R gam和mgcv之间的程序包冲突? [英] R Package conflict between gam and mgcv?

问题描述

在R中分离软件包不是一个好习惯(请参阅?detach)，但是由于某些原因，我必须在软件包gam和mgcv之间切换.一旦mgcv被附加和分离(并且卸载了命名空间中的所有依赖项！)，gam的函数就会产生一些奇怪的错误(请原谅术语).似乎-尽管先卸载了-mgcv和朋友回到了命名空间中，但函数分派还是出错了.以前有人遇到过同样的问题吗?

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()

我的会话信息为(新会话):

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

，我使用gam(1.09)和mgcv(1.7-28)的最新版本.任何提示表示赞赏！

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

推荐答案

正如您所想的那样，问题是gam和mgcv软件包都为"gam"对象安装了S3方法. 但是，如?detach文档中所述:

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:

从名称空间

注册的S3方法将不会被删除.

registered S3 methods from the namespace will not be removed.

因此，在您的情况下，很容易看到这是造成问题的原因:

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

结论:确保您从不加载mgcv

Conclusion: make sure you never load mgcv

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