On 06/05/2015 10:52 AM, Martin Maechler wrote:
Christophe Genolini <cgeno...@u-paris10.fr>
on Fri, 5 Jun 2015 00:36:42 -0700 writes:
> Hi all,
> There is a compatibility issue between the package 'lme4' and my package
> 'kml'. I define the "[" operator. It works just fine in my package (1).
If I
> try to use the lme4 package, then it does no longer work (2). Moreover,
it
> has some kind of strange behavior (3). Do you know what is wrong? Any
idea
> of how I can correct that?
> Here is a reproductible example, and the same code with the result
follows.
> Thanks for your help
> Christophe
[ ... I'm providing slightly different code below .... ]
--- 8< ----------------- Execution of the previous code -------------------
library(kml)
Le chargement a nécessité le package : clv
Le chargement a nécessité le package : cluster
Le chargement a nécessité le package : class
Le chargement a nécessité le package : longitudinalData
Le chargement a nécessité le package : rgl
Le chargement a nécessité le package : misc3d
dn <- gald(1)
###########
### (1) the "[" operator works just fine
dn["traj"]
t0 t1 t2 t3 t4 t5 t6 t7 t8 t9 t10
i1 -3.11 4.32 2.17 1.82 4.90 7.34 0.83 -2.70 5.36 4.96 3.16
i2 -7.11 1.40 -2.40 -2.96 4.31 0.50 1.25 0.52 -0.04 7.55 5.50
i3 2.80 6.23 6.08 2.87 2.58 2.88 6.58 -2.38 2.30 -1.74 -3.23
i4 2.24 0.91 6.50 10.92 11.32 7.79 7.78 10.69 9.15 1.07 -0.51
###########
### (2) using 'lme4', it does no longer work
library(lme4)
Le chargement a nécessité le package : Matrix
Le chargement a nécessité le package : Rcpp
dn["traj"]
Error in x[i, j] :
erreur d'évaluation de l'argument 'j' lors de la sélection d'une méthode
pour la fonction '[' : Erreur : l'argument "j" est manquant, avec aucune
valeur par défaut
###########
### (3) If I define again the "[", it does not work the first time I call
it, but it work the second time!
setMethod("[",
+ signature=signature(x="ClusterLongData", i="character", j="ANY",drop="ANY"),
+ definition=function (x, i, j="missing", ..., drop = TRUE){
Your file has two definitions of
setMethod("[", c("ClusterLongData", ...
I deleted the first one.
The second definition had
signature=signature(x="ClusterLongData", i="character", j="ANY",drop="ANY"),
whereas probably you mean to say that you'll handle
signature=signature(x="ClusterLongData", i="character",
j="missing", drop="ANY")
The next line says
definition=function (x, i, j="missing", ..., drop = TRUE){
which provides a default value for 'j' when j is not provided by the user. Thus
later when you say
x[i, j]
you are performing dn["traj", "missing"] when probably you meant
x[i, , drop=drop]
Making these changes, so the definition is
setMethod(
"[",
signature=signature(x="ClusterLongData", i="character", j="missing",
drop="ANY"),
definition=function (x, i, j, ..., drop = TRUE){
if (is.numeric(i)) {
stop("[ClusterLongData:getteur]: to get a clusters list, use
['ci']")
}else{}
if (i %in% c("criterionValues", "criterionValuesAsMatrix")){
j <- x['criterionActif']
}else{}
if (i %in% c(CRITERION_NAMES, "criterionActif", CLUSTER_NAMES,
"criterionValues", "criterionValuesAsMatrix", "sorted",
"initializationMethod")) {
x <- as(x, "ListPartition")
}else{
x <- as(x, "LongData")
}
x[i, , drop=drop]
})
Allows operations to work correctly.
> library(kml)
Loading required package: clv
Loading required package: cluster
Loading required package: class
Loading required package: longitudinalData
Loading required package: rgl
Loading required package: misc3d
> library(Matrix)
> x = gald(1)["traj"]
> x
t0 t1 t2 t3 t4 t5 t6 t7 t8 t9 t10
i1 -3.18 -1.19 -1.17 1.56 -0.70 1.78 -0.95 -2.00 -5.05 1.05 2.84
i2 3.51 1.72 6.97 6.09 7.81 8.33 9.54 14.38 16.14 12.82 13.86
i3 9.60 11.59 9.09 6.31 9.24 7.69 4.26 -0.80 2.70 1.63 1.21
i4 -0.54 3.80 6.05 10.41 12.60 12.32 10.33 11.05 7.89 5.21 0.67
It's hard to tell whether is an issue with the methods package, or just that
Matrix offered a better nearest 'method' than those provided by kml /
longitudinalData.
