error message. Upon my suggestion, they’ve updated their R/bioconductor and reinstalled XML package from source. The problem is still there. I am cc’ing, Duncan Temple Lang, the author of XML package in the message. Hope he may have a better idea on the cause of the problem.
Thanks!
Weijun
--------------------------------------------
On Fri, 9/6/13, Martin Morgan <mtmorgan at fhcrc.org> wrote:
Subject: Re: [BioC] bug report in pathview
To: "shang [guest]" <guest at bioconductor.org>
Date: Friday, September 6, 2013, 12:16 PM
On 09/05/2013 06:44 PM, shang [guest]
wrote:
>
> there is a segment fault when using the pathview
package data analysis in redhat el 5 64bit server, the error
report as,
>
-------------------------------------------------------
> Only KEGG ortholog gene ID is supported, make sure it
[[elided Yahoo spam]]
>
> *** caught segfault ***
> address 0x3300000000, cause 'memory not mapped'
>
> Traceback:
> 1: .Call("RS_XML_ParseTree",
as.character(file), handlers, as.logical(ignoreBla
nks),
as.logical(replaceEntities),
as.logical(asText), as.logical(trim),
as.logical(validate),
as.logical(getDTD), as.logical(isURL),
as.logical(add
AttributeNamespaces),
as.logical(useInternalNodes),
as.logical(isHTML), as.l
ogical(isSchema),
as.logical(fullNamespaceInfo),
as.character(encoding), as.
>
logical(useDotNames), xinclude,
error, addFinalizer, as.integer(options),
as
.logical(parentFirst),
PACKAGE = "XML")
> 2: xmlTreeParse(file, getDTD = FALSE)
this looks like a bug in the XML package. Is there a way
that you can reduce
your script (I don't think pathview.R is from the package?)
to a reproducible
example that others can run?
Martin
> 3: parseKGML2(file)
> 4: parseKGML2Graph2(xml.file, genes =
F, expand = expand.node, split.group = sp
lit.group)
> 5: doTryCatch(return(expr), name,
parentenv, handler)
> 6: tryCatchOne(expr, names, parentenv,
handlers[[1L]])
> 7: tryCatchList(expr, classes,
parentenv, handlers)
> 8: tryCatch(expr, error = function(e)
{ call <- conditionCall(e) if
(!is.
null(call))
{ if (identical(call[[1L]],
quote(doTryCatch)))
c
all <- sys.call(-4L)
dcall <- deparse(call)[1L]
prefix <- paste("E
rror 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(dcal
l, type
= "b") + nchar(sm[1L],
type = "b")
if (w > LONG)
prefix <- paste0(prefix, "\n ")
} else prefix <- "Error : "
msg <-
paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(ms
g[1L])) if (!silent
&& identical(getOption("show.error.messages"),
TR
>
UE)) {
cat(msg, file = stderr())
.Internal(printDeferredWarnings()
) }
invisible(structure(msg, class = "try-error", condition =
e))})
> 9: try(parseKGML2Graph2(xml.file,
genes = F, expand = expand.node,
split.gr
oup = split.group), silent = T)
> 10: pathview(gene.data = d[, 1], pathway.id = "04075",
species = "ko", kegg.
native = FALSE)
> 11: eval(expr, envir, enclos)
> 12: eval(ei, envir)
> 13: withVisible(eval(ei, envir))
> 14: source("pathview.R")
>
--------------------------------------------------------
> is any tell me how to cover it, we have test it on the
lastest version of R 3.0.1-patched 2013-09-06 version and I
have restall it ad hoc as well as update from 2.15
> all version report the same bug, very thanks
>
> -- output of sessionInfo():
>
> version 3.0.1 Patched (2013-09-05
r63850)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=zh_CN.UTF-8
LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8
LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8
LC_NAME=C
> [9] LC_ADDRESS=C
LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats
graphics grDevices utils
datasets methods
> [8] base
>
> other attached packages:
> [1] pathview_1.1.6
org.Hs.eg.db_2.9.0 RSQLite_0.11.4
> [4] DBI_0.2-7
AnnotationDbi_1.23.18
Biobase_2.21.6
> [7] BiocGenerics_0.7.4
KEGGgraph_1.17.0 graph_1.39.3
> [10] XML_3.98-1.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.29.15
digest_0.6.3 grid_3.0.1
httr_0.2
> [5] IRanges_1.19.29
KEGGREST_1.1.1 png_0.1-6
RCurl_1.95-4.1
> [9] Rgraphviz_2.5.4
stats4_3.0.1
stringr_0.6.2
tools_3.0.1
> [13] XVector_0.1.0
>
>
> --
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bioconductor.org.
>
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