[R] survival package can't find Ccoxfit6

Duncan Murdoch murdoch.duncan at gmail.com
Wed Apr 26 22:17:30 CEST 2017 

On 26/04/2017 2:51 PM, Therneau, Terry M., Ph.D. wrote:
> 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"

As far as I can see, that line doesn't appear in the current survival 
source code, it's from some earlier version of the package.  The current 
one has

coxfit <- .Call(Ccoxfit6,
                      as.integer(maxiter),
                      stime,
                      sstat,
                      x[sorted,],
                      as.double(offset[sorted]),
                      weights,
                      newstrat,
                      as.integer(method=="efron"),
                      as.double(control$eps),
                      as.double(control$toler.chol),
                      as.vector(init),
                      as.integer(1))  # internally rescale

There are several differences, the one leading to the error being the 
change from "Ccoxfit6" in quotes, to Ccoxfit6 not in quotes.  That 
corresponds to the difference between a registered symbol and an 
unregistered one.

Without seeing the code that led to the error message I can't really say 
how the error came about.  There are a few ways:

- The user has a copy of the coxph.fit function from an older version of 
survival saved in their workspace, and are using that one instead of the 
current one.

- Some part of your code returns functions, and one of those is making 
this call based on an object produced in an earlier version of survival.

- There are really two versions of survival on the search path (or 
perhaps copied bits of one), and this call isn't in survival 2.41-3 at all.

Duncan Murdoch

>>> 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
>>
>
>
> =====================================================================
>
>       Please note that this e-mail and any files transmitted from
>       Memorial Sloan Kettering Cancer Center may be privileged, confidential,
>       and protected from disclosure under applicable law. If the reader of
>       this message is not the intended recipient, or an employee or agent
>       responsible for delivering this message to the intended recipient,
>       you are hereby notified that any reading, dissemination, distribution,
>       copying, or other use of this communication or any of its attachments
>       is strictly prohibited.  If you have received this communication in
>       error, please notify the sender immediately by replying to this message
>       and deleting this message, any attachments, and all copies and backups
>       from your computer.
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

More information about the R-help mailing list