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
>>>>> 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)
Thanks Martin, that helped! G?ran On 2017-04-25 10:34, Martin Maechler wrote:>>>>>> 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) > >
On 2017-04-25 10:34, Martin Maechler wrote:>>>>>> 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)A small nuisance with this is that I end up with two versions of the survival package (and other recommended packages), since I cannot write to /usr/lib/R/library. However, this is obviously a problem suitable to present on R-SIG-Debian. See you there. G?ran> > 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) > >