[R] odfWeave 0.7.17 stutters on Debian testing 64-bit amd64 systems.

Emmanuel Charpentier emm.charpentier at free.fr
Sat May 14 11:10:02 CEST 2011


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.



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