On 28/04/2017 5:37 PM, Henric Winell wrote:
On 2017-04-26 22:17, Duncan Murdoch wrote:
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.
I think it's worthwhile to point out that non-exported symbols are
available using ':::'. See WRE Section 5.4.
So, after fixing the argument list, just use '.Call(survival:::Ccoxfit6,
<args>)' instead of '.Call("Ccoxfit6", <args>, PACKAGE = "survival")'.
Yes, and in another section it says "Using foo:::f instead of foo::f
allows access to unexported objects. This is generally not recommended,
as the semantics of unexported objects may be changed by the package
author in routine maintenance."
Duncan Murdoch
Henric Winell
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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