* using log directory 'd:/Rcompile/CRANpkg/local/3.4/survival.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 'survival/DESCRIPTION' ... OK * this is package 'survival' version '2.44-1.1' * 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 'survival' can be installed ... OK * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: doc 3.2Mb * checking package directory ... OK * checking 'build' 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 ... [60s] 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 shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... [9s] OK ** running examples for arch 'x64' ... [10s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [177s] OK Running 'aareg.R' [2s] Comparing 'aareg.Rout' to 'aareg.Rout.save' ... OK Running 'anova.R' [1s] Comparing 'anova.Rout' to 'anova.Rout.save' ... OK Running 'bladder.R' [2s] Comparing 'bladder.Rout' to 'bladder.Rout.save' ... OK Running 'book1.R' [2s] Comparing 'book1.Rout' to 'book1.Rout.save' ... OK Running 'book2.R' [1s] Comparing 'book2.Rout' to 'book2.Rout.save' ... OK Running 'book3.R' [1s] Comparing 'book3.Rout' to 'book3.Rout.save' ... OK Running 'book4.R' [1s] Comparing 'book4.Rout' to 'book4.Rout.save' ... OK Running 'book5.R' [2s] Comparing 'book5.Rout' to 'book5.Rout.save' ... OK Running 'book6.R' [2s] Comparing 'book6.Rout' to 'book6.Rout.save' ... OK Running 'book7.R' [3s] Comparing 'book7.Rout' to 'book7.Rout.save' ... OK Running 'cancer.R' [2s] Comparing 'cancer.Rout' to 'cancer.Rout.save' ... OK Running 'clogit.R' [5s] Comparing 'clogit.Rout' to 'clogit.Rout.save' ... OK Running 'concordance.R' [3s] Comparing 'concordance.Rout' to 'concordance.Rout.save' ... OK Running 'concordance2.R' [12s] Comparing 'concordance2.Rout' to 'concordance2.Rout.save' ... OK Running 'concordance3.R' [2s] Comparing 'concordance3.Rout' to 'concordance3.Rout.save' ... OK Running 'counting.R' [2s] Comparing 'counting.Rout' to 'counting.Rout.save' ... OK Running 'coxsurv.R' [1s] Comparing 'coxsurv.Rout' to 'coxsurv.Rout.save' ... OK Running 'coxsurv2.R' [2s] Comparing 'coxsurv2.Rout' to 'coxsurv2.Rout.save' ... OK Running 'coxsurv3.R' [1s] Comparing 'coxsurv3.Rout' to 'coxsurv3.Rout.save' ... OK Running 'coxsurv4.R' [1s] Comparing 'coxsurv4.Rout' to 'coxsurv4.Rout.save' ... OK Running 'detail.R' [1s] Comparing 'detail.Rout' to 'detail.Rout.save' ... OK Running 'difftest.R' [2s] Comparing 'difftest.Rout' to 'difftest.Rout.save' ... OK Running 'doaml.R' [1s] Comparing 'doaml.Rout' to 'doaml.Rout.save' ... OK Running 'doweight.R' [2s] Comparing 'doweight.Rout' to 'doweight.Rout.save' ... OK Running 'expected.R' [2s] Comparing 'expected.Rout' to 'expected.Rout.save' ... OK Running 'expected2.R' [2s] Comparing 'expected2.Rout' to 'expected2.Rout.save' ... OK Running 'factor.R' [2s] Comparing 'factor.Rout' to 'factor.Rout.save' ... OK Running 'factor2.R' [2s] Comparing 'factor2.Rout' to 'factor2.Rout.save' ... OK Running 'finegray.R' [2s] Comparing 'finegray.Rout' to 'finegray.Rout.save' ... OK Running 'fr_cancer.R' [2s] Comparing 