charles-r-nospam@plessy.org
2005-Jun-01 03:54 UTC
[R] Different versions, different results ?
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...
Best regards,
--
Charles Plessy, Ph.D. - Genome Science Laboratory
The Institute for Physical and Chemical Research (RIKEN)
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
plessy at riken.jp -- Fax: 048-462-4686 -- Tel: 048-467-9515
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, > >
On Wed, 1 Jun 2005 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") ><snip>> 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...Having multiple `id' variables in reshape() was a feature added in version 2.0.0, so you have to upgrade. -thomas