* using log directory ‘/srv/hornik/tmp/CRAN/survival.Rcheck’
* using R Under development (unstable) (2024-04-20 r86457)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘survival/DESCRIPTION’ ... OK
* this is package ‘survival’ version ‘3.6-3’
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Terry M Therneau <therneau.terry@mayo.edu>’

Size of tarball: 8058339 bytes
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘survival’ can be installed ... [30s/30s] OK
* used C compiler: ‘Debian clang version 17.0.6 (5)’
* checking package directory ... OK
* checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] 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 ... [36s/36s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'residuals.survfit.Rd':
residuals.survfit
  Code: function(object, times, type = "pstate", collapse = FALSE,
                 weighted = collapse, data.frame = FALSE, extra =
                 FALSE, ...)
  Docs: function(object, times, type = "pstate", collapse = FALSE,
                 weighted = collapse, data.frame = FALSE, ...)
  Argument names in code not in docs:
    extra
  Mismatches in argument names:
    Position: 7 Code: extra Docs: ...

* 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 ... [0s/0s] OK
* checking LazyData ... 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 GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... 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 ... [11s/11s] OK
* checking differences from ‘survival-Ex.Rout’ to ‘survival-Ex.Rout.save’ ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [104s/103s] OK
  Running ‘aareg.R’ [1s/1s]
  Comparing ‘aareg.Rout’ to ‘aareg.Rout.save’ ... OK
  Running ‘anova.R’ [1s/1s]
  Comparing ‘anova.Rout’ to ‘anova.Rout.save’ ... OK
  Running ‘bladder.R’ [1s/1s]
  Comparing ‘bladder.Rout’ to ‘bladder.Rout.save’ ... OK
  Running ‘book1.R’ [1s/1s]
  Comparing ‘book1.Rout’ to ‘book1.Rout.save’ ... OK
  Running ‘book2.R’ [1s/1s]
  Comparing ‘book2.Rout’ to ‘book2.Rout.save’ ... OK
  Running ‘book3.R’ [1s/1s]
  Comparing ‘book3.Rout’ to ‘book3.Rout.save’ ... OK
  Running ‘book4.R’ [1s/1s]
  Comparing ‘book4.Rout’ to ‘book4.Rout.save’ ... OK
  Running ‘book5.R’ [1s/1s]
  Comparing ‘book5.Rout’ to ‘book5.Rout.save’ ... OK
  Running ‘book6.R’ [1s/1s]
  Comparing ‘book6.Rout’ to ‘book6.Rout.save’ ... OK
  Running ‘book7.R’ [1s/1s]
  Comparing ‘book7.Rout’ to ‘book7.Rout.save’ ... OK
  Running ‘brier.R’ [6s/6s]
  Comparing ‘brier.Rout’ to ‘brier.Rout.save’ ... OK
  Running ‘cancer.R’ [1s/1s]
  Comparing ‘cancer.Rout’ to ‘cancer.Rout.save’ ... OK
  Running ‘checkSurv2.R’ [1s/1s]
  Comparing ‘checkSurv2.Rout’ to ‘checkSurv2.Rout.save’ ... OK
  Running ‘clogit.R’ [1s/1s]
  Comparing ‘clogit.Rout’ to ‘clogit.Rout.save’ ... OK
  Running ‘concordance.R’ [1s/1s]
  Comparing ‘concordance.Rout’ to ‘concordance.Rout.save’ ... OK
  Running ‘concordance2.R’ [3s/3s]
  Comparing ‘concordance2.Rout’ to ‘concordance2.Rout.save’ ... OK
