[R] R-3.4.0 and survival_2.41-3 ..
Göran Broström
goran.brostrom at umu.se
Tue Apr 25 10:59:42 CEST 2017
Thanks Martin,
that helped!
Göran
On 2017-04-25 10:34, Martin Maechler wrote:
>>>>>> Göran Broström <goran.brostrom at 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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