Last updated on 2025-09-12 01:53:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2-3 | 9.65 | 998.28 | 1007.93 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2-3 | 7.51 | 595.10 | 602.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2-3 | 974.43 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2-3 | 1489.91 | ERROR | |||
| r-devel-windows-x86_64 | 1.2-3 | 12.00 | 415.00 | 427.00 | OK | |
| r-patched-linux-x86_64 | 1.2-3 | 11.54 | 979.70 | 991.24 | OK | |
| r-release-linux-x86_64 | 1.2-3 | 10.41 | 976.20 | 986.61 | OK | |
| r-release-macos-arm64 | 1.2-3 | 397.00 | OK | |||
| r-release-macos-x86_64 | 1.2-3 | 885.00 | OK | |||
| r-release-windows-x86_64 | 1.2-3 | 13.00 | 425.00 | 438.00 | OK | |
| r-oldrel-macos-arm64 | 1.2-3 | 435.00 | WARN | |||
| r-oldrel-macos-x86_64 | 1.2-3 | 910.00 | WARN | |||
| r-oldrel-windows-x86_64 | 1.2-3 | 15.00 | 615.00 | 630.00 | NOTE |
Version: 1.2-3
Check: tests
Result: ERROR
Running ‘Coxph-Ex.R’ [10s/12s]
Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
Running ‘KaplanMeier-Ex.R’ [2s/2s]
Running ‘PI_OVL-Ex.R’ [2s/3s]
Running ‘Polr-Ex.R’ [2s/2s]
Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
Running ‘Survreg-Ex.R’ [3s/4s]
Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
Running ‘bugfixes.R’ [10s/13s]
Running ‘intercepts-Ex.R’ [3s/4s]
Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
Running ‘mmlt-Ex.R’ [83s/115s]
Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
Running ‘mmlt-interface.R’ [29s/38s]
Running ‘mtram-Ex.R’ [9s/10s]
Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ... OK
Running ‘stram-Ex.R’ [9s/10s]
Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
Running the tests in ‘tests/bugfixes.R’ failed.
Complete output:
>
> library("tram")
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
> library("sandwich")
> library("survival")
> library("numDeriv")
>
> ### scores for fixed parameters
> cars$int <- 1
> a0 <- Lm(dist ~ speed, data = cars)
> a1 <- Lm(dist ~ speed + int, data = cars, fixed = c("int" = 0))
>
> s0 <- estfun(a0)
> s1 <- estfun(a1)
> s2 <- estfun(a1, parm = coef(as.mlt(a1), fixed = TRUE))
>
> stopifnot(all.equal(s0[,"(Intercept)"], -s2[,"int"]))
> stopifnot(all.equal(s1[,"(Intercept)"], -s2[,"int"]))
> stopifnot(all.equal(s2[,"(Intercept)"], -s2[,"int"]))
>
> ### log_first for count data (by Sandra Siegfried)
> ### use: y + 1; log_first = TRUE, support = c(1, ...), bounds = c(1, ...)
> set.seed(29)
>
> Nsim <- 100
> n <- 4000
> b1 <- -4.5
> b0 <- 5
> theta <- 2
>
> h <- qlogis(ppois(0:100, lambda = 5))
>
> x <- runif(n, min = 0, max = 1)
> log.mu <- b0 + b1 * x
>
> h.m <- matrix(h, nrow = length(h), ncol = length(x))
> p <- (plogis(t(h.m) - b1 * x) - runif(n))^2
> y <- max.col(-p) - 1
>
> d <- data.frame(x = x, y = as.integer(y))
> d$y.p1 <- d$y + 1L
>
> m1 <- Colr(y ~ x, data = d,
+ support = c(0L, as.numeric(max(d$y))),
+ bounds = c(0L, Inf),
+ order = 10)
>
> try(m2a <- Colr(y ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y))),
+ bounds = c(1L, Inf),
+ log_first = TRUE,
+ order = 10))
Error in mlt(model = structure(list(model = structure(list(bresponse = structure(function (data, :
check(responsevar, data) is not TRUE
>
> try(m2b <- Colr(y ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y))),
+ bounds = c(0L, Inf),
+ log_first = TRUE,
+ order = 10))
Error in mlt(model = structure(list(model = structure(list(bresponse = structure(function (data, :
check(responsevar, data) is not TRUE
>
> m3 <- Colr(y.p1 ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y.p1))),
