Having read Memory leaks parsing XML in r (including linked posts) and this post on R Help and given that some time has passed again, I still think this is an unresolved issue that deserves attention as the XML
package is widely used throughout the R universe.
Thus please consider this as a follow up post and/or reference with a hopefully informative yet concise illustration of the problem.
Parsing XML/HTML documents in a way that they can be searched with XPath afterwards requires the internal use of C pointers (AFAIU). And it seems that at least on MS Windows (I'm running on Windows 8.1, 64 Bit) these references are not properly recognized by the garbage collector. Thus consumed memory is not properly released which leads to a freeze of an R process at some point.
To me it seems that XML:free
and/or gc
does/do not recognize all memory involved when parsing XML/HTML docs via xmlParse
or htmlParse
and subsequently processing them with xpathApply
or the like:
The reported memory usage of the OS task (Rterm.exe) is adding up significantly fast while the reported memory of the R process as "seen from within R" (function memory.size
) increases moderately (in comparison, that is). See list elements mem_r
, mem_os
and ratio
before and after a substantial parsing cycle below.
All in all and throwing in everything that has been recommended (free
, rm
and gc
), memory usage still always increases when xmlParse
and the like are called. It's just a question of how much. So IMHO there must still be something that's not working correctly.
I borrowed the profiling code from the Duncan's Omegahat git repository.
Some preparations:
Sys.setenv("LANGUAGE"="en")
require("compiler")
require("XML")
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] compiler stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] XML_3.98-1.1
Functions we need:
getTaskMemoryByPid <- cmpfun(function(
pid=Sys.getpid()
) {
cmd <- sprintf("tasklist /FI \"pid eq %s\" /FO csv", pid)
mem <- read.csv(text=shell(cmd, intern = TRUE), stringsAsFactors=FALSE)[,5]
mem <- as.numeric(gsub("\\.|\\s|K", "", mem))/1000
mem
}, options=list(suppressAll=TRUE))
memoryLeak <- cmpfun(function(
x=system.file("exampleData", "mtcars.xml", package="XML"),
n=10000,
use_text=FALSE,
xpath=FALSE,
free_doc=FALSE,
clean_up=FALSE,
detailed=FALSE
) {
if(use_text) {
x <- readLines(x)
}
## Before //
mem_os <- getTaskMemoryByPid()
mem_r <- memory.size()
prof_1 <- memory.profile()
mem_before <- list(mem_r=mem_r,
mem_os=mem_os, ratio=mem_os/mem_r)
## Per run //
mem_perrun <- lapply(1:n, function(ii) {
doc <- xmlParse(x, asText=use_text)
if (xpath) {
res <- xpathApply(doc=doc, path="/blah", fun=xmlValue)
rm(res)
}
if (free_doc) {
free(doc)
}
rm(doc)
out <- NULL
if (detailed) {
out <- list(
profile=memory.profile(),
size=memory.size()
)
}
out
})
has_perrun <- any(sapply(mem_perrun, length) > 0)
if (!has_perrun) {
mem_perrun <- NULL
}
## Garbage collect //
mem_gc <- NULL
if(clean_up) {
gc()
tmp <- gc()
mem_gc <- list(gc_mb=tmp["Ncells", "(Mb)"])
}
## After //
mem_os <- getTaskMemoryByPid()
mem_r <- memory.size()
prof_2 <- memory.profile()
mem_after <- list(mem_r=mem_r,
mem_os=mem_os, ratio=mem_os/mem_r)
list(
before=mem_before,
perrun=mem_perrun,
gc=mem_gc,
after=mem_after,
comparison_r=data.frame(
before=prof_1,
after=prof_2,
increase=round((prof_2/prof_1)-1, 4)
),
increase_r=(mem_after$mem_r/mem_before$mem_r)-1,
increase_os=(mem_after$mem_os/mem_before$mem_os)-1
)
}, options=list(suppressAll=TRUE))
Quick facts: garbage collection enabled, XML doc is parsed n
times but not searched via xpathApply
Notice the ratios of OS memory vs. R memory:
Before: 1.364832
After: 1.322702
res <- memoryLeak(clean_up=TRUE, n=50000)
save(res, file=file.path(tempdir(), "memory-profile-1.rdata"))
> res
$before
$before$mem_r
[1] 37.42
$before$mem_os
[1] 51.072
$before$ratio
[1] 1.364832
$perrun
NULL
$gc
$gc$gc_mb
[1] 45
$after
$after$mem_r
[1] 63.21
$after$mem_os
[1] 83.608
$after$ratio
[1] 1.322702
$comparison_r
before after increase
NULL 1 1 0.0000
symbol 7387 7392 0.0007
pairlist 190383 390633 1.0518
closure 5077 55085 9.8499
environment 1032 51032 48.4496
promise 5226 105226 19.1351
language 54675 54791 0.0021
special 44 44 0.0000
builtin 648 648 0.0000
char 8746 8763 0.0019
logical 9081 9084 0.0003
integer 22804 22807 0.0001
double 2773 2783 0.0036
complex 1 1 0.0000
character 44522 94569 1.1241
... 0 0 NaN
any 0 0 NaN
list 19946 19951 0.0003
expression 1 1 0.0000
bytecode 16049 16050 0.0001
externalptr 1487 1487 0.0000
weakref 391 391 0.0000
raw 392 392 0.0000
S4 1392 1392 0.0000
$increase_r
[1] 0.6892036
$increase_os
[1] 0.6370614
Quick facts: garbage collection enabled, free
is explicitly called, XML doc is parsed n
times but not searched via xpathApply
.