  Running ‘concordance3.R’ [1s/1s]
  Comparing ‘concordance3.Rout’ to ‘concordance3.Rout.save’ ... OK
  Running ‘counting.R’ [1s/1s]
  Comparing ‘counting.Rout’ to ‘counting.Rout.save’ ... OK
  Running ‘coxsurv.R’ [1s/1s]
  Comparing ‘coxsurv.Rout’ to ‘coxsurv.Rout.save’ ... OK
  Running ‘coxsurv2.R’ [1s/1s]
  Comparing ‘coxsurv2.Rout’ to ‘coxsurv2.Rout.save’ ... OK
  Running ‘coxsurv3.R’ [1s/1s]
  Comparing ‘coxsurv3.Rout’ to ‘coxsurv3.Rout.save’ ... OK
  Running ‘coxsurv4.R’ [1s/1s]
  Comparing ‘coxsurv4.Rout’ to ‘coxsurv4.Rout.save’ ... OK
  Running ‘coxsurv5.R’ [1s/1s]
  Comparing ‘coxsurv5.Rout’ to ‘coxsurv5.Rout.save’ ... OK
  Running ‘coxsurv6.R’ [1s/1s]
  Comparing ‘coxsurv6.Rout’ to ‘coxsurv6.Rout.save’ ... OK
  Running ‘detail.R’ [1s/1s]
  Comparing ‘detail.Rout’ to ‘detail.Rout.save’ ... OK
  Running ‘difftest.R’ [1s/1s]
  Comparing ‘difftest.Rout’ to ‘difftest.Rout.save’ ... OK
  Running ‘doaml.R’ [1s/1s]
  Comparing ‘doaml.Rout’ to ‘doaml.Rout.save’ ... OK
  Running ‘doweight.R’ [1s/1s]
  Comparing ‘doweight.Rout’ to ‘doweight.Rout.save’ ... OK
  Running ‘dropspecial.R’ [1s/1s]
  Comparing ‘dropspecial.Rout’ to ‘dropspecial.Rout.save’ ... OK
  Running ‘ekm.R’ [1s/1s]
  Comparing ‘ekm.Rout’ to ‘ekm.Rout.save’ ... OK
  Running ‘expected.R’ [1s/1s]
  Comparing ‘expected.Rout’ to ‘expected.Rout.save’ ... OK
  Running ‘expected2.R’ [1s/1s]
  Comparing ‘expected2.Rout’ to ‘expected2.Rout.save’ ... OK
  Running ‘factor.R’ [1s/1s]
  Comparing ‘factor.Rout’ to ‘factor.Rout.save’ ... OK
  Running ‘factor2.R’ [1s/1s]
  Comparing ‘factor2.Rout’ to ‘factor2.Rout.save’ ... OK
  Running ‘finegray.R’ [1s/1s]
  Comparing ‘finegray.Rout’ to ‘finegray.Rout.save’ ... OK
  Running ‘fr_cancer.R’ [1s/1s]
  Comparing ‘fr_cancer.Rout’ to ‘fr_cancer.Rout.save’ ... OK
  Running ‘fr_kidney.R’ [1s/1s]
  Comparing ‘fr_kidney.Rout’ to ‘fr_kidney.Rout.save’ ... OK
  Running ‘fr_lung.R’ [1s/1s]
  Comparing ‘fr_lung.Rout’ to ‘fr_lung.Rout.save’ ... OK
  Running ‘fr_ovarian.R’ [1s/1s]
  Comparing ‘fr_ovarian.Rout’ to ‘fr_ovarian.Rout.save’ ... OK
  Running ‘fr_rat1.R’ [1s/1s]
  Comparing ‘fr_rat1.Rout’ to ‘fr_rat1.Rout.save’ ... OK
  Running ‘fr_resid.R’ [1s/1s]
  Comparing ‘fr_resid.Rout’ to ‘fr_resid.Rout.save’ ... OK
  Running ‘fr_simple.R’ [1s/1s]
  Comparing ‘fr_simple.Rout’ to ‘fr_simple.Rout.save’ ... OK
  Running ‘frailty.R’ [1s/1s]
  Comparing ‘frailty.Rout’ to ‘frailty.Rout.save’ ... OK
  Running ‘frank.R’ [1s/1s]
  Comparing ‘frank.Rout’ to ‘frank.Rout.save’ ... OK
  Running ‘infcox.R’ [1s/1s]
  Comparing ‘infcox.Rout’ to ‘infcox.Rout.save’ ... OK
  Running ‘jasa.R’ [1s/1s]
  Comparing ‘jasa.Rout’ to ‘jasa.Rout.save’ ... OK
  Running ‘model.matrix.R’ [1s/1s]
  Comparing ‘model.matrix.Rout’ to ‘model.matrix.Rout.save’ ... OK
  Running ‘mstate.R’ [1s/1s]
  Comparing ‘mstate.Rout’ to ‘mstate.Rout.save’ ... OK
  Running ‘mstate2.R’ [1s/1s]
  Comparing ‘mstate2.Rout’ to ‘mstate2.Rout.save’ ... OK
  Running ‘mstrata.R’ [1s/1s]
