R-3.4.0 and survival_2.41-3 ..

G?ran Brostr?m <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,

    > G?ran

    >> 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)