CRAN Package Check Results for Package survival

Last updated on 2020-02-16 19:49:11 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1-8 61.18 538.18 599.36 OK
r-devel-linux-x86_64-debian-gcc 3.1-8 38.07 413.82 451.89 OK
r-devel-linux-x86_64-fedora-clang 3.1-8 727.86 NOTE
r-devel-linux-x86_64-fedora-gcc 3.1-8 714.02 OK
r-devel-windows-ix86+x86_64 3.1-8 3.00 6.00 9.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 3.1-8 148.00 787.00 935.00 NOTE
r-patched-linux-x86_64 3.1-8 43.94 483.23 527.17 OK
r-patched-solaris-x86 3.1-8 NOTE
r-release-linux-x86_64 3.1-8 42.95 490.36 533.31 OK
r-release-windows-ix86+x86_64 3.1-8 109.00 760.00 869.00 ERROR
r-release-osx-x86_64 3.1-8 NOTE
r-oldrel-windows-ix86+x86_64 3.1-8 108.00 926.00 1034.00 NOTE
r-oldrel-osx-x86_64 3.1-8 NOTE

Check Details

Version: 3.1-8
Check: installed package size
Result: NOTE
     installed size is 8.9Mb
     sub-directories of 1Mb or more:
     R 1.0Mb
     data 3.2Mb
     doc 3.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 3.1-8
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-windows-ix86+x86_64

Version: 3.1-8
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'aareg.R' [2s]
     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' [3s]
     Comparing 'book7.Rout' to 'book7.Rout.save' ... OK
     Running 'cancer.R' [4s]
     Comparing 'cancer.Rout' to 'cancer.Rout.save' ... OK
     Running 'clogit.R' [3s]
     Comparing 'clogit.Rout' to 'clogit.Rout.save' ... OK
     Running 'concordance.R' [3s]
     Comparing 'concordance.Rout' to 'concordance.Rout.save' ... OK
     Running 'concordance2.R' [15s]
     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' [3s]
     Comparing 'coxsurv4.Rout' to 'coxsurv4.Rout.save' ... OK
     Running 'coxsurv5.R' [3s]
     Comparing 'coxsurv5.Rout' to 'coxsurv5.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' [3s]
     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_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' [2s]
     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 'multi2.R' [3s]
     Comparing 'multi2.Rout' to 'multi2.Rout.save' ... OK
     Running 'multistate.R' [3s]
     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 'overlap.R' [2s]
     Comparing 'overlap.Rout' to 'overlap.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' [2s]
     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' [7s]
     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' ... OK
     Running 'survSplit.R' [2s]
     Comparing 'survSplit.Rout' to 'survSplit.Rout.save' ... OK
     Running 'survcheck.R' [2s]
     Comparing 'survcheck.Rout' to 'survcheck.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' [3s]
     Comparing 'survreg1.Rout' to 'survreg1.Rout.save' ... OK
     Running 'survreg2.R' [2s]
     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' [2s]
     Comparing 'tmerge3.Rout' to 'tmerge3.Rout.save' ... OK
     Running 'tt.R' [2s]
     Comparing 'tt.Rout' to 'tt.Rout.save' ... OK
     Running 'turnbull.R' [3s]
     Comparing 'turnbull.Rout' to 'turnbull.Rout.save' ... OK
     Running 'update.R' [2s]
     Comparing 'update.Rout' to 'update.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 'zph.R' [3s]
     Comparing 'zph.Rout' to 'zph.Rout.save' ... OK
    Running the tests in 'tests/multistate.R' failed.
    Complete output:
     > #
     > # Tests for multi-state Cox models
     > #
     > library(survival)
     >
     > aeq <- function(x,y, ...) all.equal(as.vector(x), as.vector(y), ...)
     >
     > # There are a few subjects with progression and death on the same day. In the
     > # usual multi-state data set only one will count.
     > data1 <- mgus2
     > data1$etime <- with(data1, ifelse(pstat==1, ptime, futime))
     > data1$event <- factor(ifelse(data1$pstat==1, 1, 2L*data1$death),
     + 0:2, c("censor", "PCM", "death"))
     >
     > data2 <- mgus2[rep(1:nrow(mgus2) ,2), c("id", "age", "sex", "mspike")]
     > data2$time <- rep(data1$etime, 2)
     > data2$status <- 1* c(data1$event=="PCM", data1$event=="death")
     > data2$type <- rep(c(2:3), each=nrow(mgus2))
     >
     > fit1 <- coxph(Surv(etime, event) ~ age + sex + mspike, data1, id=id, x=TRUE,
     + robust=FALSE)
     > fit1a <- coxph(Surv(etime, event=="PCM") ~ age + sex + mspike, data1)
     > fit1b <- coxph(Surv(etime, event=='death') ~ age + sex + mspike, data1)
     > fit1c <- coxph(Surv(time, status) ~ strata(type)/(age + sex+ mspike),
     + data2, x=TRUE)
     >
     > aeq(fit1$loglik, fit1a$loglik + fit1b$loglik)
     [1] TRUE
     > aeq(fit1$coef, c(fit1a$coef, fit1b$coef))
     [1] TRUE
     > aeq(fit1$var[1:3, 1:3], fit1a$var)
     [1] TRUE
     > aeq(fit1$var[4:6, 4:6], fit1b$var)
     [1] TRUE
     > aeq(fit1$x[,c(1,4,2,5,3,6)], fit1c$x)
     [1] TRUE
     > aeq(fit1$coef[c(1,4,2,5,3,6)], fit1c$coef)
     [1] TRUE
     >
     > # force a common age effect across all states
     > fit2 <- coxph(list(Surv(etime, event) ~ sex,
     + 1:0 ~ age / common),
     + data1, id=id)
     >
     > data2 <- rbind(cbind(data1, status= (data1$event=="PCM"), etype=1),
     + cbind(data1, status= (data1$event=='death'), etype=2))
     > fit2a <- coxph(Surv(etime, status) ~ age + strata(etype)/sex, data2)
     >
     > aeq(coef(fit2), coef(fit2a)[c(2,1,3)]) # not in the same order
     [1] TRUE
     > aeq(fit2$loglik, fit2a$loglik)
     [1] TRUE
     >
     > #same fit in more complex ways
     > data1$entry <- "Entry"
     > fit2b <- coxph(list(Surv(etime, event) ~ sex,
     + "Entry":"PCM" + "Entry":"death" ~ age / common),
     + istate=entry, data1, id=id)
     > fit2c <- coxph(list(Surv(etime, event) ~ sex,
     + "Entry":state(c("PCM", "death")) ~ age / common),
     + istate=entry, data1, id=id)
     >
     > aeq(fit2b$loglik, fit2$loglik)
     [1] TRUE
     > aeq(fit2c$coef, fit2$coef)
     [1] TRUE
     >
     > # mspike size as a covariate for PCM only
     > # first, 3 different ways to write the same
     > fit3 <- coxph(list(Surv(etime, event) ~ age + sex,
     + 1:state("PCM") ~ mspike),
     + data1, id=id)
     > fit3b <- coxph(list(Surv(etime, event) ~ age + sex,
     + 1:"PCM" ~ mspike),
     + data1, id=id)
     > fit3c <- coxph(list(Surv(etime, event) ~ age + sex,
     + 1:c("PCM") ~ mspike),
     + data1, id=id)
     Error in if (flag["teleport"] > 0) { :
     missing value where TRUE/FALSE needed
     Calls: coxph -> survcheck2
     Execution halted
Flavor: r-release-windows-ix86+x86_64