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memDecompress and zlib compressed base64 encoded string

3 messages · Johannes Graumann, Brian Ripley

Johannes Graumann
# 
Hi,

I have zlib compressed strings (example is attached) and would like to 
decompress them using memDecompress ...

I try this:
Error in memDecompress(as.raw(compressed), type = "g") :
  internal error -3 in memDecompress(2)
In addition: Warning messages:
1: In memDecompress(as.raw(compressed), type = "g") :
  NAs introduced by coercion
2: In memDecompress(as.raw(compressed), type = "g") :
  out-of-range values treated as 0 in coercion to raw

Can anyone nudge me into the right direction regarding this?

Thanks, Joh
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Brian Ripley
#
On Thu, 14 Jan 2010, Johannes Graumann wrote:

            

      
      
      
    

        
What is that file? Not gzip compression:

gannet% file compressed.txt
compressed.txt: ASCII text, with very long lines

since gzip uses a magic header that 'file' knows about.  And even if 
the header was stripped, such files are 8-bit and yours is ASCII.
Try

            

      
      
      
    

        
[1] "x\x9c\xf3\xca\xcfH\xcc\xcbK-Vp/J,\xcd\0052\001:\n\006\x90"

to see what a real gzipped string looks like.

            

      
      
      
    

        
You have not told us the 'at a minimum' information requested in the 
posting guide.  But you should not expect that to read a binary file, 
especially not in a MBCS locale.  We have readBin for that purpose.

            

      
      
      
    

        
I don't think you know what as.raw does: it does not convert bytes in 
a character string to raw (for which you need charToRaw).

It is always a good idea to look at each stage of your computation:

            

      
      
      
    

        
[1] 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
00 00 00
[26] 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
00 00 00

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Johannes Graumann
    

    

      
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Prof Brian Ripley wrote:

        

            

      
      
      
    

        
I am dealing with mass spectrometric data in a XML file format (mzXML). The 
biggest part of the contained data is actual mass spectra that are base64 
encoded and optionally compressed using http://zlib.net (saving quite some 
storage space). When they are compressed I just get an XML node that looks 
like this
   <peaks>CONTENT OF THE ORIGINAL ATTACHMENT HERE</peaks>
I would like to be able to decompress that string and thought that 
memDecompress was the right tool to do so ...

            

      
      
      
    

        
I'm actually reading this in as a string from the XML file ...

            

      
      
      
    

        
Yup, that was plain stupid and trying to make memDecompress run at all 
(since handing it the character string also resulted in an error.

            

      
      
      
    

        
R version 2.10.1 (2009-12-14) 
x86_64-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rkward_0.5.1

loaded via a namespace (and not attached):
[1] tools_2.10.1

Thanks for any further hints, Joh