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I am getting the following error every time I run a Cox model using the survival package in R. This error arose within the last few days. To illustrate the error, I am using a standard example command which is given at https://stat.ethz.ch/R-manual/R-devel/library/survival/html/coxph.html:

# Fit a stratified model, clustered on patients 
library(survival)
bladder1 <- bladder[bladder$enum < 5, ] 
coxph(Surv(stop, event) ~ (rx + size + number) * strata(enum) + 
      cluster(id), bladder1)

The error I get is as follows:

Error in fitter(X, Y, strats, offset, init, control, weights = weights,  : 
  object 'Ccoxmart' not found

I am using latest version of R [3.4.0 (2017-04-21) -- "You Stupid Darkness"].

I have tried to consult the survival package manual for R and researched on the internet. I am grateful for any resource or solution you may recommend.

user3487564
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2 Answers2

11

I can confirm this error. It's definitely something to do with the update from R 3.3.3 (Another Canoe) -> R 3.4.0 (You Stupid Darkness). All unit tests in my system working correctly on Friday, broken Monday.

In addition, I'm also having an issue with "Ccoxph_wtest" not being found. Must be a similar issue.

I'll start debugging later today and let you know what I find, but for now if you have to get back up and running, I'd suggest reverting to R v3.3.3 (Another Canoe). I have rerun all my unit tests using v3.3.3 and all is fine.

Here is the sessionInfo():

R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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


R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] compiler_3.4.0

My solution was to re-install the survival package. Just install it right on top of the original. install.packages("survival").

Stu Field
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0

You have to re-install packages that use C or Fortran in R 3.4.0:

update.packages(checkBuild=TRUE)

See this post

Packages which register native routines for .C or .Fortran need to be re-installed for this version (unless installed with R-devel SVN revision r72375 or later)

Denis
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