+ bounds = c(1L, Inf),
+ log_first = TRUE,
+ order = 10)
>
> l1 <- m1$logliki(coef(as.mlt(m1)), rep(1, nrow(d)))
> l3 <- m3$logliki(coef(as.mlt(m3)), rep(1, nrow(d)))
> stopifnot(cor(l1, l3) > .96)
>
> ### 0.3-0
> data("GBSG2", package = "TH.data")
> ### this model included an additional intercept
> m1 <- Coxph(Surv(time, cens) | menostat:tgrade ~ horTh, data = GBSG2)
> m2 <- Coxph(Surv(time, cens) | 0 + menostat:tgrade ~ horTh, data = GBSG2)
> stopifnot(max(abs(coef(as.mlt(m1)) - coef(as.mlt(m2)))) <
+ sqrt(.Machine$double.eps))
> ### interaction term with stratum
> m3 <- Coxph(Surv(time, cens) | horTh ~ menostat + menostat:horTh,
+ data = GBSG2)
> ci <- confint(m3)["menostatPre:horThyes",]
> stopifnot(all(!is.finite(ci)))
Error: all(!is.finite(ci)) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2-3
Check: tests
Result: ERROR
Running ‘Coxph-Ex.R’ [20s/26s]
Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
Running ‘KaplanMeier-Ex.R’
Running ‘PI_OVL-Ex.R’
Running ‘Polr-Ex.R’
Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
Running ‘Survreg-Ex.R’
Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
Running ‘bugfixes.R’ [21s/29s]
Running ‘intercepts-Ex.R’ [7s/10s]
Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
Running ‘mmlt-Ex.R’ [184s/241s]
Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
Running ‘mmlt-interface.R’ [43s/44s]
Running ‘mtram-Ex.R’ [11s/11s]
Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ... OK
Running ‘stram-Ex.R’ [11s/11s]
Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
Running the tests in ‘tests/bugfixes.R’ failed.
Complete output:
>
> library("tram")
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
> library("sandwich")
> library("survival")
> library("numDeriv")
>
> ### scores for fixed parameters
> cars$int <- 1
> a0 <- Lm(dist ~ speed, data = cars)
> a1 <- Lm(dist ~ speed + int, data = cars, fixed = c("int" = 0))
>
> s0 <- estfun(a0)
> s1 <- estfun(a1)
> s2 <- estfun(a1, parm = coef(as.mlt(a1), fixed = TRUE))
>
> stopifnot(all.equal(s0[,"(Intercept)"], -s2[,"int"]))
> stopifnot(all.equal(s1[,"(Intercept)"], -s2[,"int"]))
> stopifnot(all.equal(s2[,"(Intercept)"], -s2[,"int"]))
>
> ### log_first for count data (by Sandra Siegfried)
> ### use: y + 1; log_first = TRUE, support = c(1, ...), bounds = c(1, ...)
> set.seed(29)
>
> Nsim <- 100
> n <- 4000
> b1 <- -4.5
> b0 <- 5
> theta <- 2
>
> h <- qlogis(ppois(0:100, lambda = 5))
>
> x <- runif(n, min = 0, max = 1)
> log.mu <- b0 + b1 * x
>
> h.m <- matrix(h, nrow = length(h), ncol = length(x))
> p <- (plogis(t(h.m) - b1 * x) - runif(n))^2
> y <- max.col(-p) - 1
>
> d <- data.frame(x = x, y = as.integer(y))
> d$y.p1 <- d$y + 1L
>
> m1 <- Colr(y ~ x, data = d,
+ support = c(0L, as.numeric(max(d$y))),
+ bounds = c(0L, Inf),
+ order = 10)
>
> try(m2a <- Colr(y ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y))),
+ bounds = c(1L, Inf),
+ log_first = TRUE,
+ order = 10))
Error in mlt(model = structure(list(model = structure(list(bresponse = structure(function (data, :
check(responsevar, data) is not TRUE
>
> try(m2b <- Colr(y ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y))),
+ bounds = c(0L, Inf),
+ log_first = TRUE,
+ order = 10))
Error in mlt(model = structure(list(model = structure(list(bresponse = structure(function (data, :
check(responsevar, data) is not TRUE
>
> m3 <- Colr(y.p1 ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y.p1))),
+ bounds = c(1L, Inf),
+ log_first = TRUE,
+ order = 10)
