Source: r-cran-etm Version: 1.0.3-1 User: debian...@lists.debian.org Usertags: regression
Dear maintainers, With the upload of version 1.0.3-1 your package started to fail its autopgktest. I copied the error below. Could you please investigate, it seems you are missing a test dependency. Currently this regression is delaying the migration to testing by 13 days. Paul https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-etm/600128/log.gz autopkgtest [05:16:51]: test run-unit-test: [----------------------- Test test.etmCIF passed --- tests.etm.Rout.save_ 2018-07-13 05:17:12.927560452 +0000 +++ tests.etm.Rout_ 2018-07-13 05:17:12.931560387 +0000 @@ -246,7 +246,7 @@ 116 0.9990 116.0 4.764e-07 0.99767 1.0000 1 0 124 0.9990 124.0 4.764e-07 0.99767 1.0000 2 0 164 0.9990 164.0 4.764e-07 0.99767 1.0000 0 0 -183 1.0000 183.0 1.337e-19 1.00000 1.0000 1 1 +183 1.0000 183.0 1.032e-19 1.00000 1.0000 1 1 > > ## gonna play a bit with the state names > dd <- sir.cont @@ -585,149 +585,8 @@ > > if (!require(kmi, quietly = TRUE)) + stop("The following tests require the 'kmi' package") -> -> library(etm) -> -> data(icu.pneu) -> my.icu.pneu <- icu.pneu -> -> my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ] -> masque <- diff(my.icu.pneu$id) -> -> my.icu.pneu$from <- 0 -> my.icu.pneu$from[c(1, masque) == 0] <- 1 -> -> my.icu.pneu$to2 <- my.icu.pneu$event -> my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens" -> my.icu.pneu$to2[c(masque, 1) == 0] <- 1 -> -> -> my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2, -+ my.icu.pneu$to2) -> -> my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to", -+ "to2", "age", "sex")] -> names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit") -> -> bouh_strat <- etm(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens", 0, strata = "sex") -> -> bouh_female <- etm(my.icu.pneu[my.icu.pneu$sex == "F", ], -+ c("0", "1", "2"), tra_ill(), "cens", 0) -> -> all(bouh_strat[[1]]$est == bouh_female$est) -[1] TRUE -> -> ## Test the summary -> the_summary <- summary(bouh_strat) -> the_summary -sex == "F" - -Transition 0 0 - P time var lower upper n.risk n.event - 0.99819 1 3.276e-06 0.994641 1.00000 552 0 - 0.25589 14 3.465e-04 0.219404 0.29237 154 0 - 0.08389 29 1.406e-04 0.060653 0.10714 50 0 - 0.02876 43 5.264e-05 0.014543 0.04298 16 0 - 0.01255 57 2.458e-05 0.002833 0.02227 7 0 - 0.00000 86 0.000e+00 0.000000 0.00000 0 0 - -Transition 0 1 - P time var lower upper n.risk n.event - 0.000000 1 0.000e+00 0.00000 0.00000 552 0 - 0.052655 14 9.058e-05 0.03400 0.07131 154 1 - 0.028005 29 5.032e-05 0.01410 0.04191 50 0 - 0.014936 43 2.733e-05 0.00469 0.02518 16 0 - 0.005601 57 1.038e-05 0.00000 0.01192 7 0 - 0.000000 86 0.000e+00 0.00000 0.00000 0 0 - -Transition 0 2 - P time var lower upper n.risk n.event - 0.001812 1 3.276e-06 0.0000 0.005359 552 1 - 0.691459 14 3.880e-04 0.6529 0.730064 154 13 - 0.888101 29 1.823e-04 0.8616 0.914567 50 5 - 0.956300 43 7.840e-05 0.9389 0.973655 16 1 - 0.981848 57 3.471e-05 0.9703 0.993394 7 1 - 1.000000 86 0.000e+00 1.0000 1.000000 0 0 - -Transition 