Getting Rcpp::not_compatible when executing coxph algorithm in mapreduce job

[Ashish Patha]

I am executing coxph algorithm in map reduce and here is my code :

I have written my code in the same way for Survival it worked out for me but not working for Coxph.

Mapper function:

I have data set which consits of some fields so i am taking some required rows using cbind and passing them to reducer...

DeviceData.map.fn <- function(k,v) {

mapObject<-cbind(v[2],v[7],v[3])

keyval(1, mapObject)

}

Reducer function:

Slot,DeviceFailed,Temp are my row headers in my dataset

DeviceData.reduce.fn<-function(k,v)

{

result<-survfit(coxph(Surv(Slot,DeviceFailed)~Temp,data=v),type="aalen")

keyval(k,result)

}

i am getting following error:

Loading required package: survival
Loading required package: splines
Loading required package: rhdfs
Loading required package: methods
Loading required package: rJava
Error : .onLoad failed in loadNamespace() for 'rhdfs', details:
  call: fun(libname, pkgname)
  error: Environment variable HADOOP_CMD must be set before loading package rhdfs
Warning in FUN(c("survival", "splines", "rhdfs", "rJava", "rmr2", "reshape2",  :
  can't load rhdfs
Loading required package: rmr2
Loading required package: Rcpp
Loading required package: RJSONIO
Loading required package: bitops
Loading required package: digest
Loading required package: functional
Loading required package: stringr
Loading required package: plyr
Loading required package: reshape2
terminate called after throwing an instance of 'Rcpp::not_compatible'
  what():  expecting a single value

I need help on this

1) Is My mapper and reduce function is correct ?

2) If correct why i am getting this error for coxph as the same thing worked for Survival analysis.

[Antonio Piccolboni]

No, you are not allowed to use an object of class survfit as a value. list(survfit ... will do the job. 

2) If correct why i am getting this error for coxph as the same thing worked for Survival analysis.

I don't know.

Antonio

 

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