[R] follow-up on Error when reading a SAS transport file (with sasxport.get from Hmisc)

Jean-Louis Abitbol jlabitbol at trophos.com
Fri Oct 10 20:06:23 CEST 2008


I have done what P. Dalgaard has suggested and I don't find a
descrepancy between the number of values and the number of labels: there
15 each...

Any hint on what might go wrong here ?

Here is the output

The SAS format from proc contents

VISITF                                                                   
                . = INEXTXT                                              
              -10 = Visit 1 [Screening]                                  
                0 = Visit 2 [Baseline]                                   
                1 = CRF Tracking                                         
                6 = Visit 6                                              
                7 = Tel.Contact (day 7)                                  
               14 = Visit 3                                              
               21 = Tel.Contact (day 21)                                 
               28 = Visit 4                                              
               35 = Tel.Contact (day 35)                                 
               43 = Visit 5 [EOT]                                        
               65 = Visit 6 [Follow-up]                                  
              777 = End of Study                                         
              888 = Concomitant Med.                                     
              999 = Adverse Events   
             
the cat output with  sep=" * " (manual CR edit due to line length)    
         
Processing SAS dataset ADMIN     .x=  * 43 * 28 * 0 * 14 * 43 * 0 * 28 *
14 * 28 * 43 * 14 * 0 * 28 * 14 * 0 
* 43 * 43 * 28 * 14 * 0 * 0 * 43 * 28 * 14  * 0 * 43 * 28 * 14 * 0 * 14
* 0 * 43 * 28 * 43 * 28 * 14 * 0 * 43 
* 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 14 * 0 * 0 * 43 * 28 * 14 * 0 *
43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 
* 14 * 0 * 43 * 28 * 0 * 28 * 43 * 14 * 14 * 0 * 28 * 43 * 0 * 43 * 0 *
43 * 14 * 0 * 28 * 0 * 43 * 28 * 14 * 43 
* 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 * 43 * 28 *
14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14
 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
 * 14 * 0 * 28 * 14 * 0 * 43 * 14 * 0 * 43 
 * 28 * 0 * 14 * 43 * 28 * 14 * 43 * 28 * 0 * 28 * 14 * 0 * 43 * 0 * 43
 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
 * 14 * 0 * 0 * 28 * 14 * 0 * 43 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 *
 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 
 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28
 * 14 * 0 * 14 * 28 * 43 * 0 * 43 * 14
  * 28 * 0 * 28 * 14 * 43 * 0 * 0 * 14 * 0 * 28 * 43 * 43 * 28 * 14 * 0
  * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
   * 14 * 0 * 43 * 28 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
   14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
   * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 14 * 0 * 43 * 28 * 0
   * 43 * 28 * 14 * 28 * 43 * 0 * 14
    * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
    14 * 0 * 43 * 28 * 14 * 0 * 43 
    * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 14 * 0 * 28 * 14 * 0 * 14 * 0 *
    43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 
    * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 *
    28 * 14 * 0 * 14 * 43 * 28 * 28 * 14 
    * 0 * 43 * 43 * 28 * 0 * 14 * 28 * 0 * 14 * 43 * 43 * 28 * 14 * 0 *
    43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 
    * 28 * 14 * 0 * 43 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
    14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
    * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 28 * 14 * 0 * 0 * 14 * 0 * 43 * 28
    * 0 * 43 * 14 * 28 * 14 * 43 * 28 
    * 0 * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 *
    28 * 14 * 0 * 43 * 14 * 0 * 43 * 28 
    * 14 * 0 * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 *
    43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 
    * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 *
    28 * 14 * 0 * 14 * 28 * 43 * 14 * 28 
    * 0 * 43 * 43 * 28 * 0 * 14 * 28 * 0 * 14 * 43 * 43 * 28 * 14 * 0 *
    43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 
    * 28 * 14 * 0 * 43 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
    14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
    * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28 * 14 * 0 * 43 *
    14 * 0 * 28 * 43 * 14 * 0 * 43 * 28 
    * 43 * 28 * 0 * 14 * 43 * 14 * 0 * 28 * 0 * 43 * 28 * 14 * 43 * 28 *
    14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
    * 14 * 0 * 0 * 43 * 28 * 14 * 14 * 0 * 28 * 14 * 0 * 43 * 28 * 14 *
    0 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
    * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28 * 14 * 0 * 43 *
    14 * 0 * 43 * 28 * 14 * 28 * 0 * 28 
    * 43 * 0 * 14 * 43 * 28 * 14 * 0 * 14 * 0 * 43 * 28 * 43 * 28 * 14 *
    0 * 43 * 28 * 14 * 0 * 0 * 43 * 28 
    * 14 * 0 * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 *
    43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 
    * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 *
    28 * 14 * 14 * 43 * 28 * 0 * 14 * 0 
    * 14 * 0 * 43 * 28 * 43 * 14 * 0 * 28 * 0 * 43 * 28 * 14 * 43 * 28 *
    14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 
    * 14 * 0 * 0 * 28 * 14 * 28 * 14 * 0 * 
f$value=  * NA * -10 * 0 * 1 * 6 * 7 * 14 * 21 * 28 * 35 * 43 * 65 * 777
* 888 * 999 * 
f$label=  * INEXTXT * Visit 1 [Screening] * Visit 2 [Baseline] * CRF
Tracking * Visit 6 * Tel.Contact (day 7) * Visit 3 
* Tel.Contact (day 21) * Visit 4 * Tel.Contact (day 35) * Visit 5 [EOT]
* Visit 6 [Follow-up] * End of Study * Concomitant Med. * Adverse Events
* 
Erreur dans factor(x, f$value, f$label) : 
  invalid labels; length 15 should be 1 or 14

Thanks again, JL


On Thu, 09 Oct 2008 17:33:06 +0200, "Peter Dalgaard"
<P.Dalgaard at biostat.ku.dk> said:
> Jean-Louis Abitbol wrote:
> > Dear All,
> >
> > I get the following error when using either SASxport or Hmisc to read an
> > .xpt file:
> >
> >   
> >> w <- read.xport("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt")
> >>     
> > Erreur dans factor(x, f$value, f$label) : 
> >   invalid labels; length 15 should be 1 or 14
> >   
> >> z<- sasxport.get("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt")
> >>     
> > Erreur dans factor(x, f$value, f$label) : 
> >   invalid labels; length 15 should be 1 or 14
> >
> > I don't understand what is wrong with the labels ! Is there a limit for
> > their length ?
> > Could the problem be in the formats label ? 
> >   
> Hmmnoo...
> 
> This is happening in R code, and the error is the same as you'd get from
> 
> > factor(1,levels=1:4,labels=1:5)
> Error in factor(1, levels = 1:4, labels = 1:5) :
>   invalid labels; length 5 should be 1 or 4
> 
> So, not going into the actual code, I would suspect that it is
> encountering a problem where a user format has values and labels out of
> sync. This could well be a bug in the package(s), but I wouldn't rule
> out that your data could have gotten into some inconsistent state. You
> might try debugging to the trouble spot and see what is actually in
> f$value and f$label at that point.
> 
> > Just in case this might help this is the  output from 
> > test <- lookup.xport("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt") 
> > print(test)
> >
> > for the first SAS dataset:
> > SAS xport file
> > --------------
> > Filename: `D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt'
> >
> > Variables in data set `ADMIN':
> >  dataset     name      type  format flength fdigits iformat iflength
> >  ifdigits                                  label nobs
> >    ADMIN      CEN   numeric               5       0                0    
> >       0                                 Centre  696
> >    ADMIN      PNO   numeric               6       0                0    
> >       0                      Pat./Subj. number  696
> >    ADMIN    VISIT   numeric  VISITF       0       0                0    
> >       0                              Visit no.  696
> >    ADMIN   VISITR   numeric               0       0                0    
> >       0                           Visit repeat  696
> >    ADMIN      PRO character               0       0                0    
> >       0                         Project number  696
> >    ADMIN    STUDY character               0       0                0    
> >       0                           Study number  696
> >    ADMIN  COLLDAT   numeric    DATE       7       0                0    
> >       0      Date collected (study medication)  696
> >    ADMIN   COMM_O character               0       0                0    
> >       0                                Comment  696
> >    ADMIN  INEXMET   numeric  YESNOF       0       0                0    
> >       0      In-/exclusion criteria still met?  696
> >    ADMIN LABEL_NO   numeric               4       0                0    
> >       0              Medication number (label)  696
> >    ADMIN  RAND_NO   numeric               4       0                0    
> >       0 Lowest randomisation/medication number  696
> >    ADMIN   RETMED   numeric               4       0                0    
> >       0            Number of capsules returned  696
> >    ADMIN     PAGE   numeric               0       0                0    
> >       0                                   Page  696
> >    ADMIN    PAGER   numeric               0       0                0    
> >       0                            Page repeat  696
> >    ADMIN CT_RECID character       $      40       0       $       40    
> >       0         for merge with notes and flags  696
> >    ADMIN      RNO   numeric               4       0                0    
> >       0                   Randomisation number  696
> >    ADMIN      SAF   numeric NOYESZF       0       0                0    
> >       0                                         696
> >    ADMIN      ITT   numeric NOYESZF       0       0                0    
> >       0                                         696
> >    ADMIN       PP   numeric NOYESZF       0       0                0    
> >       0                                         696
> >    ADMIN      SEX   numeric    SEXF       0       0                0    
> >       0                                    Sex  696
> >    ADMIN    AGE_C   numeric               4       0                0    
> >       0                               Age calc  696
> >    ADMIN      TRT   numeric    TRTF       0       0                0    
> >       0                                         696
> >    ADMIN CRF_VERS character               0       0                0    
> >       0                        CRF Version no.  696
> >
> > Thanks for any help,
> >
> > Best wishes, Jean-Louis
> >
> > PS: sessionInfo()
> > R version 2.7.1 RC (2008-06-20 r45965) 
> > i386-pc-mingw32 
> >
> > locale:
> > LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base     
> >
> > other attached packages:
> > [1] SASxport_1.2.3 Hmisc_3.4-3    foreign_0.8-29 RWinEdt_1.8-0 
> >
> > loaded via a namespace (and not attached):
> > [1] chron_2.3-24    cluster_1.11.11 grid_2.7.1      lattice_0.17-15
> >
> >
> > Jean-Louis Abitbol, MD
> > Chief Medical Officer
> > Trophos SA, Parc scientifique de Luminy, Case 931
> > Luminy Biotech Entreprises
> > 13288 Marseille Cedex 9 France
> > Email: jlabitbol at trophos.com ---- Backup Email: abitbol at sent.com
> > Cellular: (33) (0)6 24 47 59 34
> > Direct Line: (33) (0)4 91 82 82 73-Switchboard: (33) (0)4 91 82 82 82  
> > Fax: (33) (0)4 91 82 82 89
> >
> > ______________________________________________
> > R-help at 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.
> >   
> 
> 
> -- 
>    O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
>   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>  (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907
> 
> 
> 



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