Notice the ratios of OS memory vs. R memory:
Before: 1.315249
After: 1.222143
res <- memoryLeak(clean_up=TRUE, free_doc=TRUE, n=50000)
save(res, file=file.path(tempdir(), "memory-profile-2.rdata"))
> res
$before
$before$mem_r
[1] 63.48
$before$mem_os
[1] 83.492
$before$ratio
[1] 1.315249
$perrun
NULL
$gc
$gc$gc_mb
[1] 69.3
$after
$after$mem_r
[1] 95.92
$after$mem_os
[1] 117.228
$after$ratio
[1] 1.222143
$comparison_r
before after increase
NULL 1 1 0.0000
symbol 7454 7454 0.0000
pairlist 392455 592466 0.5096
closure 55104 105104 0.9074
environment 51032 101032 0.9798
promise 105226 205226 0.9503
language 55592 55592 0.0000
special 44 44 0.0000
builtin 648 648 0.0000
char 8847 8848 0.0001
logical 9141 9141 0.0000
integer 23109 23111 0.0001
double 2802 2807 0.0018
complex 1 1 0.0000
character 94775 144781 0.5276
... 0 0 NaN
any 0 0 NaN
list 20174 20177 0.0001
expression 1 1 0.0000
bytecode 16265 16265 0.0000
externalptr 1488 1487 -0.0007
weakref 392 391 -0.0026
raw 393 392 -0.0025
S4 1392 1392 0.0000
$increase_r
[1] 0.5110271
$increase_os
[1] 0.4040627
Quick facts: garbage collection enabled, free
is explicitly called, XML doc is parsed n
times and searched via xpathApply
each time.
Notice the ratios of OS memory vs. R memory:
Before: 1.220429
After: 13.15629
(!)
res <- memoryLeak(clean_up=TRUE, free_doc=TRUE, xpath=TRUE, n=50000)
save(res, file=file.path(tempdir(), "memory-profile-3.rdata"))
res
$before
$before$mem_r
[1] 95.94
$before$mem_os
[1] 117.088
$before$ratio
[1] 1.220429
$perrun
NULL
$gc
$gc$gc_mb
[1] 93.4
$after
$after$mem_r
[1] 124.64
$after$mem_os
[1] 1639.8
$after$ratio
[1] 13.15629
$comparison_r
before after increase
NULL 1 1 0.0000
symbol 7454 7460 0.0008
pairlist 592458 793042 0.3386
closure 105104 155110 0.4758
environment 101032 151032 0.4949
promise 205226 305226 0.4873
language 55592 55882 0.0052
special 44 44 0.0000
builtin 648 648 0.0000
char 8847 8867 0.0023
logical 9142 9162 0.0022
integer 23109 23112 0.0001
double 2802 2832 0.0107
complex 1 1 0.0000
character 144775 194819 0.3457
... 0 0 NaN
any 0 0 NaN
list 20174 20177 0.0001
expression 1 1 0.0000
bytecode 16265 16265 0.0000
externalptr 1488 1487 -0.0007
weakref 392 391 -0.0026
raw 393 392 -0.0025
S4 1392 1392 0.0000
$increase_r
[1] 0.2991453
$increase_os
[1] 13.00485
I also tried different versions. Well, I tried to try ;-)
FYI: latest Rtools 3.1 is installed and included in the Windows PATH
(e.g. installing stringr
form the source code worked just fine).
