* using log directory 'd:/Rcompile/CRANpkg/local/3.4/ISwR.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'ISwR/DESCRIPTION' ... OK * this is package 'ISwR' version '2.0-7' * 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 for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'ISwR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over 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 * 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 loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking 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 ... [2s] 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 examples ... [2s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [12s] OK Running 'allexercises.R' [6s] Comparing 'allexercises.Rout' to 'allexercises.Rout.save' ...724c724 < 60-64:4 Hist.ctr. :6 Median :104.0 Median : 169261 --- > 60-64:4 Hist.ctr. :6 Median :104.0 Median : 169260 1896c1896 < Chisq= 6.6 on 1 degrees of freedom, p= 0.01 --- > Chisq= 6.6 on 1 degrees of freedom, p= 0.0105 1911,1914c1911,1915 < Concordance= 0.671 (se = 0.052 ) < Likelihood ratio test= 6.19 on 1 df, p=0.01 < Wald test = 5.83 on 1 df, p=0.02 < Score (logrank) test = 6.55 on 1 df, p=0.01 --- > Concordance= 0.671 (se = 0.061 ) > Rsquare= 0.154 (max possible= 0.957 ) > Likelihood ratio test= 6.19 on 1 df, p=0.01286 > Wald test = 5.83 on 1 df, p=0.01577 > Score (logrank) test = 6.55 on 1 df, p=0.01046 1940,1943c1941,1945 < Concordance= 0.748 (se = 0.065 ) < Likelihood ratio test= 14.33 on 5 df, p=0.01 < Wald test = 14.86 on 5 df, p=0.01 < Score (logrank) test = 17.48 on 5 df, p=0.004 --- > Concordance= 0.748 (se = 0.074 ) > Rsquare= 0.321 (max possible= 0.957 ) > Likelihood ratio test= 14.33 on 5 df, p=0.01367 > Wald test = 14.86 on 5 df, p=0.01097 > Score (logrank) test = 17.48 on 5 df, p=0.003679 1967,1970c1969,1973 < Concordance= 0.66 (se = 0.013 ) < Likelihood ratio test= 158.6 on 2 df, p=<2e-16 < Wald test = 137.7 on 2 df, p=<2e-16 < Score (logrank) test = 136.3 on 2 df, p=<2e-16 --- > Concordance= 0.66 (se = 0.014 ) > Rsquare= 0.174 (max possible= 0.999 ) > Likelihood ratio test= 158.6 on 2 df, p=0 > Wald test = 137.7 on 2 df, p=0 > Score (logrank) test = 136.3 on 2 df, p=0 1986,1989c1989,1993 < Concordance= 0.547 (se = 0.011 ) < Likelihood ratio test= 14.97 on 1 df, p=1e-04 < Wald test = 14.47 on 1 df, p=1e-04 < Score (logrank) test = 14.63 on 1 df, p=1e-04 --- > Concordance= 0.547 (se = 0.012 ) > Rsquare= 0.018 (max possible= 0.999 ) > Likelihood ratio test= 14.97 on 1 df, p=0.0001091 > Wald test = 14.47 on 1 df, p=0.0001428 > Score (logrank) test = 14.63 on 1 df, p=0.0001311 2017,2020c2021,2025 < Concordance= 0.66 (se = 0.013 ) < Likelihood ratio test= 158.6 on 2 df, p=<2e-16 < Wald test = 137.7 on 2 df, p=<2e-16 < Score (logrank) test = 136.3 on 2 df, p=<2e-16 --- > Concordance= 0.66 (se = 0.014 ) > Rsquare= 0.063 (max possible= 0.918 ) > Likelihood ratio test= 158.6 on 2 df, p=0 > Wald test = 137.7 on 2 df, p=0 > Score (logrank) test = 136.3 on 2 df, p=0 2159c2164 < alpha 180.77123 1.93392 93.474 < 2e-16 *** --- > alpha 180.77131 1.93393 93.474 < 2e-16 *** 2162c2167 < da 62.03692 11.26004 5.509 4.46e-08 *** --- > da 62.03691 11.26006 5.509 4.46e-08 *** 2171c2176 < Achieved convergence tolerance: 1.743e-06 --- > Achieved convergence tolerance: 2.021e-06 Running 'allscripts.R' [5s] Comparing 'allscripts.Rout' to 'allscripts.Rout.save' ...486c486 < [1] 192 --- > [1] 186 518c518 < [1] "D:/temp/RtmpALaFcL/RLIBS_ebd81c107af2/ISwR/rawdata/thuesen.txt" --- > [1] "/Users/pd/BIOSTAT/books/ISWR-2nd-ed/ISwR.Rcheck/ISwR/rawdata/thuesen.txt" 3619,3620c3619,3620 < n events median 0.95LCL 0.95UCL < 205 57 NA NA NA --- > records n.max n.start events median 0.95LCL 0.95UCL > 205 205 205 57 NA NA NA 3697c3697 < Chisq= 6.5 on 1 degrees of freedom, p= 0.01 --- > Chisq= 6.5 on 1 degrees of freedom, p= 0.011 3706c3706 < Chisq= 3.3 on 1 degrees of freedom, p= 0.07 --- > Chisq= 3.3 on 1 degrees of freedom, p= 0.0687 3721,3724c3721,3725 < Concordance= 0.59 (se = 0.034 ) < Likelihood ratio test= 6.15 on 1 df, p=0.01 < Wald test = 6.24 on 1 df, p=0.01 < Score (logrank) test = 6.47 on 1 df, p=0.01 --- > Concordance= 0.59 (se = 0.033 ) > Rsquare= 0.03 (max possible= 0.937 ) > Likelihood ratio test= 6.15 on 1 df, p=0.01314 > Wald test = 6.24 on 1 df, p=0.01251 > Score (logrank) test = 6.47 on 1 df, p=0.01098 3743,3746c3744,3748 < Concordance= 0.673 (se = 0.039 ) < Likelihood ratio test= 13.3 on 2 df, p=0.001 < Wald test = 12.88 on 2 df, p=0.002 < Score (logrank) test = 12.98 on 2 df, p=0.002 --- > Concordance= 0.673 (se = 0.058 ) > Rsquare= 0.063 (max possible= 0.9 ) > Likelihood ratio test= 13.3 on 2 df, p=0.001296 > Wald test = 12.88 on 2 df, p=0.001598 > Score (logrank) test = 12.98 on 2 df, p=0.00152 4175c4177 < Achieved convergence tolerance: 7.238e-09 --- > Achieved convergence tolerance: 1.582e-08 4212c4214 < Achieved convergence tolerance: 5.256e-06 --- > Achieved convergence tolerance: 5.243e-06 4228c4230 < alpha 255.97694 15.03920 17.021 <2e-16 *** --- > alpha 255.97696 15.03921 17.021 <2e-16 *** 4237c4239 < Achieved convergence tolerance: 2.764e-06 --- > Achieved convergence tolerance: 2.681e-06 4282c4284 < Achieved convergence tolerance: 5.543e-06 --- > Achieved convergence tolerance: 5.506e-06 4291c4293 < alpha 233.5007561 294.76267623 --- > alpha 233.5007560 294.76267652 4296,4298c4298,4300 < alpha 226.50064250 285.45323176 < beta 1.13125577 1.24772847 < gamma 0.05443819 0.08622691 --- > alpha 226.50065351 285.4532669 > beta 1.13125577 1.2477285 > gamma 0.05443818 0.0862269 * checking PDF version of manual ... OK * DONE Status: OK