Your message dated Mon, 10 Sep 2018 07:50:12 +0000
with message-id <[email protected]>
and subject line Bug#903719: fixed in r-cran-etm 1.0.4-2
has caused the Debian Bug report #903719,
regarding r-cran-etm: autopkgtest regression: there is no package called 'kmi'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
903719: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=903719
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: r-cran-etm
Version: 1.0.3-1
User: [email protected]
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: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: r-cran-etm
Source-Version: 1.0.4-2
We believe that the bug you reported is fixed in the latest version of
r-cran-etm, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated r-cran-etm package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 10 Sep 2018 09:19:56 +0200
Source: r-cran-etm
Binary: r-cran-etm
Architecture: source
Version: 1.0.4-2
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
r-cran-etm - GNU R empirical transition matrix
Closes: 903672 903719
Changes:
r-cran-etm (1.0.4-2) unstable; urgency=medium
.
* Test-Depends: r-cran-kmi
Closes: #903672, #903719
* Standards-Version: 4.2.1
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