Last updated on 2026-10-24 01:51:36 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 25.46 | 419.04 | 444.50 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 20.15 | 260.57 | 280.72 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 23.00 | 297.39 | 320.39 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 20.00 | 268.83 | 288.83 | OK | |
| r-devel-windows-x86_64 | 0.2.0 | 36.00 | 583.00 | 619.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 28.58 | 394.78 | 423.36 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 25.53 | 392.77 | 418.30 | OK | |
| r-release-macos-arm64 | 0.2.0 | 7.00 | 90.00 | 97.00 | OK | |
| r-release-macos-x86_64 | 0.2.0 | 20.00 | 425.00 | 445.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 33.00 | 507.00 | 540.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.0 | 18.00 | 225.00 | 243.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 47.00 | 608.00 | 655.00 | OK |
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘icmstate-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.probtrans.subjects
> ### Title: Plot an object of class '"probtrans.subjects"'
> ### Aliases: plot.probtrans.subjects
>
> ### ** Examples
>
> if(require("mstate")){
+ data(ebmt3)
+ n <- nrow(ebmt3)
+ tmat <- transMat(x = list(c(2, 3), c(3), c()), names = c("Tx",
+ "PR", "RelDeath"))
+ ebmt3$prtime <- ebmt3$prtime/365.25
+ ebmt3$rfstime <- ebmt3$rfstime/365.25
+ covs <- c("dissub", "age", "drmatch", "tcd", "prtime")
+ msbmt <- msprep(time = c(NA, "prtime", "rfstime"), status = c(NA,
+ "prstat", "rfsstat"), data = ebmt3, trans = tmat, keep = covs)
+ #Expand covariates so that we can have transition specific covariates
+ msbmt <- expand.covs(msbmt, covs, append = TRUE, longnames = FALSE)
+
+ #Simple model, transition specific covariates, each transition own baseline hazard
+ c1 <- coxph(Surv(Tstart, Tstop, status) ~ dissub1.1 + dissub2.1 +
+ age1.1 + age2.1 + drmatch.1 + tcd.1 + dissub1.2 + dissub2.2 +
+ age1.2 + age2.2 + drmatch.2 + tcd.2 + dissub1.3 + dissub2.3 +
+ age1.3 + age2.3 + drmatch.3 + tcd.3 + strata(trans), data = msbmt,
+ method = "breslow")
+ #We need to make a data.frame containing all subjects of interest
+ ttmat <- to.trans2(tmat)[, c(2, 3, 1)]
+ names(ttmat)[3] <- "trans"
+ nd_n <- NULL
+ for (j in 1:30) {
+ # Select global covariates of subject j
+ cllj <- ebmt3[j, covs]
+ nd2 <- cbind(ttmat, rep(j, 3), rbind(cllj, cllj, cllj))
+ colnames(nd2)[4] <- "id"
+ # Make nd2 of class msdata to use expand.covs
+ attr(nd2, "trans") <- tmat
+ class(nd2) <- c("msdata", "data.frame")
+ nd2 <- expand.covs(nd2, covs=covs, longnames = FALSE)
+ nd_n <- rbind(nd_n, nd2)
+ }
+
+ icmstate_pt <- probtrans_coxph(c1, predt = 0, direction = "forward",
+ newdata = nd_n, trans = tmat)
+
+ #plot transition probabilities for subject 2
+ plot(icmstate_pt, id = 2)
+ }
Loading required package: mstate
Loading required package: survival
Error in a$specials[[i]] : subscript out of bounds
Calls: probtrans_coxph ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(icmstate)
>
> test_check("icmstate")
[1] "Frydman Support"
[1] "MSM Support"
Loading required package: survival
Saving _problems/test-probtrans_coxph-87.R
Saving _problems/test-probtrans_coxph-152.R
[ FAIL 2 | WARN 0 | SKIP 9 | PASS 66 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• TRUE is TRUE (8): 'test-estimateSupportMSM.R:2:3', 'test-icmstate.R:2:3',
'test-npmsm.R:174:3', 'test-probtrans_coxph.R:195:3', 'test-profiling.R:2:3',
'test-sim_id_weib.R:2:3', 'test-supportHeinEM.R:3:3',
'test-visualise_data.R:2:3'
• empty test (1): 'test-npmsm.R:67:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-probtrans_coxph.R:87:3'): Do we recover the same baseline hazards as msfit? ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─mstate::msfit(c1, newdata = newd, trans = tmat) at test-probtrans_coxph.R:87:3
2. ├─stats::model.matrix(object, data = mf)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-probtrans_coxph.R:152:5'): Do we recover the same transition probabilities as msfit + probtrans? ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─mstate::msfit(c2, newdata = nd, trans = tmat) at test-probtrans_coxph.R:152:5
2. ├─stats::model.matrix(object, data = mf)
3. └─survival:::model.matrix.coxph(object, data = mf)
4. └─stats::delete.response(object$terms)
5. └─stats (local) off(a$specials[[i]])
[ FAIL 2 | WARN 0 | SKIP 9 | PASS 66 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc