[R] Different versions, different results ?

[Uwe Ligges]

charles-r-nospam at plessy.org wrote:

> Dear all,
> 
> I wrote the following batch script on a iMac, and ran it on a linux
> mosix cluster.
> 
> tu <- read.table("cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshape.table")
> tu_reshaped <- t(reshape(tu[1:50,], direction="wide", timevar="tu", idvar=c("rna","lib")))
> write.table(tu_reshaped, "cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table")
> q(sav="no")
> 
> (I will remove the [1:50,] later, the table has 153,646 rows)
> 
> The original tables are identical on both machines :
> 
> $ head cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshape.table 
> "rna" "lib" "tu" "x"
> "1" "CAA" "114BA" "1" 2
> "2" "CAB" "114BA" "1" 5
> "3" "CAC" "114BA" "1" 1
> "4" "CAD" "114BA" "1" 5
> "5" "CAG" "114BA" "1" 4
> "6" "CAH" "114BA" "1" 2
> "7" "CAI" "114BA" "1" 6
> "8" "CAJ" "114BA" "1" 2
> "9" "CAA" "114BB" "1" 1
> 
> The written table, however, is different :
> 
> GSLC8|Reproducibility|$ head cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table 
> "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "27" "35" "38" "44" "47" "50"
> "rna" "CAA" "CAB" "CAC" "CAD" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAE" "CAF" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAG" "CAH" "CAI" "CAJ" "CAE" "CAE" "CAE" "CAJ" "CAF" "CAD"
> "lib" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BC" "114BC" "114BC" "114BC" "114BC" "114BC" "114BC" "114BC" "114BA" "061AA" "061AA" "114BA" "062AA"
> "x.1" " 2" " 5" " 1" " 5" " 4" " 2" " 6" " 2" " 1" " 5" " 3" " 4" " 2" " 2" " 1" " 2" " 1" " 1" " 2" " 1" " 1" " 1" " 1" " 2" NA NA NA NA NA NA
> "x.2" NA " 1" NA NA NA NA NA NA NA NA " 1" NA NA NA NA NA NA NA NA NA NA NA NA NA " 1" NA NA NA NA NA
> "x.4" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA " 1" NA NA NA NA NA NA NA NA NA NA
> "x.5" NA NA NA NA NA NA " 2" " 1" NA " 2" " 1" NA NA NA NA NA " 1" NA NA NA NA NA " 1" NA NA NA NA NA NA NA
> "x.7" NA NA NA NA NA NA " 1" NA " 1" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA " 1" NA NA NA NA
> "x.24" " 1" " 2" NA NA NA NA NA NA NA NA " 3" NA " 1" NA NA NA NA NA NA NA NA NA NA NA " 1" NA " 1" NA NA NA
> "x.114" NA NA " 1" NA NA NA " 1" NA NA NA NA NA NA NA NA NA NA NA " 1" NA NA NA NA NA NA " 1" NA " 1" " 1" NA
> 
> charles at tofu:~$ head cage.mm5.tags.rna_lib.CAA-CAJ.tu-reshaped.table
> "X1" "X2" "X3" "X4" "X5" "X6" "X7" "X8" "X9" "X10" "X11" "X12" "X13" "X14" "X15" "X16" "X17" "X18" "X19" "X20" "X21" "X22" "X23" "X24" "X27" "X35" "X38" "X44" "X47" "X50"
> "rna" "CAA" "CAB" "CAC" "CAD" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAE" "CAF" "CAG" "CAH" "CAI" "CAJ" "CAA" "CAB" "CAD" "CAG" "CAH" "CAI" "CAJ" "CAE" "CAE" "CAE" "CAJ" "CAF" "CAD"
> "lib" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BA" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BB" "114BC" "114BC" "114BC" "114BC" "114BC" "114BC" "114BC" "114BC" "114BA" "061AA" "061AA" "114BA" "062AA"
> "x.1" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5" "2" "5"
> "x.2" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.4" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.5" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.7" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA""x.24" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
> "x.114" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"
> 
> There is something obviously wrong in the second one. The versions are:
> 
> GSLC8|Reproducibility|$ R --version
> R 2.1.0 Patched (2005-05-12).
> 
> charles at tofu:~$ R --version
> R 1.5.1 (2002-06-17).
> 
> I am wondering wether there is a fix or I have to ask the admin of the mosix cluster to upgrade R...


Yes, yes:
Yes there is a fix: R has been fixed more than once in the last 3 year. 
More precisely, there have been 12 *releases* in the meantime.

So please upgrade!

Uwe Ligges


> Best regards,
> 
>