* using log directory 'd:/Rcompile/CRANpkg/local/3.3/MASS.Rcheck' * using R version 3.3.3 (2017-03-06) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'MASS/DESCRIPTION' ... OK * this is package 'MASS' version '7.3-49' * 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 'MASS' 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 * 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 ** checking use of S3 registration ... 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 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 ... 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 compiled code ... OK * checking examples ... ** running examples for arch 'i386' ... [14s] OK ** checking differences from 'MASS-Ex_i386.Rout' to 'MASS-Ex.Rout.save' ... OK 582c582 < Likelihood ratio test=9.85 on 1 df, p=0.002 --- > Likelihood ratio test=9.85 on 1 df, p=0.0017 596c596 < Likelihood ratio test=15.45 on 4 df, p=0.004 --- > Likelihood ratio test=15.4 on 4 df, p=0.00385 607c607 < Likelihood ratio test=15.15 on 1 df, p=1e-04 --- > Likelihood ratio test=15.2 on 1 df, p=9.93e-05 870c870 < -2.42080777 -0.61510520 -0.03573836 0.81641138 2.15153497 --- > -2.42080780 -0.61510520 -0.03573836 0.81641138 2.15153499 1528c1528 < factor(subject)2 -2.890e-16 2.828e-01 0.000 1.000000 --- > factor(subject)2 -2.300e-15 2.828e-01 0.000 1.000000 1988c1988 < Chisq= 30.27 on 21 degrees of freedom, p= 0.0866 --- > Chisq= 30.27 on 21 degrees of freedom, p= 0.087 1995,1996c1995,1996 < (Intercept) 3.686 0.333 11.06 < 2e-16 < treatcontrol -1.527 0.398 -3.83 0.00013 --- > (Intercept) 3.69 0.333 11.06 2.00e-28 > treatcontrol -1.53 0.398 -3.83 1.27e-04 2011,2013c2011,2013 < (Intercept) 3.516 0.252 13.96 < 2e-16 < treatcontrol -1.267 0.311 -4.08 4.5e-05 < Log(scale) -0.312 0.147 -2.12 0.034 --- > (Intercept) 3.516 0.252 13.96 2.61e-44 > treatcontrol -1.267 0.311 -4.08 4.51e-05 > Log(scale) -0.312 0.147 -2.12 3.43e-02 2040,2042c2040,2042 < Likelihood ratio test= 16.35 on 1 df, p=5e-05 < Wald test = 14.53 on 1 df, p=1e-04 < Score (logrank) test = 17.25 on 1 df, p=3e-05 --- > Likelihood ratio test= 16.35 on 1 df, p=5.261e-05 > Wald test = 14.53 on 1 df, p=0.0001378 > Score (logrank) test = 17.25 on 1 df, p=3.283e-05 2378c2378 < ContHigh 1.271e-15 1.690e-01 0.000 1.000000 --- > ContHigh -1.490e-15 1.690e-01 0.000 1.000000 3025,3027c3025,3027 < Likelihood ratio test= 15.64 on 2 df, p=4e-04 < Wald test = 15.06 on 2 df, p=5e-04 < Score (logrank) test = 16.49 on 2 df, p=3e-04 --- > Likelihood ratio test= 15.64 on 2 df, p=0.0004014 > Wald test = 15.06 on 2 df, p=0.0005365 > Score (logrank) test = 16.49 on 2 df, p=0.0002629 3203c3203 < -3.631e+01 7.292e-01 4.167e-01 -1.647e-16 --- > -3.631e+01 7.292e-01 4.167e-01 -8.131e-17 3286,3288c3286,3288 < (Intercept) 16.31852 0.62296 26.2 < 2e-16 < temp -0.04531 0.00319 -14.2 < 2e-16 < Log(scale) -1.09564 0.21480 -5.1 3.4e-07 --- > (Intercept) 16.3185 0.62296 26.2 3.03e-151 > temp -0.0453 0.00319 -14.2 6.74e-46 > Log(scale) -1.0956 0.21480 -5.1 3.38e-07 3320,3322c3320,3322 < Likelihood ratio test= 25.56 on 1 df, p=4e-07 < Wald test = 11.27 on 1 df, p=8e-04 < Score (logrank) test = 22.73 on 1 df, p=2e-06 --- > Likelihood ratio test= 25.56 on 1 df, p=4.299e-07 > Wald test = 11.27 on 1 df, p=0.0007863 > Score (logrank) test = 22.73 on 1 df, p=1.862e-06 3366c3366 < 0.07776401 3.08304824 3.30137838 3.44562531 2.80464433 --- > 0.07776401 3.08304824 3.30137838 3.44562531 2.80464434 3368c3368 < 2.60835015 3.03357724 3.52301734 3.38711844 3.46709395 --- > 2.60835015 3.03357725 3.52301734 3.38711844 3.46709396 3370c3370 < 3.81438456 3.73878664 3.51332580 3.39741114 3.47088607 --- > 3.81438456 3.73878664 3.51332581 3.39741115 3.47088608 3372c3372 < 3.72895847 3.31863862 3.37938672 2.96452195 3.58468686 --- > 3.72895847 3.31863862 3.37938673 2.96452195 3.58468686 3374c3374 < 3.39628029 3.36998871 -2.96015461 --- > 3.39628029 3.36998872 -2.96015460 3397c3397 < Achieved convergence tolerance: 4.939e-06 --- > Achieved convergence tolerance: 4.923e-06 3533c3533 < (Intercept) 2.78706 (Intr) --- > (Intercept) 2.78707 (Intr) 5132c5132 < Achieved convergence tolerance: 4.354e-06 --- > Achieved convergence tolerance: 4.324e-06 Warning message: running command 'diff -bw "D:\temp\RtmpGSsrVd\Rdiffa1b8584ec52906" "D:\temp\RtmpGSsrVd\Rdiffb1b8584a9a3f40"' had status 1 ** running examples for arch 'x64' ... [15s] OK ** checking differences from 'MASS-Ex_x64.Rout' to 'MASS-Ex.Rout.save' ... OK 582c582 < Likelihood ratio test=9.85 on 1 df, p=0.002 --- > Likelihood ratio test=9.85 on 1 df, p=0.0017 596c596 < Likelihood ratio test=15.45 on 4 df, p=0.004 --- > Likelihood ratio test=15.4 on 4 df, p=0.00385 607c607 < Likelihood ratio test=15.15 on 1 df, p=1e-04 --- > Likelihood ratio test=15.2 on 1 df, p=9.93e-05 1988c1988 < Chisq= 30.27 on 21 degrees of freedom, p= 0.0866 --- > Chisq= 30.27 on 21 degrees of freedom, p= 0.087 1995,1996c1995,1996 < (Intercept) 3.686 0.333 11.06 < 2e-16 < treatcontrol -1.527 0.398 -3.83 0.00013 --- > (Intercept) 3.69 0.333 11.06 2.00e-28 > treatcontrol -1.53 0.398 -3.83 1.27e-04 2011,2013c2011,2013 < (Intercept) 3.516 0.252 13.96 < 2e-16 < treatcontrol -1.267 0.311 -4.08 4.5e-05 < Log(scale) -0.312 0.147 -2.12 0.034 --- > (Intercept) 3.516 0.252 13.96 2.61e-44 > treatcontrol -1.267 0.311 -4.08 4.51e-05 > Log(scale) -0.312 0.147 -2.12 3.43e-02 2040,2042c2040,2042 < Likelihood ratio test= 16.35 on 1 df, p=5e-05 < Wald test = 14.53 on 1 df, p=1e-04 < Score (logrank) test = 17.25 on 1 df, p=3e-05 --- > Likelihood ratio test= 16.35 on 1 df, p=5.261e-05 > Wald test = 14.53 on 1 df, p=0.0001378 > Score (logrank) test = 17.25 on 1 df, p=3.283e-05 3025,3027c3025,3027 < Likelihood ratio test= 15.64 on 2 df, p=4e-04 < Wald test = 15.06 on 2 df, p=5e-04 < Score (logrank) test = 16.49 on 2 df, p=3e-04 --- > Likelihood ratio test= 15.64 on 2 df, p=0.0004014 > Wald test = 15.06 on 2 df, p=0.0005365 > Score (logrank) test = 16.49 on 2 df, p=0.0002629 3286,3288c3286,3288 < (Intercept) 16.31852 0.62296 26.2 < 2e-16 < temp -0.04531 0.00319 -14.2 < 2e-16 < Log(scale) -1.09564 0.21480 -5.1 3.4e-07 --- > (Intercept) 16.3185 0.62296 26.2 3.03e-151 > temp -0.0453 0.00319 -14.2 6.74e-46 > Log(scale) -1.0956 0.21480 -5.1 3.38e-07 3320,3322c3320,3322 < Likelihood ratio test= 25.56 on 1 df, p=4e-07 < Wald test = 11.27 on 1 df, p=8e-04 < Score (logrank) test = 22.73 on 1 df, p=2e-06 --- > Likelihood ratio test= 25.56 on 1 df, p=4.299e-07 > Wald test = 11.27 on 1 df, p=0.0007863 > Score (logrank) test = 22.73 on 1 df, p=1.862e-06 Warning message: running command 'diff -bw "D:\temp\RtmpmcEEXF\Rdiffa93c010925a41" "D:\temp\RtmpmcEEXF\Rdiffb93c0709e7e61"' had status 1 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [7s] OK Running 'confint.R' [1s] Running 'fitdistr.R' [1s] Comparing 'fitdistr.Rout' to 'fitdistr.Rout.save' ... OK Running 'glm.nb.R' [1s] Running 'hubers.R' [0s] Running 'lme.R' [1s] Running 'polr.R' [1s] Running 'profile.R' [1s] Running 'regression.R' [1s] Comparing 'regression.Rout' to 'regression.Rout.save' ... OK Running 'rlm.R' [1s] Running 'scripts.R' [1s] ** running tests for arch 'x64' ... [9s] OK Running 'confint.R' [1s] Running 'fitdistr.R' [1s] Comparing 'fitdistr.Rout' to 'fitdistr.Rout.save' ... OK Running 'glm.nb.R' [1s] Running 'hubers.R' [1s] Running 'lme.R' [1s] Running 'polr.R' [1s] Running 'profile.R' [1s] Running 'regression.R' [1s] Comparing 'regression.Rout' to 'regression.Rout.save' ... OK Running 'rlm.R' [1s] Running 'scripts.R' [1s] * checking PDF version of manual ... OK * DONE Status: OK