[R] survival package can't find Ccoxfit6

Therneau, Terry M., Ph.D. therneau at mayo.edu
Wed Apr 26 20:51:10 CEST 2017


A user contacted me directly about this, I answered with my best understanding of the 
recent R-help discussion of the issue, and their response to my response shows that I'm 
not quite right.

I am emphatically not an MS Windows user so am asking for help -- which I will cut/paste 
to this user and to the next dozen who will invariably contact me directly.

Thanks,
   Terry Therneau



-------- Forwarded Message --------
Subject: RE: survival package
Date: Wed, 26 Apr 2017 18:05:30 +0000
From: SeshanV at mskcc.org
To: Therneau, Terry M., Ph.D. <therneau at mayo.edu>

Thank you for the quick response. The session info command for v3.4.0 does in fact report 
survival_2.41-3. Furthermore, while both v3.3.1 and v3.40 are on the same computer the 
library paths do not have any directory in common:

> .libPaths()
[1] "C:/Program Files/R/R-3.4.0/library"
>

and
> .libPaths()
[1] "C:/Program Files/R/R-3.3.1/library"
>


Thanks,
Venkat


-----Original Message-----
From: Therneau, Terry M., Ph.D. [mailto:therneau at mayo.edu] Sent: Wednesday, April 26, 2017 
1:42 PM
To: Seshan, Venkatraman E./Epidemiology-Biostatistics
Subject: Re: survival package

This has been discussed in R-help by multiple people.  You have a pre-3.4 version of the 
survival package somewhere on your search path, and the method for resolving .C calls has 
changed.   The sessionInfo command should report survival version 2.41-3.

Terry T.


On 04/26/2017 12:17 PM, SeshanV at mskcc.org wrote:
> Dear Prof. Therneau,
>
> I am encountering an error message when I try to use the coxfit6 routine from the survival package under the 3.4.0 version of R. The minimal function and the script are in the attached file. This function worked under earlier versions of R.
>
> ----------------------------------------------------------------------
> -------------------------
>
> ***************************
> **  Works under R-3.3.1  **
> ***************************
>
>> source("coxfit6-issue.R")
> [1] -0.4838181
>
>> sessionInfo()
> R version 3.3.1 (2016-06-21)
> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64
> (build 7601) Service Pack 1
>
> locale:
> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] survival_2.39-4
>
> loaded via a namespace (and not attached):
> [1] Matrix_1.2-6    splines_3.3.1   grid_3.3.1      lattice_0.20-33
>
> ----------------------------------------------------------------------
> -------------------------
>
> ***********************************
> **  Does not work under R-3.4.0  **
> ***********************************
>
>> library(survival)
>> source("coxfit6-issue.R")
> Error in .Call("Ccoxfit6", as.integer(control$iter.max), stime, as.integer(sstat),  :
>    "Ccoxfit6" not available for .Call() for package "survival"
>> sessionInfo()
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64
> (build 7601) Service Pack 1
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] survival_2.41-3
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0  Matrix_1.2-9    splines_3.4.0   grid_3.4.0
> [5] lattice_0.20-35
>
> ----------------------------------------------------------------------
> -------------------------
>
> When I remove the quotes surrounding Ccoxfit6 in the function both versions give the error:
>
> Error in phcoefs(stim[ii], sts[ii], as.matrix(as.double(cvt[ii])), oo$coefficients,  :
>    object 'Ccoxfit6' not found
>
>
> I would greatly appreciate your help in resolving this.
>
> Thanks,
> Venkat Seshan
>


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