>>>>> Göran Broström <goran.brost...@umu.se>
>>>>> on Tue, 25 Apr 2017 10:22:48 +0200 writes:
> I installed R-3.4.0 and got problems with the survival package, for
instance
> ------------
>> library(survival)
>> mort <- data.frame(exit = 1:4, event = rep(1, 4), x = c(0, 1, 0, 1))
>> fit <- coxph(Surv(exit, event) ~ x, data = mort)
> Error in fitter(X, Y, strats, offset, init, control, weights = weights, :
> object 'Ccoxmart' not found
> -------------
> No problems with R-3.3.3 and the same (latest) survival version, which
> makes me think that something is going on in my R installation rather
> than in the survival package.
> Thanks for any hint,
> Göran
>> sessionInfo()
> R version 3.4.0 (2017-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.2 LTS
> Matrix products: default
> BLAS: /usr/lib/openblas-base/libblas.so.3
> LAPACK: /usr/lib/libopenblasp-r0.2.18.so
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=sv_SE.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C
> 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_1.2-8 splines_3.4.0 grid_3.4.0
> [5] lattice_0.20-35
I'm 99.5% sure that you are using more than just the default
library of package (a very good thing - we have been doing the
same for years).
We have in NEWS for R 3.4.0
> PACKAGE INSTALLATION:
> [...........]
> [...........]
> • Packages which register native routines for .C or .Fortran need
> to be re-installed for this version (unless installed with
> R-devel SVN revision r72375 or later).
and Prof Brian Ripley did announce that nicely and early on R-devel.
==> https://hypatia.math.ethz.ch/pipermail/r-devel/2017-March/073940.html
==> You have to re-install quite a few packages for R 3.4.0,
__if__ they use .C() or .Fortran()
When we've e-talked about the issue within R-core,
Uwe Ligges noted we should really ask everyone to run
update.packages(checkBuilt=TRUE)
after an update to a new major (meaning "R-x.y.0") release of R
and **not** re-use packages {inside R-x.y.z}
that were installed with R-x.(y-1).z' ..
and of course Uwe is right:
We should ask others to do it _and_ do it ourselves.
Anyway it _is_ considerably more important for the 3.4.0
release.
Martin Maechler
ETH Zurich (and R Core team)
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