'fr_cancer.Rout' to 'fr_cancer.Rout.save' ... OK Running 'fr_kidney.R' [2s] Comparing 'fr_kidney.Rout' to 'fr_kidney.Rout.save' ... OK Running 'fr_lung.R' [2s] Comparing 'fr_lung.Rout' to 'fr_lung.Rout.save' ... OK Running 'fr_ovarian.R' [2s] Comparing 'fr_ovarian.Rout' to 'fr_ovarian.Rout.save' ... OK Running 'fr_rat1.R' [2s] Comparing 'fr_rat1.Rout' to 'fr_rat1.Rout.save' ... OK Running 'fr_rat2.R' [2s] Comparing 'fr_rat2.Rout' to 'fr_rat2.Rout.save' ... OK Running 'fr_resid.R' [2s] Comparing 'fr_resid.Rout' to 'fr_resid.Rout.save' ... OK Running 'fr_simple.R' [1s] Comparing 'fr_simple.Rout' to 'fr_simple.Rout.save' ... OK Running 'frailty.R' [2s] Comparing 'frailty.Rout' to 'frailty.Rout.save' ... OK Running 'frank.R' [1s] Comparing 'frank.Rout' to 'frank.Rout.save' ... OK Running 'infcox.R' [1s] Comparing 'infcox.Rout' to 'infcox.Rout.save' ... OK Running 'jasa.R' [2s] Comparing 'jasa.Rout' to 'jasa.Rout.save' ... OK Running 'model.matrix.R' [1s] Comparing 'model.matrix.Rout' to 'model.matrix.Rout.save' ... OK Running 'mstate.R' [2s] Comparing 'mstate.Rout' to 'mstate.Rout.save' ... OK Running 'nested.R' [2s] Comparing 'nested.Rout' to 'nested.Rout.save' ... OK Running 'ovarian.R' [2s] Comparing 'ovarian.Rout' to 'ovarian.Rout.save' ... OK Running 'prednew.R' [2s] Comparing 'prednew.Rout' to 'prednew.Rout.save' ... OK Running 'pspline.R' [2s] Comparing 'pspline.Rout' to 'pspline.Rout.save' ... OK Running 'pyear.R' [2s] Comparing 'pyear.Rout' to 'pyear.Rout.save' ... OK Running 'quantile.R' [2s] Comparing 'quantile.Rout' to 'quantile.Rout.save' ... OK Running 'r_donnell.R' [3s] Comparing 'r_donnell.Rout' to 'r_donnell.Rout.save' ... OK Running 'r_lung.R' [1s] Comparing 'r_lung.Rout' to 'r_lung.Rout.save' ... OK Running 'r_peterson.R' [1s] Comparing 'r_peterson.Rout' to 'r_peterson.Rout.save' ... OK Running 'r_resid.R' [2s] Comparing 'r_resid.Rout' to 'r_resid.Rout.save' ... OK Running 'r_sas.R' [6s] Comparing 'r_sas.Rout' to 'r_sas.Rout.save' ... OK Running 'r_scale.R' [2s] Comparing 'r_scale.Rout' to 'r_scale.Rout.save' ... OK Running 'r_stanford.R' [2s] Comparing 'r_stanford.Rout' to 'r_stanford.Rout.save' ... OK Running 'r_strata.R' [2s] Comparing 'r_strata.Rout' to 'r_strata.Rout.save' ... OK Running 'r_tdist.R' [2s] Comparing 'r_tdist.Rout' to 'r_tdist.Rout.save' ... OK Running 'r_user.R' [1s] Comparing 'r_user.Rout' to 'r_user.Rout.save' ... OK Running 'ratetable.R' [2s] Comparing 'ratetable.Rout' to 'ratetable.Rout.save' ... OK Running 'singtest.R' [1s] Comparing 'singtest.Rout' to 'singtest.Rout.save' ... OK Running 'strata2.R' [1s] Comparing 'strata2.Rout' to 'strata2.Rout.save' ... OK Running 'stratatest.R' [2s] Comparing 'stratatest.Rout' to 'stratatest.Rout.save' ... OK Running 'summary_survfit.R' [2s] Comparing 'summary_survfit.Rout' to 'summary_survfit.Rout.save' ... OK Running 'surv.R' [2s] Comparing 'surv.Rout' to 'surv.Rout.save' ...54c54 < [1] "Mean relative difference: 0.5882353" --- > [1] TRUE 56c56 < [1] "Mean relative difference: 0.5714286" --- > [1] TRUE 58,59c58 < [1] "Attributes: < Component \"dim\": Mean relative difference: 0.2857143 >" < [2] "Numeric: lengths (7, 5) differ" --- > [1] TRUE 63c62 < [1] "Mean relative difference: 0.6666667" --- > [1] TRUE 71,72c70 < [1] "Attributes: < Component \"dim\": Mean relative difference: 0.1666667 >" < [2] "Numeric: lengths (6, 5) differ" --- > [1] TRUE 74c72 < [1] "'is.NA' value mismatch: 1 in current 1 in target" --- > [1] TRUE Running 'survSplit.R' [1s] Comparing 'survSplit.Rout' to 'survSplit.Rout.save' ... OK Running 'survfit1.R' [2s] Comparing 'survfit1.Rout' to 'survfit1.Rout.save' ... OK Running 'survfit2.R' [1s] Comparing 'survfit2.Rout' to 'survfit2.Rout.save' ... OK Running 'survreg1.R' [1s] Running 'survreg2.R' [2s] Comparing 'survreg2.Rout' to 'survreg2.Rout.save' ... OK Running 'survtest.R' [1s] Comparing 'survtest.Rout' to 'survtest.Rout.save' ... OK Running 'testci.R' [2s] Comparing 'testci.Rout' to 'testci.Rout.save' ... OK Running 'testci2.R' [1s] Comparing 'testci2.Rout' to 'testci2.Rout.save' ... OK Running 'testnull.R' [2s] Comparing 'testnull.Rout' to 'testnull.Rout.save' ... OK Running 'testreg.R' [2s] Comparing 'testreg.Rout' to 'testreg.Rout.save' ... OK Running 'tiedtime.R' [2s] Comparing 'tiedtime.Rout' to 'tiedtime.Rout.save' ... OK Running 'tmerge.R' [2s] Comparing 'tmerge.Rout' to 'tmerge.Rout.save' ... OK Running 'tmerge2.R' [2s] Comparing 'tmerge2.Rout' to 'tmerge2.Rout.save' ... OK Running 'tmerge3.R' [2s] Comparing 'tmerge3.Rout' to 'tmerge3.Rout.save' ... OK Running 'tt.R' [12s] Comparing 'tt.Rout' to 'tt.Rout.save' ... OK Running 'turnbull.R' [2s] Comparing 'turnbull.Rout' to 'turnbull.Rout.save' ... OK Running 'yates0.R' [0s] Comparing 'yates0.Rout' to 'yates0.Rout.save' ... OK Running 'yates1.R' [2s] Comparing 'yates1.Rout' to 'yates1.Rout.save' ... OK Running 'yates2.R' [2s] ** running tests for arch 'x64' ... [210s] OK Running 'aareg.R' [4s] Comparing 'aareg.Rout' to 'aareg.Rout.save' ... OK Running 'anova.R' [2s] Comparing 'anova.Rout' to 'anova.Rout.save' ... OK Running 'bladder.R' [2s] Comparing 'bladder.Rout' to 'bladder.Rout.save' ... OK Running 'book1.R' [2s] Comparing 'book1.Rout' to 'book1.Rout.save' ... OK Running 'book2.R' [2s] Comparing 'book2.Rout' to 'book2.Rout.save' ... OK Running 'book3.R' [2s] Comparing 'book3.Rout' to 'book3.Rout.save' ... OK Running 'book4.R' [2s] Comparing 'book4.Rout' to 'book4.Rout.save' ... OK Running 'book5.R' [2s] Comparing 'book5.Rout' to 'book5.Rout.save' ... OK Running 'book6.R' [2s] Comparing 'book6.Rout' to 'book6.Rout.save' ... OK Running 'book7.R' [2s] Comparing 'book7.Rout' to 'book7.Rout.save' ... OK Running 'cancer.R' [2s] Comparing 'cancer.Rout' to 'cancer.Rout.save' ... OK Running 'clogit.R' [5s] Comparing 'clogit.Rout' to 'clogit.Rout.save' ... OK Running 'concordance.R' [4s] Comparing 'concordance.Rout' to 'concordance.Rout.save' ... OK Running 'concordance2.R' [16s] Comparing 'concordance2.Rout' to 'concordance2.Rout.save' ... OK Running 'concordance3.R' [2s] Comparing 'concordance3.Rout' to 'concordance3.Rout.save' ... OK Running 'counting.R' [2s] Comparing 'counting.Rout' to 'counting.Rout.save' ... OK Running 'coxsurv.R' [2s] Comparing 'coxsurv.Rout' to 'coxsurv.Rout.save' ... OK Running 'coxsurv2.R' [2s] Comparing 'coxsurv2.Rout' to 'coxsurv2.Rout.save' ... OK Running 'coxsurv3.R' [2s] Comparing 'coxsurv3.Rout' to 'coxsurv3.Rout.save' ... OK Running 'coxsurv4.R' [2s] Comparing 'coxsurv4.Rout' to 'coxsurv4.Rout.save' ... OK Running 'detail.R' [2s] Comparing 'detail.Rout' to 'detail.Rout.save' ... OK Running 'difftest.R' [2s] Comparing 'difftest.Rout' to 'difftest.Rout.save' ... OK Running 'doaml.R' [2s] Comparing 'doaml.Rout' to 'doaml.Rout.save' ... OK Running 'doweight.R' [2s] Comparing 'doweight.Rout' to 'doweight.Rout.save' ... OK Running 'expected.R' [2s] Comparing 'expected.Rout' to 'expected.Rout.save' ... OK Running 'expected2.R' [2s] Comparing 'expected2.Rout' to 'expected2.Rout.save' ... OK Running 'factor.R' [2s] Comparing 'factor.Rout' to 'factor.Rout.save' ... OK Running 'factor2.R' [2s] Comparing 'factor2.Rout' to 'factor2.Rout.save' ... OK Running 'finegray.R' [2s] Comparing 'finegray.Rout' to 'finegray.Rout.save' ... OK Running 'fr_cancer.R' [2s] Comparing 'fr_cancer.Rout' to 'fr_cancer.Rout.save' ... OK Running 'fr_kidney.R' [2s] Comparing 'fr_kidney.Rout' to 'fr_kidney.Rout.save' ... OK Running 'fr_lung.R' [2s] Comparing 'fr_lung.Rout' to 'fr_lung.Rout.save' ... OK Running 'fr_ovarian.R' [2s] Comparing 'fr_ovarian.Rout' to 'fr_ovarian.Rout.save' ... OK Running 'fr_rat1.R' [1s] Comparing 'fr_rat1.Rout' to 'fr_rat1.Rout.save' ... OK Running 'fr_rat2.R' [2s] Comparing 'fr_rat2.Rout' to 'fr_rat2.Rout.save' ... OK Running 'fr_resid.R' [2s] Comparing 'fr_resid.Rout' to 'fr_resid.Rout.save' ... OK Running 'fr_simple.R' [2s] Comparing 'fr_simple.Rout' to 'fr_simple.Rout.save' ... OK Running 'frailty.R' [2s] Comparing 'frailty.Rout' to 'frailty.Rout.save' ... OK Running 'frank.R' [2s] Comparing 'frank.Rout' to 'frank.Rout.save' ... OK Running 'infcox.R' [3s] Comparing 'infcox.Rout' to 'infcox.Rout.save' ... OK Running 'jasa.R' [2s] Comparing 'jasa.Rout' to 'jasa.Rout.save' ... OK Running 'model.matrix.R' [2s] Comparing 'model.matrix.Rout' to 'model.matrix.Rout.save' ... OK Running 'mstate.R' [2s] Comparing 'mstate.Rout' to 'mstate.Rout.save' ... OK Running 'nested.R' [2s] Comparing 'nested.Rout' to 'nested.Rout.save' ... OK Running 'ovarian.R' [2s] Comparing 'ovarian.Rout' to 'ovarian.Rout.save' ... OK Running 'prednew.R' [2s] Comparing 'prednew.Rout' to 'prednew.Rout.save' ... OK Running 'pspline.R' [2s] Comparing 'pspline.Rout' to 'pspline.Rout.save' ... OK Running 'pyear.R' [2s] Comparing 'pyear.Rout' to 'pyear.Rout.save' ... OK Running 'quantile.R' [2s] Comparing 'quantile.Rout' to 'quantile.Rout.save' ... OK Running 'r_donnell.R' [3s] Comparing 'r_donnell.Rout' to 'r_donnell.Rout.save' ... OK Running 'r_lung.R' [3s] Comparing 'r_lung.Rout' to 'r_lung.Rout.save' ... OK Running 'r_peterson.R' [2s] Comparing 'r_peterson.Rout' to 'r_peterson.Rout.save' ... OK Running 'r_resid.R' [2s] Comparing 'r_resid.Rout' to 'r_resid.Rout.save' ... OK Running 