Did you try taking out P7, which is text? Moreover, if you get a message
saying ' the standard deviation is zero', it means that the entire column is
constant. By definition, the covariance of a constant with a random variable
is 0, but your data consists of values, so cor() understandably throws a
warning that one or more of your columns are constant. Applying the
following to your data (which I named expd instead),  we get

sapply(expd[, -12], var)
          P1           P2           P3           P4           P5
P6
5.433333e-01 1.083333e+00 5.766667e-01 1.083333e+00 6.433333e-01
5.566667e-01
          P8           P9          P10          P11          P12
SITE
5.733333e-01 3.193333e+00 5.066667e-01 2.500000e-01 5.500000e+00
2.493333e+00
      Errors     warnings       Manual        Total        H_tot
HP1.1
9.072840e+03 2.081334e+04 7.433333e-01 3.823500e+04 3.880250e+03
2.676667e+00
       HP1.2        HP1.3        HP1.4       HP_tot        HO1.1
HO1.2
0.000000e+00 2.008440e+03 3.057067e+02 3.827250e+03 8.400000e-01
0.000000e+00
       HO1.3        HO1.4       HO_tot        HU1.1        HU1.2
HU1.3
0.000000e+00 0.000000e+00 8.400000e-01 0.000000e+00 2.100000e-01
2.266667e-01
      HU_tot           HR        L_tot        LP1.1        LP1.2
LP1.3
6.233333e-01 7.433333e-01 3.754610e+03 3.209333e+01 0.000000e+00
2.065010e+03
       LP1.4       LP_tot        LO1.1        LO1.2        LO1.3
LO1.4
2.246233e+02 3.590040e+03 3.684000e+01 0.000000e+00 0.000000e+00
2.840000e+00
      LO_tot        LU1.1        LU1.2        LU1.3       LU_tot
LR_tot
6.000000e+01 0.000000e+00 1.440000e+00 3.626667e+00 8.373333e+00
4.943333e+00
      SP_tot        SP1.1        SP1.2        SP1.3        SP1.4
SP_tot.1
6.911067e+02 4.225000e+01 0.000000e+00 1.009600e+02 4.161600e+02
3.071600e+02
       SO1.1        SO1.2        SO1.3        SO1.4       SO_tot
SU1.1
4.543333e+00 2.500000e-01 0.000000e+00 2.100000e-01 5.250000e+00
0.000000e+00
       SU1.2        SU1.3       SU_tot           SR
1.556667e+00 4.225000e+01 3.504000e+01 4.225000e+01

Which columns are constant?
which(sapply(expd[, -12], var) < .Machine$double.eps)
HP1.2 HO1.2 HO1.3 HO1.4 HU1.1 LP1.2 LO1.2 LO1.3 LU1.1 SP1.2 SO1.3 SU1.1
   19    24    25    26    28    35    40    41    44    51    57    60

I suspect that in your real data set, there aren't so many constant columns,
but this is one way to check.

HTH,
Dennis

On Wed, Sep 8, 2010 at 12:35 PM, Stephane Vaucher <vauchers@iro.umontreal.ca
> wrote:

> Hi everyone,
>
> I'm observing what I believe is weird behaviour when attempting to do
> something very simple. I want a correlation matrix, but my matrix seems to
> contain correlation values that are not found when executed on pairs:
>
>  test2$P2
>>
>  [1] 2 2 4 4 1 3 2 4 3 3 2 3 4 1 2 2 4 3 4 1 2 3 2 1 3
>
>> test2$HP_tot
>>
>  [1]  10  10  10  10  10  10  10  10 136 136 136 136 136 136 136 136 136
> 136  15
> [20]  15  15  15  15  15  15 c=cor(test2$P3,test2$HP_tot,method='spearman')
>
>> c
>>
> [1] -0.2182876
>
>> c=cor(test2,method='spearman')
>>
> Warning message:
> In cor(test2, method = "spearman") : the standard deviation is zero
>
>> write(c,file='out.csv')
>>
>
> from my spreadsheet
> -0.25028783918741
>
> Most cells are correct, but not that one.
>
> If this is expected behaviour, I apologise for bothering you, I read the
> documentation, but I do not know if the calculation of matrices and pairs is
> done using the same function (eg, with respect to equal value observations).
>
> If this is not a desired behaviour, I noticed that it only occurs with a
> relatively large matrix (I couldn't reproduce on a simple 2 column data
> set). There might be a naming error.
>
>  names(test2)
>>
>  [1] "ID"                   "NOMBRE"               "MAIL"
>  [4] "Age"                  "SEXO"                 "Studies"
>  [7] "Hours_Internet"       "Vision.Disabilities"  "Other.disabilities"
> [10] "Technology_Knowledge" "Start_Time"           "End_Time"
> [13] "Duration"             "P1"                   "P1Book"
> [16] "P1DVD"                "P2"                   "P3"
> [19] "P4"                   "P5"                   "P6"
> [22] "P8"                   "P9"                   "P10"
> [25] "P11"                  "P12"                  "P7"
> [28] "SITE"                 "Errors"               "warnings"
> [31] "Manual"               "Total"                "H_tot"
> [34] "HP1.1"                "HP1.2"                "HP1.3"
> [37] "HP1.4"                "HP_tot"               "HO1.1"
> [40] "HO1.2"                "HO1.3"                "HO1.4"
> [43] "HO_tot"               "HU1.1"                "HU1.2"
> [46] "HU1.3"                "HU_tot"               "HR"
> [49] "L_tot"                "LP1.1"                "LP1.2"
> [52] "LP1.3"                "LP1.4"                "LP_tot"
> [55] "LO1.1"                "LO1.2"                "LO1.3"
> [58] "LO1.4"                "LO_tot"               "LU1.1"
> [61] "LU1.2"                "LU1.3"                "LU_tot"
> [64] "LR_tot"               "SP_tot"               "SP1.1"
> [67] "SP1.2"                "SP1.3"                "SP1.4"
> [70] "SP_tot.1"             "SO1.1"                "SO1.2"
> [73] "SO1.3"                "SO1.4"                "SO_tot"
> [76] "SU1.1"                "SU1.2"                "SU1.3"
> [79] "SU_tot"               "SR"
>
> Thank you in advance,
> Stephane Vaucher
>
> ______________________________________________
> R-help@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.
>

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