R devel - Nov 2014 - Unexplicable difference between 2 R installations regarding reading numbers

Dear all,

A colleague of mine reported a problem that I fail to understand
completely. He has a number of .csv files that look all very
straightforward, and they all read in perfectly well using read.csv() on
both his and my computer.

When we try the exact same R version on the university server however,
suddenly all numeric variables turn into factors. The problem is resolved
by deleting the last digits of every number in the .csv file.  Using
as.numeric() on the values works as well.

Anybody a clue as to what might cause this problem? If needed, I can send
an example of a .csv file.

Example output on server:
> X <- read.csv("Originelen/Originelen/heavymetals.csv")
> levels(X[[2]])
 [1] "11.140969600635804" "11.548972671055257"
"11.98554898321271"
 [4] "16.317868213178677" "17.179218967921898"
"18.596573461949852"
 [7] "18.786014405762298" "18.87978032658098" 
"23.604106448719225"
[10] "26.75482955698816"  "27.33829851044687" 
"29.26619704952923"
[13] "33.07842352705811"  "39.296270581233884"
"4.8696848424212105"
[16] "5.5751725517655295" "6.0256909109049195"
"9.117975845892804"
[19] "9.26944194868723"
> str(X)
'data.frame':   19 obs. of  18 variables:
 $ ID   : int  1 2 3 4 5 6 7 8 9 10 ...
 $ Cd5  : Factor w/ 19 levels "11.140969600635804",..: 3 8 6 12 11 10
2 5
14 13 ...
 $ Cd20 : Factor w/ 19 levels "10.160499999999999",..: 2 8 10 12 5 6
18 9
11 4 ...
 $ Cr5  : Factor w/ 19 levels "118.43421710855425",..: 6 11 10 17 16
15 7
13 19 18 ...
 $ Cr20 : Factor w/ 19 levels "100.48101898101898",..: 9 15 14 17 13
11 6
16 18 12 ...
 $ Cu5  : Factor w/ 19 levels "101.8005401620486",..: 8 17 16 15 14 12
9 18
19 1 ...
 $ Cu20 : Factor w/ 19 levels "103.67346938775509",..: 11 18 19 2 16
17 14
3 4 1 ...
 $ Fe5  : Factor w/ 19 levels "17239.349496158833",..: 3 8 10 9 12 14
7 16
19 18 ...
 $ Fe20 : Factor w/ 19 levels "17701.77893264042",..: 3 14 16 18 10 15
6 17
19 13 ...
 $ Mn5  : Factor w/ 19 levels "440.37211163349",..: 10 14 4 5 3 17 2 7
18 6
...
 $ Mn20 : Factor w/ 19 levels "375.19156134938805",..: 12 2 6 3 1 9 11
7 8
5 ...
 $ Ni5  : Factor w/ 19 levels "19.54255213010077",..: 4 12 8 10 11 16
6 14
19 18 ...
 $ Ni20 : Factor w/ 19 levels "21.295222866280234",..: 8 13 15 18 12
16 7
17 19 14 ...
 $ Pb5  : Factor w/ 19 levels "125.5616926977306",..: 1 11 14 9 13 8 5
12
15 16 ...
 $ Pb20 : Factor w/ 19 levels "106.96930306969303",..: 3 8 11 12 9 10
4 13
14 15 ...
 $ Zn5  : Factor w/ 19 levels "1024.909963985594",..: 17 4 7 5 8 3 18
6 9
10 ...
 $ Zn20 : Factor w/ 19 levels "1247.816195886593",..: 15 4 5 7 2 1 16
6 8 3
...
 $ river: int  1 1 1 1 1 1 1 1 1 1 ...

Using as.numeric(levels(X[[2]])) works perfectly fine though...

Session info both server and my own computer :
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252
[3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Belgium.1252

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

loaded via a namespace (and not attached):
[1] tools_3.1.0

-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel :  +32 (0)9 264 61 79
Joris.Meys at Ugent.be
-------------------------------
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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R version.

NEWS for 3.1.0:

      type.convert() (and hence by default
      read.table() returns a character vector or factor when
      representing a numeric input as a double would lose accuracy.
      Similarly for complex inputs.

NEWS for 3.1.1:

      type.convert(), read.table() and similar
      read.*() functions get a new numerals argument,
      specifying how numeric input is converted when its conversion to
      double precision loses accuracy.  The default value,
      allow.loss allows accuracy loss, as in R versions before
      3.1.0.


