Emmanuel Charpentier
2011-May-14 09:10 UTC
[R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.
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 n?cessit? le package : lattice
Le chargement a n?cessit? 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 syst?me ?coul?
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 syst?me ?coul?
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.
Prof Brian Ripley
2011-May-14 10:52 UTC
[R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.
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. 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 n?cessit? le package : lattice > Le chargement a n?cessit? 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 syst?me ?coul? > 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 syst?me ?coul? > 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