I've finally narrowed down a puzzling problem: here is the short test case. tmt34% R --vanilla R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0> temp <- matrix(runif(50), ncol=2) > t(temp) %*% temp[,1] [,2] [1,] 7.916016 6.049698 [2,] 6.049698 7.650694> library(kinship)Loading required package: survival Loading required package: splines Loading required package: nlme Loading required package: lattice> t(temp) %*% temp`__Deferred_Default_Marker__` ----------------------------------------- Within the library is a definition of %*% for bdsmatrix objects, which is perhaps the issue. But I'm only guessing since I don't have a clear idea what the error message means. Any hints are appreciated. The new coxme/bsdmatrix packages need only a couple more functions to be a complete replacement for kinship, at which point we will depreciate it. (Pedigrees and plotting were finished last weekend!) But I can't quite do that yet. The error does not arise with these newer libraries. There have been no changes to kinship for some time. Terry Therneau> sessionInfo()R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] kinship_1.1.0-11 lattice_0.17-26 nlme_3.1-96 survival_2.35-9 loaded via a namespace (and not attached): [1] grid_2.10.0>
Terry, I don't see the problem in R 2.11.0 or R 2.10.1 Patched (session info for R 2.10.1 below) with Windows (Vista). I do get warnings about kinship having been built under R 2.11.0 when I use R 2.10.1. But I notice that your version of kinship looks somewhat dated. Is that intentional? -Peter Ehlers > sessionInfo() R version 2.10.1 Patched (2010-01-05 r50896) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] kinship_1.1.0-23 lattice_0.18-3 nlme_3.1-96 survival_2.35-8 loaded via a namespace (and not attached): [1] grid_2.10.1 On 2010-04-23 9:20, Terry Therneau wrote:> I've finally narrowed down a puzzling problem: here is the short test > case. > > tmt34% R --vanilla > > R version 2.10.0 (2009-10-26) > Copyright (C) 2009 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > >> temp<- matrix(runif(50), ncol=2) >> t(temp) %*% temp > [,1] [,2] > [1,] 7.916016 6.049698 > [2,] 6.049698 7.650694 > >> library(kinship) > Loading required package: survival > Loading required package: splines > Loading required package: nlme > Loading required package: lattice >> t(temp) %*% temp > `__Deferred_Default_Marker__` > > ----------------------------------------- > > Within the library is a definition of %*% for bdsmatrix objects, which > is perhaps the issue. But I'm only guessing since I don't have a clear > idea what the error message means. Any hints are appreciated. > > The new coxme/bsdmatrix packages need only a couple more functions to be > a complete replacement for kinship, at which point we will depreciate > it. (Pedigrees and plotting were finished last weekend!) But I can't > quite do that yet. The error does not arise with these newer libraries. > There have been no changes to kinship for some time. > > Terry Therneau > > >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] splines stats graphics grDevices utils datasets > methods > [8] base > other attached packages: > [1] kinship_1.1.0-11 lattice_0.17-26 nlme_3.1-96 survival_2.35-9 > > loaded via a namespace (and not attached): > [1] grid_2.10.0 >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >-- Peter Ehlers University of Calgary
Hi Terry, Not aware about the issue, e.g., from $ uname -a Linux c06.mrc-epid.private.cam.ac.uk 2.6.9-89.0.23.ELsmp #1 SMP Fri Mar 5 23:27:13 EST 2010 x86_64 x86_64 x86_64 GNU/Linux I got> library(kinship)Loading required package: survival Loading required package: splines Loading required package: nlme Loading required package: lattice [1] "kinship is loaded"> temp <- matrix(runif(50), ncol=2) > temp <- matrix(runif(50), ncol=2) > t(temp) %*% temp[,1] [,2] [1,] 8.327462 6.531409 [2,] 6.531409 9.129242> t(temp) %*% temp[,1] [,2] [1,] 8.327462 6.531409 [2,] 6.531409 9.129242> version_ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 11.0 year 2010 month 04 day 22 svn rev 51801 language R version.string R version 2.11.0 (2010-04-22) or $ /genetics/data/software/R-2.11.0/bin/R --vanilla R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.> temp <- matrix(runif(50), ncol=2) > t(temp) %*% temp[,1] [,2] [1,] 9.379705 7.471682 [2,] 7.471682 9.046881> library(kinship)Loading required package: survival Loading required package: splines Loading required package: nlme Loading required package: lattice [1] "kinship is loaded"> t(temp) %*% temp[,1] [,2] [1,] 9.379705 7.471682 [2,] 7.471682 9.046881 I look forward to the availability of a complete replacement of bdsmatrix/coxme/pedigree packages. There have been simple yet sticky issues such as allowing for unknown status in the affection status which would benefit from an overhaul implementation than revising the present one. Jing Hua> From: therneau@mayo.edu > To: r-devel@r-project.org > Date: Fri, 23 Apr 2010 10:20:39 -0500 > Subject: [Rd] Deferred Default Marker > > I've finally narrowed down a puzzling problem: here is the short test > case. > > tmt34% R --vanilla > > R version 2.10.0 (2009-10-26) > Copyright (C) 2009 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > > temp <- matrix(runif(50), ncol=2) > > t(temp) %*% temp > [,1] [,2] > [1,] 7.916016 6.049698 > [2,] 6.049698 7.650694 > > > library(kinship) > Loading required package: survival > Loading required package: splines > Loading required package: nlme > Loading required package: lattice > > t(temp) %*% temp > `__Deferred_Default_Marker__` > > ----------------------------------------- > > Within the library is a definition of %*% for bdsmatrix objects, which > is perhaps the issue. But I'm only guessing since I don't have a clear > idea what the error message means. Any hints are appreciated. > > The new coxme/bsdmatrix packages need only a couple more functions to be > a complete replacement for kinship, at which point we will depreciate > it. (Pedigrees and plotting were finished last weekend!) But I can't > quite do that yet. The error does not arise with these newer libraries. > There have been no changes to kinship for some time. > > Terry Therneau > > > > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] splines stats graphics grDevices utils datasets > methods > [8] base > other attached packages: > [1] kinship_1.1.0-11 lattice_0.17-26 nlme_3.1-96 survival_2.35-9 > > loaded via a namespace (and not attached): > [1] grid_2.10.0 > > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel_________________________________________________________________ Do you have a story that started on Hotmail? Tell us now [[alternative HTML version deleted]]