[R] survival package can't find Ccoxfit6
Duncan Murdoch
murdoch.duncan at gmail.com
Thu Apr 27 03:06:22 CEST 2017
On 26/04/2017 5:20 PM, SeshanV at mskcc.org wrote:
> Attaching the code that generates the error. The function phcoefs in the attached was modeled after coxph.fit from which all the preprocessing has been stripped so that just coxfit6 (C code) can be called to estimate the coefficients.
>
>> library(survival)
>> source("coxfit6-issue.R")
> Error in .Call("Ccoxfit6", as.integer(control$iter.max), stime, as.integer(sstat), :
> "Ccoxfit6" not available for .Call() for package "survival"
>
> Same file with the quotes surrounding "Ccoxfit6" removed
>
>> source("coxfit6-issue.R")
> Error in phcoefs(stim[ii], sts[ii], as.matrix(as.double(cvt[ii])), oo$coefficients, :
> object 'Ccoxfit6' not found
>>
>
> I can confirm that this error occurs in linux (Ubuntu 14.0.4.5) as well.
That's misuse of the package. As far as I know, the Ccoxfit6 function
has never been exported from the survival package. Using unexported
internals from a package is very dangerous and likely to lead to errors.
(As I pointed out, there were other changes to the call besides the
use of "Ccoxfit6" versus Ccoxfit6.
Duncan Murdoch
>
> Thanks,
> Venkat
>
> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
> Sent: Wednesday, April 26, 2017 4:18 PM
> To: Therneau, Terry M., Ph.D.; R-help
> Cc: Seshan, Venkatraman E./Epidemiology-Biostatistics
> Subject: Re: [R] survival package can't find Ccoxfit6
>
> 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
>>>
>>
>>
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>
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> Please note that this e-mail and any files transmitted from
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