[R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sat May 14 13:59:45 CEST 2011
On Sat, 14 May 2011, Emmanuel Charpentier wrote:
> Dear Brian,
>
> Thank you very much for this answer. However ...
>
> Le samedi 14 mai 2011 à 11:52 +0100, Prof Brian Ripley a écrit :
>> 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.
>
> Do you mean the XML R package ? Or the libxml2 Debian package ? I am
Only the R package is called XML. Why would I write XML if I meant
libxml2?
> worried by the diference in behaviour of i386 and amd64 versions (and,
> on amd64, the discrepancies between Ubuntu 11.04 and Debian testing,
> which are easier to explain : Debian has slightly more recent version).
>
> I'll try to downgrade the R xml package (easier) and report results.
>
> Again, thank you very much !
>
> Emmanuel Charpentier
>
>
>> 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
>
>
>
--
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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