Dear Brian, You are right (as usual...) : downgrading XML to 3.2.0 (the next-to-most-recent version) enables me to compile my minimalistic example correctly.
And yes, there is no other XML than XML. Silly me... Now, I have to understand why the i386 and Ubuntu machines were *not* "upgraded" to 3.4.0 by the "update.packages(ask=FALSE)" I'm used to do ... Thank you again ! Now I can again use a multiprocessor eficiently to run the same analyses on 18 datasets (thanks to mclapply (multicore)). A serious win in my case... Emmanuel Charpentier Le samedi 14 mai 2011 à 12:59 +0100, Prof Brian Ripley a écrit : > 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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.