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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