R Package conflict between gam and mgcv?

Question

Detaching packages in R isnt good practice (see ?detach), but for some reasons I have to switch between the packages gam and mgcv. Once mgcv was attached and detached (and all the dependencies in the namespace unloaded!), functions of gam produce some strange errors (please forgive the terminology). It seems that - even though unloaded one step before - mgcv and friends are back in the namespace and function dispatching goes wrong. Does anyone had the same problem before?

# fresh session
t.s1 <- search()
t.lN1 <- loadedNamespaces()

# some dummy data
data <-data.frame(is.exc=sample(x=c(0,1),size=100,replace=T),
year=1:100,doy=rep(1:5,times=20))
t.dof <- 2

# everything works fine
library(gam)
t.gam1 <- gam::gam(is.exc~s(year,df=t.dof)+s(doy,df=t.dof),data=data,family=poisson)
t.pred1 <- gam::predict.gam(t.gam1,newdata=data,type='terms')
detach('package:gam',unload=T,character.only=T)
detach('package:splines',unload=T,character.only=T)

# compare attached packages and namespaces with fresh session
t.s2 <- search()
t.lN2 <- loadedNamespaces()
identical(t.s1,t.s2)
identical(t.lN1,t.lN2)

# attach and detach mgcv
library(mgcv)
detach('package:mgcv',unload=T,character.only=T)
unloadNamespace('nlme')
unloadNamespace('Matrix')
unloadNamespace('lattice')
unloadNamespace('grid')

# compare again attached packages and namespaces with fresh session
t.s2 <- search()
t.lN2 <- loadedNamespaces()
identical(t.s1,t.s2)
identical(t.lN1,t.lN2)

# use package gam again and produce errors
library(gam)
t.gam2 <- gam::gam(is.exc~s(year,df=t.dof)+s(doy,df=t.dof),data=data,family=poisson)
gam::summary.gam(t.gam2)
t.pred2 <- gam::predict.gam(t.gam2,newdata=data,type='terms')

# why do we have mgcv and friends in the namespace?
loadedNamespaces()

My session infos are (fresh session):

R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8         LC_COLLATE=en_US.UTF-8    
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
[9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] tools_3.0.2

and I use the latest versions of gam (1.09) and mgcv (1.7-28). Any hints are appreciated!

Answer 1

The problem, as you ANTICIPATED, is that both gam and mgcv packages install S3 methods for "gam" objects. But, as stated in the ?detach documentation:

registered S3 methods from the namespace will not be removed.

So in your case it is easy to see that is the cause of your problems:

library(gam)
# installs gam::print.summary.gam
identical(getS3method('print', 'summary.gam'), gam:::print.summary.gam)
[1] TRUE


library(mgcv)
# installs mgcv::print.summary.gam
identical(getS3method('print', 'summary.gam'), mgcv:::print.summary.gam)
[1] TRUE

# save a pointer before unloading namespaces
mgcv_psgam <- mgcv:::print.summary.gam

detach('package:mgcv',unload = TRUE, character.only = TRUE)
# after the detach, the method from mgcv is still installed !!!
identical(getS3method('print', 'summary.gam'), mgcv_psgam)
[1] TRUE

Conclusion: make sure you never load mgcv