Re: [R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sat, 14 May 2011 11:52:48 +0100 (BST)

Note the difference in XML versions.

odfWeave does not work correctly with XML 3.4-x: this has been reported to the maintainer (and can be seen on the CRAN package checks at http://cran.r-project.org/web/checks/check_results_odfWeave.html). I suggest you try downgrading to an earlier version of XML.

On Sat, 14 May 2011, Emmanuel Charpentier wrote:

> Dear list,
>
> This is a copy of a mail sent to Max Kuhn, original author and
> maintainer of the odfWeave package, which seems not to have received it.
> It reports a problem that seems to be very implementation specific
> (reproductible on three Debian testing amd64 machine, does *not* happen
> on two i686 Debian testing systems, does *not* happen on an Ubuntu 11.06
> amd64 machine) and therefore not attributable to odfWeave itself (which
> is pure R) but to a software component it uses (XML and the underlying
> libxml2, R itself, etc ...), but I need to know how to track this
> problem.
>
> Apologies fror cross-posting to r-help and r-debian-sig, but I think
> that the issue is ... complicated and might not be as Debian-specific as
> it seems at first view.
>
> Sincerely,
>
> Emmanuel Charpentier
>
> Dear Max,
>
> A few days ago, I started to have problems with odfWeave 0.7.17 on a
> couple of amd64 systems : the compiled files contained numerous copies
> of the source files, more or less interlaced, "and a few copies of the
> target productions.
>
> Then I noticed that using an older 32-bit system resulted in correct
> files. An attempt with yet another machine (recent i686 netbook)
> confirmed that 32-bit systems gave okay results.
>
> Setup : in all machines, I use Debian testing with updates. My packages
> are self-compiled (i. e. installed via install.packages()).
>
> I enclose a very minimalist source and the resulting targets. Logs of
> execution on 32- and 64-bit systems are affixed after this message.
>
> Since odfWeave is pure R, I doubt that it could be the source of the
> problem. This leaves us with two obvious targets : R itself (the Debian
> package is current), or the XML library.
>
> Do you have any idea about how to proceed to find the source of the
> problem (and how to fix in) ?
>
> Sincerely,
>
> Emmanuel Charpentier
>
> Execution on a 32-bit system :
>
>> library(odfWeave)
> Le chargement a nécessité le package : lattice
> Le chargement a nécessité le package : XML
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i486-pc-linux-gnu (32-bit)
>
> locale:
> [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C
> [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8
> [5] LC_MONETARY=C LC_MESSAGES=fr_FR.utf8
> [7] LC_PAPER=fr_FR.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] odfWeave_0.7.17 XML_3.2-0 lattice_0.19-26
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.0
>> system.time(odfWeave("In1.odt", "Out1-32.odt"))
> Copying In1.odt
> Setting wd to /tmp/RtmpS8lBt8/odfWeave11161739126
> Unzipping ODF file using unzip -o In1.odt
> Archive: In1.odt
> extracting: mimetype
> creating: Configurations2/statusbar/
> inflating: Configurations2/accelerator/current.xml
> creating: Configurations2/floater/
> creating: Configurations2/popupmenu/
> creating: Configurations2/progressbar/
> creating: Configurations2/toolpanel/
> creating: Configurations2/menubar/
> creating: Configurations2/toolbar/
> creating: Configurations2/images/Bitmaps/
> inflating: content.xml
> inflating: manifest.rdf
> inflating: styles.xml
> extracting: meta.xml
> extracting: Thumbnails/thumbnail.png
> inflating: settings.xml
> inflating: META-INF/manifest.xml
>
> Removing In1.odt
> Creating a Pictures directory
>
> Pre-processing the contents
> Sweaving content.Rnw
>
> Writing to file content_1.xml
> Processing code chunks ...
>
> 'content_1.xml' has been Sweaved
>
> Removing content.xml
>
> Post-processing the contents
> Removing content.Rnw
> Removing styles.xml
> Renaming styles_2.xml to styles.xml
> Removing manifest.xml
> Renaming manifest_2.xml to manifest.xml
> Removing extra files
>
> Packaging file using zip -r In1.odt .
