Re: [Rd] conflict between lme4 and RMySQL packages (PR#9753)

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue, 26 Jun 2007 10:51:03 +0100 (BST)

You have three summary() functions here:

> library(RMySQL)

Loading required package: DBI
> library(lme4)

Loading required package: Matrix
Loading required package: lattice
> find("summary")

[1] "package:Matrix" "package:DBI" "package:base"

and this is simply a namespace issue (note the environments):

> summary

standardGeneric for "summary" defined from package "base"

function (object, ...)
standardGeneric("summary")
<environment: 0x15122d0>
Methods may be defined for arguments: object

> Matrix:::summary

standardGeneric for "summary" defined from package "base"

function (object, ...)
standardGeneric("summary")
<environment: 0x26c6640>
Methods may be defined for arguments: object

> DBI:::summary

standardGeneric for "summary" defined from package "base"

function (object, ...)
standardGeneric("summary")
<environment: 0x15122d0>
Methods may be defined for arguments: object

so the visible summary() from package:Matrix is a copy of that in the DBI namespace, not that in the Matrix namespace. Since lme4 imports all of Matrix, it imports its take-over of summary. So the issue is not *S4* dispatch per se, but how the 'methods' package copes with two or more packages presenting the same generic.

If you dig a bit deeper,

> ls(environment(summary)$".AllMTable")

  [1] "ANY"             "DBIObject"       "MySQLConnection" "MySQLDriver"
  [5] "MySQLResult"     "lmer2"           "mer"             "sparseMatrix"
  [9] "summary.lmer2"   "summary.mer"

> ls(environment(summary)$".AllMTable")
[1] "ANY" "DBIObject" "MySQLConnection" "MySQLDriver" [5] "MySQLResult" "lmer2" "mer" "sparseMatrix"
  [9] "summary.lmer2" "summary.mer"
> ls(environment(Matrix:::summary)$".AllMTable")
[1] "ANY" "sparseMatrix"
> ls(environment(DBI:::summary)$".AllMTable")
  [1] "ANY"             "DBIObject"       "MySQLConnection" "MySQLDriver"
  [5] "MySQLResult"     "lmer2"           "mer"             "sparseMatrix"
  [9] "summary.lmer2"   "summary.mer"

shows the issue: the methods do not get stored on the version in the Matrix namespace, but rather on the version in package:Matrix which was copied from the existing export and not Matrix:::summary.

Clearly there is going to be a namespace problem one way round: what seems undocumented is which.

On Tue, 26 Jun 2007, maechler_at_stat.math.ethz.ch wrote:

> Thank you, Dale.
>
> I think you've revealed a bug in the method dispatch mechanism.
> I'm adding here a script which confirms your finding and add
> slightly more insight:
>
> library(RMySQL)
> library(lme4)
>
> data(sleepstudy)
> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
>
> ## MM: First save, then print -- the error is in "print" i.e. show() :
> s1 <- summary(fm1)
> s1 #-> error in printMer() which is hidden :
>
> debug(lme4:::printMer)
> s1 # --> printMer(x, ..) calls so <- summary(x) at the very beginning
> ## and indeed, summary(x) -- *inside* printMer() dispatches wrongly !!!!
> ## whereas top-level, there is no problem :
>
> ## maybe here, or then later
> undebug(lme4:::printMer)
>
> ## This works fine top-level, but gives non-sense when inside printMer() !!
> ##
> so <- summary(s1) ## does nothing, since s1 *is* already summary.lmer :
> stopifnot(identical(so, s1)) # ok
>
> ## one other symptom of the same problem:
> showMethods(summary) ## is fine top-level
>
> ## whereas it does not see the correct methods when used from inside printMer()
> ## i.e., also when debugging
>
>
>
>>>>>> "db" == dale barr <dale.barr_at_ucr.edu>
>>>>>> on Tue, 26 Jun 2007 00:57:22 +0200 (CEST) writes:
>
> db> Full_Name: Dale Barr
> db> Version: 2.5.1 (patched)
> db> OS: Ubuntu linux x86_64
> db> Submission from: (NULL) (138.23.70.108)
>
>
> db> When RMySQL is loaded in before lme4, the summary() function for lmer objects in
> db> the lme4 packages produces the following error:
>
> db> Error in printMer(object) : no slot of name "status" for this object of class
> db> "table"
>
> db> When RMySQL is loaded AFTER lme4, however, no such error arises. For example,
> db> the following code gives the error:
>
> >> library(RMySQL)
> db> Loading required package: DBI
> >> library(lme4)
> db> Loading required package: Matrix
> db> Loading required package: lattice
> >> data(sleepstudy)
> >> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> >> summary(fm1)
> db> Error in printMer(object) : no slot of name "status" for this object of class
> db> "table"
>
> db> Now, here is the exact same code except that lme4 is loaded before RMySQL. The
> db> summary function works properly.
>
> >> library(lme4)
> db> Loading required package: Matrix
> db> Loading required package: lattice
> db> library(RMySQL)> library(RMySQL)
> db> Loading required package: DBI
> >> data(sleepstudy)
> >> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> >> summary(fm1)
> db> Linear mixed-effects model fit by REML
> db> Formula: Reaction ~ Days + (Days | Subject)
> db> Data: sleepstudy
> db> AIC BIC logLik MLdeviance REMLdeviance
> db> 1754 1770 -871.8 1752 1744
> db> Random effects:
> db> Groups Name Variance Std.Dev. Corr
> db> Subject (Intercept) 610.835 24.7151
> db> Days 35.056 5.9208 0.067
> db> Residual 655.066 25.5943
> db> number of obs: 180, groups: Subject, 18
>
> db> Fixed effects:
> db> Estimate Std. Error t value
> db> (Intercept) 251.405 6.820 36.86
> db> Days 10.467 1.546 6.77
>
> db> Correlation of Fixed Effects:
> db> (Intr)
> db> Days -0.137
>
>
> db> MY SESSION INFO:
> db> R version 2.5.1 RC (2007-06-22 r42030)
> db> x86_64-unknown-linux-gnu
>
> db> locale:
> db> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> db> attached base packages:
> db> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
> db> [7] "base"
>
> db> other attached packages:
> db> RMySQL DBI lme4 Matrix lattice
> db> "0.6-0" "0.2-3" "0.99875-2" "0.99875-2" "0.15-11"
>
> db> ______________________________________________
> db> R-devel_at_r-project.org mailing list
> db> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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