* using log directory 'd:/Rcompile/CRANpkg/local/2.14/coxme.Rcheck' * using R version 2.14.2 (2012-02-29) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'coxme/DESCRIPTION' ... OK * this is package 'coxme' version '2.2-3' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking whether package 'coxme' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in tests ... OK * checking tests ... ** running tests for arch 'i386' OK Running 'bdstest.R' Comparing 'bdstest.Rout' to 'bdstest.Rout.save' ...14,22d13 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'lmekin1.R' Comparing 'lmekin1.Rout' to 'lmekin1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'lmekin2.R' Comparing 'lmekin2.Rout' to 'lmekin2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'nest1.R' Comparing 'nest1.Rout' to 'nest1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'nest2.R' Comparing 'nest2.Rout' to 'nest2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine.R' Comparing 'refine.Rout' to 'refine.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine1.R' Comparing 'refine1.Rout' to 'refine1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine2.R' Comparing 'refine2.Rout' to 'refine2.Rout.save' ...16,24d15 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine3.R' Comparing 'refine3.Rout' to 'refine3.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'shrink.R' Comparing 'shrink.Rout' to 'shrink.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope1.R' Comparing 'slope1.Rout' to 'slope1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope2.R' Comparing 'slope2.Rout' to 'slope2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' 106c97 < [1] "Mean relative difference: 1.95117e-08" --- > [1] TRUE Running 'slope3.R' Comparing 'slope3.Rout' to 'slope3.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope4.R' Comparing 'slope4.Rout' to 'slope4.Rout.save' ...30,38d29 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'strata1.R' Comparing 'strata1.Rout' to 'strata1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test0.R' Comparing 'test0.Rout' to 'test0.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test1.R' Comparing 'test1.Rout' to 'test1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test2.R' Comparing 'test2.Rout' to 'test2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test3.R' Comparing 'test3.Rout' to 'test3.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test4.R' Comparing 'test4.Rout' to 'test4.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'twoterm.R' Comparing 'twoterm.Rout' to 'twoterm.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' ** running tests for arch 'x64' OK Running 'bdstest.R' Comparing 'bdstest.Rout' to 'bdstest.Rout.save' ...14,22d13 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'lmekin1.R' Comparing 'lmekin1.Rout' to 'lmekin1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'lmekin2.R' Comparing 'lmekin2.Rout' to 'lmekin2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'nest1.R' Comparing 'nest1.Rout' to 'nest1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'nest2.R' Comparing 'nest2.Rout' to 'nest2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine.R' Comparing 'refine.Rout' to 'refine.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine1.R' Comparing 'refine1.Rout' to 'refine1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine2.R' Comparing 'refine2.Rout' to 'refine2.Rout.save' ...16,24d15 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'refine3.R' Comparing 'refine3.Rout' to 'refine3.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'shrink.R' Comparing 'shrink.Rout' to 'shrink.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope1.R' Comparing 'slope1.Rout' to 'slope1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope2.R' Comparing 'slope2.Rout' to 'slope2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope3.R' Comparing 'slope3.Rout' to 'slope3.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'slope4.R' Comparing 'slope4.Rout' to 'slope4.Rout.save' ...30,38d29 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'strata1.R' Comparing 'strata1.Rout' to 'strata1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test0.R' Comparing 'test0.Rout' to 'test0.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test1.R' Comparing 'test1.Rout' to 'test1.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test2.R' Comparing 'test2.Rout' to 'test2.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test3.R' Comparing 'test3.Rout' to 'test3.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'test4.R' Comparing 'test4.Rout' to 'test4.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' Running 'twoterm.R' Comparing 'twoterm.Rout' to 'twoterm.Rout.save' ...11,19d10 < < Attaching package: 'Matrix' < < The following object(s) are masked from 'package:base': < < det < < Warning message: < replacing previous import 'diag' when loading 'Matrix' 96c87 < [1] TRUE --- > [1] "Component 2: Mean relative difference: 2.069803e-08" * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... OK * checking re-building of vignette PDFs ... OK * checking PDF version of manual ... OK