1 1 - P time var lower upper n.risk n.event - 1.00000 1 0.000000 1.00000 1.0000 0 0 - 0.89474 14 0.004957 0.75674 1.0000 27 0 - 0.35627 29 0.006364 0.19992 0.5126 17 0 - 0.19001 43 0.003916 0.06736 0.3127 8 0 - 0.07125 57 0.001608 0.00000 0.1499 3 0 - 0.00000 86 0.000000 0.00000 0.0000 1 0 - -Transition 1 2 - P time var lower upper n.risk n.event - 0.0000 1 0.000e+00 0.0000 0.0000 0 0 - 0.1053 14 4.957e-03 0.0000 0.2433 27 0 - 0.6437 29 6.364e-03 0.4874 0.8001 17 2 - 0.8100 43 3.916e-03 0.6873 0.9326 8 0 - 0.9287 57 1.608e-03 0.8501 1.0000 3 0 - 1.0000 86 4.770e-18 1.0000 1.0000 1 1 - -sex == "M" - -Transition 0 0 - P time var lower upper n.risk n.event - 0.976347 2 3.035e-05 0.965550 0.98714 761 0 - 0.186247 19 2.012e-04 0.158445 0.21405 151 0 - 0.071497 35 9.063e-05 0.052838 0.09016 54 0 - 0.018589 54 2.580e-05 0.008634 0.02854 15 0 - 0.007746 77 1.148e-05 0.001105 0.01439 5 0 - 0.000000 460 0.000e+00 0.000000 0.00000 1 0 - -Transition 0 1 - P time var lower upper n.risk n.event - 0.000000 2 0.000e+00 0.00000 0.000000 761 0 - 0.052695 19 6.577e-05 0.03680 0.068590 151 0 - 0.025063 35 3.371e-05 0.01368 0.036444 54 0 - 0.013247 54 1.866e-05 0.00478 0.021713 15 0 - 0.003312 77 5.279e-06 0.00000 0.007815 5 0 - 0.000000 460 0.000e+00 0.00000 0.000000 1 0 - -Transition 0 2 - P time var lower upper n.risk n.event - 0.02365 2 3.035e-05 0.01286 0.03445 761 18 - 0.76106 19 2.410e-04 0.73063 0.79149 151 12 - 0.90344 35 1.193e-04 0.88204 0.92484 54 4 - 0.96816 54 4.374e-05 0.95520 0.98113 15 2 - 0.98894 77 1.668e-05 0.98094 0.99695 5 0 - 1.00000 460 1.016e-20 1.00000 1.00000 1 1 - -Transition 1 1 - P time var lower upper n.risk n.event - 1.0000 2 0.000000 1.00000 1.00000 0 0 - 0.5620 19 0.005905 0.41137 0.71259 43 0 - 0.2024 35 0.002450 0.10542 0.29945 18 0 - 0.1012 54 0.001182 0.03384 0.16859 9 0 - 0.0253 77 0.000314 0.00000 0.06003 3 0 - 0.0000 460 0.000000 0.00000 0.00000 0 0 - -Transition 1 2 - P time var lower upper n.risk n.event - 0.0000 2 0.000e+00 0.0000 0.0000 0 0 - 0.4380 19 5.905e-03 0.2874 0.5886 43 3 - 0.7976 35 2.450e-03 0.7005 0.8946 18 1 - 0.8988 54 1.182e-03 0.8314 0.9662 9 0 - 0.9747 77 3.140e-04 0.9400 1.0000 3 1 - 1.0000 460 3.686e-18 1.0000 1.0000 0 0 - -> -> ## Test trprob -> all(trprob(bouh_strat, "0 1")[[1]] == trprob(bouh_female, "0 1")) -[1] TRUE -> all(trprob(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trprob(bouh_female, "0 1", c(0, 5, 10, 15))) -[1] TRUE -> -> ## Test trcov -> all(trcov(bouh_strat, "0 1")[[1]] == trcov(bouh_female, "0 1")) -[1] TRUE -> all(trcov(bouh_strat, c("0 1", "0 2"))[[1]] == trcov(bouh_female, c("0 1", "0 2"))) -[1] TRUE -> all(trcov(bouh_strat, "0 1", c(0, 5, 10, 15))[[1]] == trcov(bouh_female, "0 1", c(0, 5, 10, 15))) -[1] TRUE -> -> options(old) -> +Error: The following tests require the 'kmi' package +In addition: Warning message: +In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : + there is no package called 'kmi' +Execution halted autopkgtest [05:17:13]: test run-unit-test: -----------------------]
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