+ x <- as(x, "LongData")
+ return(x[i, j])
+ }
+ )
[1] "["
### No working the first time I use it
dn["traj"]
Error in dn["traj"] :
l'argument "j" est manquant, avec aucune valeur par défaut
### But working the second time
dn["traj"]
t0 t1 t2 t3 t4 t5 t6 t7 t8 t9 t10
i1 -3.11 4.32 2.17 1.82 4.90 7.34 0.83 -2.70 5.36 4.96 3.16
i2 -7.11 1.40 -2.40 -2.96 4.31 0.50 1.25 0.52 -0.04 7.55 5.50
i3 2.80 6.23 6.08 2.87 2.58 2.88 6.58 -2.38 2.30 -1.74 -3.23
i4 2.24 0.91 6.50 10.92 11.32 7.79 7.78 10.69 9.15 1.07 -0.51
I have made some investigations, but have to stop for now, and
leave this hopefully to others knowledgable about S4 method
dispatch, etc :
1) I am confident to say that you have uncovered an "unfelicity if
not a bug" in R.
2) I am also pretty confident that the "[" methods that you
define in 'kml' and in the package '
3) Diagnosing is not easy: As you have shown yourself above,
in some situations the bug "bites" and if you repeat the *same*
code, things work.
This is related to the fact that S4 methods are __cached__
(so next time they are found more quickly) under some
circumstances, and the cache is cleared under other such circumstances.
3b) Actually, I am sure that we have seen +/- the same problem many
months ago, in other contexts but did not get "down to it";
and at the moment, I cannot quickly find where to look for
the problem there...
##--- 8< ------------Commented (incl output) reproducible code--------------
library(kml)
### Creating some data
dn <- gald(1)
(dnt <- dn["traj"])
showMethods("[")
## Function: [ (package base)
## x="ClusterLongData", i="character"
## x="ListPartition", i="ANY"
## x="LongData", i="ANY"
## x="LongData", i="character"
## (inherited from: x="LongData", i="ANY")
## x="LongData3d", i="ANY"
## x="nonStructure", i="ANY"
## x="ParChoice", i="ANY"
## x="ParKml", i="ANY"
## x="ParLongData", i="ANY"
## x="Partition", i="ANY"
## x="ParWindows", i="ANY"
### using Matrix (or lme4, which 'Depends' on Matrix; hence same effect)
library(Matrix)
dn["traj"]
## Error in x[i, j] :
## error in evaluating the argument 'j' in selecting a method for function '[': Error:
argument "j" is missing, with no default
traceback()
## 3: x[i, j]
## 2: dn["traj"]
## 1: dn["traj"]
(ms <- methods(`[`)) ## 81 methods
##---- MM: debugging :
trace("[", browser, signature=c("ClusterLongData", "character", "missing",
"missing"))
trace("[", browser, signature=c("LongData", "character", "character",
"missing"))
dn["traj"]
## -> you get into the browser, just press "c" twice (once for each "trace")
## ==> it works !!
## Remove the tracing :
untrace("[", signature=c("ClusterLongData", "character", "missing",
"missing"))
untrace("[", signature=c("LongData", "character", "character",
"missing"))
dn["traj"]
## Error in dn["traj"] : argument "j" is missing, with no default
## Debugging only the *inner* function:
trace("[", browser, signature=c("LongData", "character", "character",
"missing"))
dn["traj"]
## Error ....
untrace("[", signature=c("LongData", "character", "character",
"missing"))
## Debugging only the *outer* function:
trace("[", browser, signature=c("ClusterLongData", "character", "missing",
"missing"))
dn["traj"] ## -> debugger, press 'c'
## it works!
## t0 t1 t2 t3 t4 t5 t6 t7 t8 t9 t10
## i1 7.38 4.80 4.80 0.73 0.58 2.22 0.55 -1.05 0.79 5.20 4.43
## i2 1.55 2.01 -0.29 2.12 4.44 7.33 9.09 4.76 12.18 5.92 8.06
## i3 13.60 14.72 10.15 9.25 8.70 8.34 6.71 5.84 3.44 2.10 2.17
## i4 -7.49 -1.80 0.08 2.51 6.61 4.56 8.96 3.05 3.41 -2.62 -4.09
untrace("[", signature=c("ClusterLongData", "character", "missing",
"missing"))
##--- {end of reproducible code} --------------
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