'r_sas.R' [8s] Comparing 'r_sas.Rout' to 'r_sas.Rout.save' ... OK Running 'r_scale.R' [2s] Comparing 'r_scale.Rout' to 'r_scale.Rout.save' ... OK Running 'r_stanford.R' [2s] Comparing 'r_stanford.Rout' to 'r_stanford.Rout.save' ... OK Running 'r_strata.R' [2s] Comparing 'r_strata.Rout' to 'r_strata.Rout.save' ... OK Running 'r_tdist.R' [2s] Comparing 'r_tdist.Rout' to 'r_tdist.Rout.save' ... OK Running 'r_user.R' [2s] Comparing 'r_user.Rout' to 'r_user.Rout.save' ... OK Running 'ratetable.R' [2s] Comparing 'ratetable.Rout' to 'ratetable.Rout.save' ... OK Running 'singtest.R' [2s] Comparing 'singtest.Rout' to 'singtest.Rout.save' ... OK Running 'strata2.R' [2s] Comparing 'strata2.Rout' to 'strata2.Rout.save' ... OK Running 'stratatest.R' [2s] Comparing 'stratatest.Rout' to 'stratatest.Rout.save' ... OK Running 'summary_survfit.R' [2s] Comparing 'summary_survfit.Rout' to 'summary_survfit.Rout.save' ... OK Running 'surv.R' [2s] Comparing 'surv.Rout' to 'surv.Rout.save' ...54c54 < [1] "Mean relative difference: 0.5882353" --- > [1] TRUE 56c56 < [1] "Mean relative difference: 0.5714286" --- > [1] TRUE 58,59c58 < [1] "Attributes: < Component \"dim\": Mean relative difference: 0.2857143 >" < [2] "Numeric: lengths (7, 5) differ" --- > [1] TRUE 63c62 < [1] "Mean relative difference: 0.6666667" --- > [1] TRUE 71,72c70 < [1] "Attributes: < Component \"dim\": Mean relative difference: 0.1666667 >" < [2] "Numeric: lengths (6, 5) differ" --- > [1] TRUE 74c72 < [1] "'is.NA' value mismatch: 1 in current 1 in target" --- > [1] TRUE Running 'survSplit.R' [2s] Comparing 'survSplit.Rout' to 'survSplit.Rout.save' ... OK Running 'survfit1.R' [2s] Comparing 'survfit1.Rout' to 'survfit1.Rout.save' ... OK Running 'survfit2.R' [2s] Comparing 'survfit2.Rout' to 'survfit2.Rout.save' ... OK Running 'survreg1.R' [2s] Running 'survreg2.R' [3s] Comparing 'survreg2.Rout' to 'survreg2.Rout.save' ... OK Running 'survtest.R' [2s] Comparing 'survtest.Rout' to 'survtest.Rout.save' ... OK Running 'testci.R' [2s] Comparing 'testci.Rout' to 'testci.Rout.save' ... OK Running 'testci2.R' [2s] Comparing 'testci2.Rout' to 'testci2.Rout.save' ... OK Running 'testnull.R' [2s] Comparing 'testnull.Rout' to 'testnull.Rout.save' ... OK Running 'testreg.R' [2s] Comparing 'testreg.Rout' to 'testreg.Rout.save' ... OK Running 'tiedtime.R' [2s] Comparing 'tiedtime.Rout' to 'tiedtime.Rout.save' ... OK Running 'tmerge.R' [2s] Comparing 'tmerge.Rout' to 'tmerge.Rout.save' ... OK Running 'tmerge2.R' [2s] Comparing 'tmerge2.Rout' to 'tmerge2.Rout.save' ... OK Running 'tmerge3.R' [1s] Comparing 'tmerge3.Rout' to 'tmerge3.Rout.save' ... OK Running 'tt.R' [16s] Comparing 'tt.Rout' to 'tt.Rout.save' ... OK Running 'turnbull.R' [2s] Comparing 'turnbull.Rout' to 'turnbull.Rout.save' ... OK Running 'yates0.R' [0s] Comparing 'yates0.Rout' to 'yates0.Rout.save' ... OK Running 'yates1.R' [2s] Comparing 'yates1.Rout' to 'yates1.Rout.save' ... OK Running 'yates2.R' [2s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [107s] OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE