[R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.
Emmanuel Charpentier
emm.charpentier at free.fr
Sat May 14 14:18:21 CEST 2011
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, 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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