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.
Thanks,
Venkat
-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.dun...@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: sesh...@mskcc.org
To: Therneau, Terry M., Ph.D. <thern...@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:thern...@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, sesh...@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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