  Comparing ‘mstrata.Rout’ to ‘mstrata.Rout.save’ ... OK
  Running ‘multi2.R’ [1s/1s]
  Comparing ‘multi2.Rout’ to ‘multi2.Rout.save’ ... OK
  Running ‘multi3.R’ [1s/1s]
  Comparing ‘multi3.Rout’ to ‘multi3.Rout.save’ ... OK
  Running ‘multistate.R’ [1s/1s]
  Comparing ‘multistate.Rout’ to ‘multistate.Rout.save’ ... OK
  Running ‘neardate.R’ [1s/1s]
  Comparing ‘neardate.Rout’ to ‘neardate.Rout.save’ ... OK
  Running ‘nested.R’ [1s/1s]
  Comparing ‘nested.Rout’ to ‘nested.Rout.save’ ... OK
  Running ‘nsk.R’ [1s/1s]
  Comparing ‘nsk.Rout’ to ‘nsk.Rout.save’ ... OK
  Running ‘ovarian.R’ [1s/1s]
  Comparing ‘ovarian.Rout’ to ‘ovarian.Rout.save’ ... OK
  Running ‘overlap.R’ [1s/1s]
  Comparing ‘overlap.Rout’ to ‘overlap.Rout.save’ ... OK
  Running ‘prednew.R’ [1s/1s]
  Comparing ‘prednew.Rout’ to ‘prednew.Rout.save’ ... OK
  Running ‘pseudo.R’ [1s/1s]
  Comparing ‘pseudo.Rout’ to ‘pseudo.Rout.save’ ...342,372d341
< > #
< > # a data set with a missing value, and with a group that has only one obs
< > #  a good test of edge cases
< > #
< > lfit1 <- survfit(Surv(time, status) ~ ph.ecog, lung)
< > # This will warn about points beyond the curve; ph.ecog==3 has a single point
< > # at time=118, and it will have one fewer obs than the data
< > p1 <- pseudo(lfit1, times=c(100, 200))
< Warning message:
< In pseudo(lfit1, times = c(100, 200)) :
<   requested time points are beyond the end of one or more curves
< > aeq(dim(p1), c(nrow(lung)-1, 2))
< [1] TRUE
< > 
< > 
< > # This will have rows that match the data
< > lfit2 <- survfit(Surv(time, status) ~ ph.ecog, lung, na.action= na.exclude)
< > p2 <- pseudo(lfit2, time=c(100, 200))
< Warning message:
< In pseudo(lfit2, time = c(100, 200)) :
<   requested time points are beyond the end of one or more curves
< > aeq(dim(p2), c(nrow(lung), 2))
< [1] TRUE
< > all(is.na(p2[is.na(lung$ph.ecog)]))  # a row of missing was inserted
< [1] TRUE
< > 
< > row3 <- which(!is.na(lung$ph.ecog) & lung$ph.ecog ==3)  # the singleton row
< > all(p2[row3,] == c(1, 0))
< [1] TRUE
< > 
< > 
  Running ‘pspline.R’ [1s/1s]
  Comparing ‘pspline.Rout’ to ‘pspline.Rout.save’ ... OK
  Running ‘pyear.R’ [1s/1s]
  Comparing ‘pyear.Rout’ to ‘pyear.Rout.save’ ... OK
  Running ‘quantile.R’ [1s/1s]
  Comparing ‘quantile.Rout’ to ‘quantile.Rout.save’ ... OK
  Running ‘r_lung.R’ [1s/1s]
  Comparing ‘r_lung.Rout’ to ‘r_lung.Rout.save’ ... OK
  Running ‘r_resid.R’ [1s/1s]
  Comparing ‘r_resid.Rout’ to ‘r_resid.Rout.save’ ... OK
  Running ‘r_sas.R’ [3s/3s]
  Comparing ‘r_sas.Rout’ to ‘r_sas.Rout.save’ ... OK
  Running ‘r_scale.R’ [1s/1s]
  Comparing ‘r_scale.Rout’ to ‘r_scale.Rout.save’ ... OK
  Running ‘r_stanford.R’ [1s/1s]
  Comparing ‘r_stanford.Rout’ to ‘r_stanford.Rout.save’ ... OK
  Running ‘r_strata.R’ [1s/1s]
  Comparing ‘r_strata.Rout’ to ‘r_strata.Rout.save’ ... OK
  Running ‘r_tdist.R’ [1s/1s]
  Comparing ‘r_tdist.Rout’ to ‘r_tdist.Rout.save’ ... OK
  Running ‘r_user.R’ [1s/1s]
  Comparing ‘r_user.Rout’ to ‘r_user.Rout.save’ ... OK
  Running ‘ratetable.R’ [1s/1s]
  Comparing ‘ratetable.Rout’ to ‘ratetable.Rout.save’ ... OK
  Running ‘residsf.R’ [1s/1s]
  Comparing ‘residsf.Rout’ to ‘residsf.Rout.save’ ... OK
  Running ‘royston.R’ [1s/1s]
  Comparing ‘royston.Rout’ to ‘royston.Rout.save’ ... OK
  Running ‘rttright.R’ [1s/1s]
  Comparing ‘rttright.Rout’ to ‘rttright.Rout.save’ ... OK
  Running ‘singtest.R’ [1s/1s]
  Comparing ‘singtest.Rout’ to ‘singtest.Rout.save’ ... OK
  Running ‘strata2.R’ [1s/1s]
  Comparing ‘strata2.Rout’ to ‘strata2.Rout.save’ ... OK
  Running ‘stratatest.R’ [1s/1s]
  Comparing ‘stratatest.Rout’ to ‘stratatest.Rout.save’ ... OK
  Running ‘summary_survfit.R’ [1s/1s]
  Comparing ‘summary_survfit.Rout’ to ‘summary_survfit.Rout.save’ ... OK
  Running ‘surv.R’ [1s/1s]
  Comparing ‘surv.Rout’ to ‘surv.Rout.save’ ... OK
  Running ‘survSplit.R’ [1s/1s]
  Comparing ‘survSplit.Rout’ to ‘survSplit.Rout.save’ ... OK
  Running ‘survcheck.R’ [1s/1s]
  Comparing ‘survcheck.Rout’ to ‘survcheck.Rout.save’ ... OK
  Running ‘survfit1.R’ [1s/1s]
  Comparing ‘survfit1.Rout’ to ‘survfit1.Rout.save’ ... OK
  Running ‘survfit2.R’ [1s/1s]
  Comparing ‘survfit2.Rout’ to ‘survfit2.Rout.save’ ... OK
  Running ‘survreg1.R’ [1s/1s]
  Comparing ‘survreg1.Rout’ to ‘survreg1.Rout.save’ ... OK
  Running ‘survreg2.R’ [1s/1s]
  Comparing ‘survreg2.Rout’ to ‘survreg2.Rout.save’ ... OK
  Running ‘survtest.R’ [1s/1s]
  Comparing ‘survtest.Rout’ to ‘survtest.Rout.save’ ... OK
  Running ‘testci.R’ [1s/1s]
  Comparing ‘testci.Rout’ to ‘testci.Rout.save’ ... OK
  Running ‘testci2.R’ [1s/1s]
  Comparing ‘testci2.Rout’ to ‘testci2.Rout.save’ ... OK
  Running ‘testnull.R’ [1s/1s]
  Comparing ‘testnull.Rout’ to ‘testnull.Rout.save’ ... OK
  Running ‘testreg.R’ [1s/1s]
  Comparing ‘testreg.Rout’ to ‘testreg.Rout.save’ ... OK
  Running ‘tiedtime.R’ [1s/1s]
  Comparing ‘tiedtime.Rout’ to ‘tiedtime.Rout.save’ ... OK
  Running ‘tmerge.R’ [1s/1s]
  Comparing ‘tmerge.Rout’ to ‘tmerge.Rout.save’ ... OK
  Running ‘tmerge2.R’ [1s/1s]
  Comparing ‘tmerge2.Rout’ to ‘tmerge2.Rout.save’ ... OK
  Running ‘tmerge3.R’ [1s/1s]
  Comparing ‘tmerge3.Rout’ to ‘tmerge3.Rout.save’ ... OK
  Running ‘tt.R’ [1s/1s]
  Comparing ‘tt.Rout’ to ‘tt.Rout.save’ ... OK
  Running ‘tt2.R’ [1s/1s]
  Comparing ‘tt2.Rout’ to ‘tt2.Rout.save’ ... OK
  Running ‘turnbull.R’ [1s/1s]
  Comparing ‘turnbull.Rout’ to ‘turnbull.Rout.save’ ... OK
  Running ‘update.R’ [1s/1s]
  Comparing ‘update.Rout’ to ‘update.Rout.save’ ... OK
  Running ‘yates0.R’ [0s/0s]
  Comparing ‘yates0.Rout’ to ‘yates0.Rout.save’ ... OK
  Running ‘yates1.R’ [1s/1s]
  Comparing ‘yates1.Rout’ to ‘yates1.Rout.save’ ... OK
  Running ‘yates2.R’ [1s/1s]
  Running ‘zph.R’ [1s/1s]
  Comparing ‘zph.Rout’ to ‘zph.Rout.save’ ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [63s/63s] OK
* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [4s/4s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 1 NOTE