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,                  rip...@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,                  rip...@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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