[R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.
Emmanuel Charpentier
emm.charpentier at free.fr
Sat May 14 13:57:23 CEST 2011
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
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
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