[Debian-med-packaging] Bug#903719: r-cran-etm: autopkgtest regression: there is no package called 'kmi'
Paul Gevers
elbrus at debian.org
Fri Jul 13 18:25:49 BST 2018
Source: r-cran-etm
Version: 1.0.3-1
User: debian-ci at 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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