Sort of an obvious approach, but after every upgrade (regardless if it is
major/minor), I just delete my entire personal library and reinstall everything
from scratch. For this, I have a script that includes just a bunch of
install.packages() calls. Like:
install.packages(c("lme4", "glmmML", "MCMCglmm"))
install.packages(c("psych", "GPArotation", "sem", "lavaan"))
[...]
I split things up a bit, based on the purpose/topic (along the lines of
http://www.wvbauer.com/doku.php/rpackages) to keep things organized.
This may not be the most efficient method if you use hundreds of packages, but
works for me.
Best,
Wolfgang
--
Wolfgang Viechtbauer, Ph.D., Statistician | Department of Psychiatry and
Neuropsychology | Maastricht University | P.O. Box 616 (VIJV1) | 6200 MD
Maastricht, The Netherlands | +31 (43) 388-4170 | http://www.wvbauer.com
>-----Original Message-----
>From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Göran
>Broström
>Sent: Tuesday, April 25, 2017 11:00
>To: Martin Maechler
>Cc: r-help@r-project.org
>Subject: Re: [R] R-3.4.0 and survival_2.41-3 ..
>
>Thanks Martin,
>
>that helped!
>
>Göran
>
>On 2017-04-25 10:34, Martin Maechler wrote:
>>>>>>> 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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