> install.packages("XML", repos="http://www.omegahat.org/R", type="source")
trying URL 'http://www.omegahat.org/R/src/contrib/XML_3.98-1.tar.gz'
Content type 'application/x-gzip' length 1543387 bytes (1.5 Mb)
opened URL
downloaded 1.5 Mb
* installing *source* package 'XML' ...
Please define LIB_XML (and LIB_ZLIB, LIB_ICONV)
Warning: running command 'sh ./configure.win' had status 1
ERROR: configuration failed for package 'XML'
* removing 'R:/home/apps/lsqmapps/apps/r/R-3.1.0/library/XML'
* restoring previous 'R:/home/apps/lsqmapps/apps/r/R-3.1.0/library/XML'
The downloaded source packages are in
'C:\Users\rappster_admin\AppData\Local\Temp\RtmpQFZ2Ck\downloaded_packages'
Warning messages:
1: running command '"R:/home/apps/lsqmapps/apps/r/R-3.1.0/bin/x64/R" CMD INSTALL -l "R:\home\apps\lsqmapps\apps\r\R-3.1.0\library" C:\Users\RAPPST~1\AppData\Local\Temp\RtmpQFZ2Ck/downloaded_packages/XML_3.98-1.tar.gz' had status 1
2: In install.packages("XML", repos = "http://www.omegahat.org/R", :
installation of package 'XML' had non-zero exit status
I did not follow the recommendations in the README on the github repo as it points to this directory that only contains a tar.gz
of version 3.94-0
(while we're at 3.98-1.1
on CRAN).
Even though it is stated that the gihub repo is not in a standard R package structure, I tried it anyway with install_github
- and failed ;-)
require("devtools")
> install_github(repo="XML", username="omegahat")
Installing github repo XML/master from omegahat
Downloading master.zip from https://github.com/omegahat/XML/archive/master.zip
Installing package from C:\Users\RAPPST~1\AppData\Local\Temp\RtmpQFZ2Ck/master.zip
Installing XML
"R:/home/apps/lsqmapps/apps/r/R-3.1.0/bin/x64/R" --vanilla CMD INSTALL \
"C:\Users\rappster_admin\AppData\Local\Temp\RtmpQFZ2Ck\devtools15c82d7c2b4c\XML-master" \
--library="R:/home/apps/lsqmapps/apps/r/R-3.1.0/library" --with-keep.source \
--install-tests
* installing *source* package 'XML' ...
Please define LIB_XML (and LIB_ZLIB, LIB_ICONV)
Warning: running command 'sh ./configure.win' had status 1
ERROR: configuration failed for package 'XML'
* removing 'R:/home/apps/lsqmapps/apps/r/R-3.1.0/library/XML'
* restoring previous 'R:/home/apps/lsqmapps/apps/r/R-3.1.0/library/XML'
Error: Command failed (1)
The usual fix is to reboot. Freeing up the operating system for reuse of the space that has been taken over by memory leaks is called garbage collection. In the past, programs have had to explicitly request storage and then return it to the system when it was no longer needed.
Press Windows+R to open the Run dialog; enter "resmon" and click OK. With Resource Monitor open, select the Memory tab. Looking at Physical Memory, start by confirming the correct amount is displayed as installed, to ensure that there isn't a hardware issue.
Memory leak occurs when programmers create a memory in heap and forget to delete it. The consequences of memory leak is that it reduces the performance of the computer by reducing the amount of available memory.
Whilst it is still in its infancy (only a couple of months old!), and has a few quirks, Hadley Wickham has written a library for XML parsing, xml2
, that can be found on Github at https://github.com/hadley/xml2. It is restricted to reading rather than writing XML, but for parsing XML I've been experimenting and it looks like it will do the job, without the memory leaks of the xml package! It provides functions including:
read_xml()
to read an XML filexml_children()
to get the child nodes of a nodexml_text()
to get the text within a tagxml_attrs()
to get a character vector of the attributes and values of a node, that can be cast to a named list with as.list()
Note that you still need to ensure that you rm()
the XML node objects after you're done with them, and force a garbage collection with gc()
, but the memory then does actually get released to the O/S (Disclaimer: Only tested on Windows 7 but this seems to be the most 'memory leaky' platform anyway).
Hope this helps someone!
Following Matthew Wise's answer above for using xml2, I found the function that really releases memory is xml_remove()
followed by gc()
, not rm()
.
If you love us? You can donate to us via Paypal or buy me a coffee so we can maintain and grow! Thank you!
Donate Us With