> adding: manifest.rdf (deflated 54%)
> adding: mimetype (stored 0%)
> adding: Pictures/ (stored 0%)
> adding: Configurations2/ (stored 0%)
> adding: Configurations2/images/ (stored 0%)
> adding: Configurations2/images/Bitmaps/ (stored 0%)
> adding: Configurations2/menubar/ (stored 0%)
> adding: Configurations2/progressbar/ (stored 0%)
> adding: Configurations2/toolbar/ (stored 0%)
> adding: Configurations2/floater/ (stored 0%)
> adding: Configurations2/accelerator/ (stored 0%)
> adding: Configurations2/accelerator/current.xml (stored 0%)
> adding: Configurations2/popupmenu/ (stored 0%)
> adding: Configurations2/toolpanel/ (stored 0%)
> adding: Configurations2/statusbar/ (stored 0%)
> adding: content.xml (deflated 75%)
> adding: META-INF/ (stored 0%)
> adding: META-INF/manifest.xml (deflated 83%)
> adding: Thumbnails/ (stored 0%)
> adding: Thumbnails/thumbnail.png (deflated 60%)
> adding: meta.xml (deflated 56%)
> adding: styles.xml (deflated 83%)
> adding: settings.xml (deflated 84%)
> Copying In1.odt
> Resetting wd
> Removing /tmp/RtmpS8lBt8/odfWeave11161739126
>
> Done
> utilisateur système écoulé
> 0.448 0.020 0.568
>
> Execution on a 64-bit system :
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=fr_FR.UTF-8
> [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] odfWeave_0.7.17 XML_3.4-0 lattice_0.19-26
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.0
>> system.time(odfWeave("In1.odt", "Out1-64.odt"))
> Copying In1.odt
> Setting wd to /tmp/Rtmpfw3Ow2/odfWeave11162204556
> Unzipping ODF file using unzip -o In1.odt
> Archive: In1.odt
> extracting: mimetype
> creating: Configurations2/statusbar/
> inflating: Configurations2/accelerator/current.xml
> creating: Configurations2/floater/
> creating: Configurations2/popupmenu/
> creating: Configurations2/progressbar/
> creating: Configurations2/toolpanel/
> creating: Configurations2/menubar/
> creating: Configurations2/toolbar/
> creating: Configurations2/images/Bitmaps/
> inflating: content.xml
> inflating: manifest.rdf
> inflating: styles.xml
> extracting: meta.xml
> extracting: Thumbnails/thumbnail.png
> inflating: settings.xml
> inflating: META-INF/manifest.xml
>
> Removing In1.odt
> Creating a Pictures directory
>
> Pre-processing the contents
> Sweaving content.Rnw
>
> Writing to file content_1.xml
> Processing code chunks ...
>
> 'content_1.xml' has been Sweaved
>
> Removing content.xml
>
> Post-processing the contents
> Removing content.Rnw
> Removing styles.xml
> Renaming styles_2.xml to styles.xml
> Removing manifest.xml
> Renaming manifest_2.xml to manifest.xml
> Removing extra files
>
> Packaging file using zip -r In1.odt .
> adding: manifest.rdf (deflated 54%)
> adding: Configurations2/ (stored 0%)
> adding: Configurations2/toolpanel/ (stored 0%)
> adding: Configurations2/images/ (stored 0%)
> adding: Configurations2/images/Bitmaps/ (stored 0%)
> adding: Configurations2/progressbar/ (stored 0%)
> adding: Configurations2/popupmenu/ (stored 0%)
> adding: Configurations2/statusbar/ (stored 0%)
> adding: Configurations2/menubar/ (stored 0%)
> adding: Configurations2/floater/ (stored 0%)
> adding: Configurations2/accelerator/ (stored 0%)
> adding: Configurations2/accelerator/current.xml (stored 0%)
> adding: Configurations2/toolbar/ (stored 0%)
> adding: content.xml (deflated 98%)
> adding: mimetype (stored 0%)
> adding: Pictures/ (stored 0%)
> adding: settings.xml (deflated 84%)
> adding: META-INF/ (stored 0%)
> adding: META-INF/manifest.xml (deflated 83%)
> adding: meta.xml (deflated 56%)
> adding: Thumbnails/ (stored 0%)
> adding: Thumbnails/thumbnail.png (deflated 60%)
> adding: styles.xml (deflated 92%)
> Copying In1.odt
> Resetting wd
> Removing /tmp/Rtmpfw3Ow2/odfWeave11162204556
>
> Done
> utilisateur système écoulé
> 0.756 0.012 0.775
>
> One could note that the user time is almost double of the 32-bit system system time, notwhistanding the fact that the 64-bit system is about 10x faster than the 32-bit system.
>
>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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Received on Sat 14 May 2011 - 11:01:28 GMT

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