segfault

[slowkow]

Hi Christian,

Thanks for the great package! It is a life saver.

Unfortunately, I ran into a problem. I hope you can help me fix this.

Here is the file I'm reading. I get a segfault when I try to extract the second table:

motif1.info.html.txt

(I had to add .txt to upload to this issue.)

Anyway, I think I'll have to find another way to extract the information out of the file. It turns out that the information I want is actually spread across multiple tables, not just one table. If you have any tips, I'd appreciate it!

library(htmltab)
htmltab("motif1.info.html", which = 2)

 *** caught segfault ***
address 0x11000080, cause 'memory not mapped'

Traceback:
 1: .Call("RS_XML_internalNodeNamespaceDefinitions", x, as.logical(recursive),     PACKAGE = "XML")
 2: xmlNamespaceDefinitions.XMLInternalNode(node)
 3: xmlNamespaceDefinitions(node)
 4: getEffectiveNamespaces(node)
 5: getEffectiveNamespaces(node)
 6: match(ns[i], names(nsDefs))
 7: checkAttrNamespaces(getEffectiveNamespaces(node), .attrs, suppressNamespaceWarning)
 8: addAttributes(node, .attrs = value, suppressNamespaceWarning = suppressNamespaceWarning,     append = append)
 9: addAttributes(node, .attrs = value, suppressNamespaceWarning = suppressNamespaceWarning,     append = append)
10: XML::`xmlAttrs<-`(`*tmp*`, value = 2L)
11: XML::`xmlAttrs<-`(`*tmp*`, value = 2L)
12: FUN(X[[i]], ...)
13: lapply(1:n.trs, function(index) XML::xmlAttrs(trs[[index]]) <- c(HTMLTABtrindex = index))
14: normalize_tr(table.Node = table.Node)
15: htmltab::htmltab("homerResults/motif1.info.html", which = 2)

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

Session info

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago)

Matrix products: default
BLAS: /apps/lib-osver/R/3.4.0/lib64/R/lib/libRblas.so
LAPACK: /apps/lib-osver/R/3.4.0/lib64/R/lib/libRlapack.so

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=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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] XML_3.98-1.9   htmltab_0.7.1  colorout_1.1-2

loaded via a namespace (and not attached):
[1] compiler_3.4.0

[marijnschraagen]

This issue is not specific for htmltab, it occurs within the XML package that htmltab uses internally. This package in turn calls the system library libxml2. This library may be outdated and updating it might solve the issue.

To check the currently installed version of libxml2 from R:

> library(XML)
> libxmlVersion()
$major
[1] "2"

$minor
[1] "09"

$patch
[1] "03"

In this example the version is 2.9.3, the most recent is 2.9.7. RPMs are available on ftp://xmlsoft.org/libxml2/.

[peeter-t2]

I encountered a similar memory leak. Finally found that the issue was caused in a table within a table html files. Since this was there just once in each file, I simply used sed to remove that table within table, and the memory leak was gone. Not sure if this can be helped somehow.

Problem existed both with 2.9.4 and 2.9.9 of libxml2.