On Nov 3, 2014, at 10:07 AM, Joris Meys <jorismeys at gmail.com> wrote:
> Dear all,
> 
> A colleague of mine reported a problem that I fail to understand
> completely. He has a number of .csv files that look all very
> straightforward, and they all read in perfectly well using read.csv() on
> both his and my computer.
> 
> When we try the exact same R version on the university server however,
> suddenly all numeric variables turn into factors. The problem is resolved
> by deleting the last digits of every number in the .csv file.  Using
> as.numeric() on the values works as well.
> 
> Anybody a clue as to what might cause this problem? If needed, I can send
> an example of a .csv file.
> 
> Example output on server:
> 
>> X <- read.csv("Originelen/Originelen/heavymetals.csv")
>> levels(X[[2]])
> [1] "11.140969600635804" "11.548972671055257"
"11.98554898321271"
> [4] "16.317868213178677" "17.179218967921898"
"18.596573461949852"
> [7] "18.786014405762298" "18.87978032658098" 
"23.604106448719225"
> [10] "26.75482955698816"  "27.33829851044687" 
"29.26619704952923"
> [13] "33.07842352705811"  "39.296270581233884"
"4.8696848424212105"
> [16] "5.5751725517655295" "6.0256909109049195"
"9.117975845892804"
> [19] "9.26944194868723"
>> str(X)
> 'data.frame':   19 obs. of  18 variables:
> $ ID   : int  1 2 3 4 5 6 7 8 9 10 ...
> $ Cd5  : Factor w/ 19 levels "11.140969600635804",..: 3 8 6 12 11
10 2 5
> 14 13 ...
> $ Cd20 : Factor w/ 19 levels "10.160499999999999",..: 2 8 10 12 5
6 18 9
> 11 4 ...
> $ Cr5  : Factor w/ 19 levels "118.43421710855425",..: 6 11 10 17
16 15 7
> 13 19 18 ...
> $ Cr20 : Factor w/ 19 levels "100.48101898101898",..: 9 15 14 17
13 11 6
> 16 18 12 ...
> $ Cu5  : Factor w/ 19 levels "101.8005401620486",..: 8 17 16 15
14 12 9 18
> 19 1 ...
> $ Cu20 : Factor w/ 19 levels "103.67346938775509",..: 11 18 19 2
16 17 14
> 3 4 1 ...
> $ Fe5  : Factor w/ 19 levels "17239.349496158833",..: 3 8 10 9 12
14 7 16
> 19 18 ...
> $ Fe20 : Factor w/ 19 levels "17701.77893264042",..: 3 14 16 18
10 15 6 17
> 19 13 ...
> $ Mn5  : Factor w/ 19 levels "440.37211163349",..: 10 14 4 5 3 17
2 7 18 6
> ...
> $ Mn20 : Factor w/ 19 levels "375.19156134938805",..: 12 2 6 3 1
9 11 7 8
> 5 ...
> $ Ni5  : Factor w/ 19 levels "19.54255213010077",..: 4 12 8 10 11
16 6 14
> 19 18 ...
> $ Ni20 : Factor w/ 19 levels "21.295222866280234",..: 8 13 15 18
12 16 7
> 17 19 14 ...
> $ Pb5  : Factor w/ 19 levels "125.5616926977306",..: 1 11 14 9 13
8 5 12
> 15 16 ...
> $ Pb20 : Factor w/ 19 levels "106.96930306969303",..: 3 8 11 12 9
10 4 13
> 14 15 ...
> $ Zn5  : Factor w/ 19 levels "1024.909963985594",..: 17 4 7 5 8 3
18 6 9
> 10 ...
> $ Zn20 : Factor w/ 19 levels "1247.816195886593",..: 15 4 5 7 2 1
16 6 8 3
> ...
> $ river: int  1 1 1 1 1 1 1 1 1 1 ...
> 
> Using as.numeric(levels(X[[2]])) works perfectly fine though...
> 
> Session info both server and my own computer :
> 
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252
> [3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
> [5] LC_TIME=Dutch_Belgium.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
> 
> -- 
> Joris Meys
> Statistical consultant
> 
> Ghent University
> Faculty of Bioscience Engineering
> Department of Mathematical Modelling, Statistics and Bio-Informatics
> 
> tel :  +32 (0)9 264 61 79
> Joris.Meys at Ugent.be
> -------------------------------
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
> 
> 	[[alternative HTML version deleted]]
> 
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