[R] R-3.4.0 and survival_2.41-3 ..

[Viechtbauer Wolfgang (SP)]

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-bounces at r-project.org] On Behalf Of Göran
>Broström
>Sent: Tuesday, April 25, 2017 11:00
>To: Martin Maechler
>Cc: r-help at 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.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)