htmlParse() segfault error in R XML package: 'memory not mapped'

Question

I am using R 2.11.1 and XML package 3.1-0, and I was going through an example from R2GoogleMaps when I encountered a segfault error.

#library(RJSONIO)
library(R2GoogleMaps)
library(XML)
#library(RCurl)

load("b.rda") # find in the sampleDocs folder in source file of R2GoogleMaps

center = c(mean(range(b$lat)), mean(range(b$long)))
code = addOverlay(gpolyline(b))

d = googleMapsDoc(code, center, zoom = 11, dim = c(750, 700), file = "simplePolyline.html")

Below is an easily reproducible code that gets the same error:

> library(XML)
> a <- htmlParse("http://bm2.genes.nig.ac.jp/RGM2/R_current/library/XML/man/xmlTreeParse.html")
> a

 *** caught segfault ***
address 0x55aa44, cause 'memory not mapped'

Traceback:
 1: .Call("RS_XML_dumpHTMLDoc", doc, as.integer(indent), as.character(encoding),     as.logical(indent), PACKAGE = "XML")
 2: saveXML(from)
 3: saveXML(from)
 4: asMethod(object)
 5: as(x, "character")
 6: cat(as(x, "character"), "\n")
 7: print.XMLInternalDocument(<pointer: 0x1016363f0>)
 8: print(<pointer: 0x1016363f0>)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
aborting ...

Process R segmentation fault at Sat Jul 31 22:07:02 2010

The problem also seems to be doing a saveXML() on the htmlParse() file.

When I was writing up another code that used htmlParse(), I don't recall ever encountering this problem (although I don't remember if I called a htmlParse() object explicitly). So I'm not entirely sure if this is a recent problem or not. The only difference between then and now (that I can remember) is that I've installed many of the OmegaHat packages from source.

I was curious if anyone else was getting this error. To explore if the cause lies with my laptop, I have restarted and upgraded my OS as a basic step. What might be the problem? Thanks.

edit: just for ref:

> sessionInfo()
R version 2.11.1 (2010-05-31) 
x86_64-apple-darwin9.8.0 

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  grid      methods  
[8] base     

other attached packages:
[1] XML_3.1-0     digest_0.4.2  reshape_0.8.3 plyr_0.1.9    proto_0.3-8  

loaded via a namespace (and not attached):
[1] ggplot2_0.8.7

Answer 1

I think that almost by definition a segmentation fault constitutes a bug. Your example works for me (see below).

I would (a) make sure you have the latest version of XML and that the error still occurs there; (b) contact the maintainer of the XML package (try

maintainer("XML") ) and provide your example and the results of sessionInfo()

good luck.

=============

library(XML) a <- htmlParse("http://bm2.genes.nig.ac.jp/RGM2/R_current/library/XML/man/xmlTreeParse.html")

sessionInfo() R version 2.11.1 (2010-05-31) i486-pc-linux-gnu

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C 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] stats graphics grDevices utils datasets grid methods
[8] base

other attached packages: [1] XML_3.1-0 reshape_0.8.3 plyr_1.0.3 proto_0.3-8

loaded via a namespace (and not attached): [1] ggplot2_0.8.8