>
> l1 <- m1$logliki(coef(as.mlt(m1)), rep(1, nrow(d)))
> l3 <- m3$logliki(coef(as.mlt(m3)), rep(1, nrow(d)))
> stopifnot(cor(l1, l3) > .96)
>
> ### 0.3-0
> data("GBSG2", package = "TH.data")
> ### this model included an additional intercept
> m1 <- Coxph(Surv(time, cens) | menostat:tgrade ~ horTh, data = GBSG2)
> m2 <- Coxph(Surv(time, cens) | 0 + menostat:tgrade ~ horTh, data = GBSG2)
> stopifnot(max(abs(coef(as.mlt(m1)) - coef(as.mlt(m2)))) <
+ sqrt(.Machine$double.eps))
> ### interaction term with stratum
> m3 <- Coxph(Surv(time, cens) | horTh ~ menostat + menostat:horTh,
+ data = GBSG2)
> ci <- confint(m3)["menostatPre:horThyes",]
> stopifnot(all(!is.finite(ci)))
Error: all(!is.finite(ci)) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2-3
Check: tests
Result: ERROR
Running ‘Coxph-Ex.R’ [21s/60s]
Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
Running ‘KaplanMeier-Ex.R’
Running ‘PI_OVL-Ex.R’ [5s/11s]
Running ‘Polr-Ex.R’ [4s/10s]
Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
Running ‘Survreg-Ex.R’ [7s/19s]
Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
Running ‘bugfixes.R’ [22s/48s]
Running ‘intercepts-Ex.R’ [7s/29s]
Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
Running ‘mmlt-Ex.R’ [241s/417s]
Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
Running ‘mmlt-interface.R’ [75s/76s]
Running ‘mtram-Ex.R’ [20s/21s]
Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ... OK
Running ‘stram-Ex.R’ [22s/23s]
Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
Running the tests in ‘tests/bugfixes.R’ failed.
Complete output:
>
> library("tram")
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
> library("sandwich")
> library("survival")
> library("numDeriv")
>
> ### scores for fixed parameters
> cars$int <- 1
> a0 <- Lm(dist ~ speed, data = cars)
> a1 <- Lm(dist ~ speed + int, data = cars, fixed = c("int" = 0))
>
> s0 <- estfun(a0)
> s1 <- estfun(a1)
> s2 <- estfun(a1, parm = coef(as.mlt(a1), fixed = TRUE))
>
> stopifnot(all.equal(s0[,"(Intercept)"], -s2[,"int"]))
> stopifnot(all.equal(s1[,"(Intercept)"], -s2[,"int"]))
> stopifnot(all.equal(s2[,"(Intercept)"], -s2[,"int"]))
>
> ### log_first for count data (by Sandra Siegfried)
> ### use: y + 1; log_first = TRUE, support = c(1, ...), bounds = c(1, ...)
> set.seed(29)
>
> Nsim <- 100
> n <- 4000
> b1 <- -4.5
> b0 <- 5
> theta <- 2
>
> h <- qlogis(ppois(0:100, lambda = 5))
>
> x <- runif(n, min = 0, max = 1)
> log.mu <- b0 + b1 * x
>
> h.m <- matrix(h, nrow = length(h), ncol = length(x))
> p <- (plogis(t(h.m) - b1 * x) - runif(n))^2
> y <- max.col(-p) - 1
>
> d <- data.frame(x = x, y = as.integer(y))
> d$y.p1 <- d$y + 1L
>
> m1 <- Colr(y ~ x, data = d,
+ support = c(0L, as.numeric(max(d$y))),
+ bounds = c(0L, Inf),
+ order = 10)
>
> try(m2a <- Colr(y ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y))),
+ bounds = c(1L, Inf),
+ log_first = TRUE,
+ order = 10))
Error in mlt(model = structure(list(model = structure(list(bresponse = structure(function (data, :
check(responsevar, data) is not TRUE
>
> try(m2b <- Colr(y ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y))),
+ bounds = c(0L, Inf),
+ log_first = TRUE,
+ order = 10))
Error in mlt(model = structure(list(model = structure(list(bresponse = structure(function (data, :
check(responsevar, data) is not TRUE
>
> m3 <- Colr(y.p1 ~ x, data = d,
+ support = c(1L, as.numeric(max(d$y.p1))),
+ bounds = c(1L, Inf),
+ log_first = TRUE,
+ order = 10)
>
> l1 <- m1$logliki(coef(as.mlt(m1)), rep(1, nrow(d)))
> l3 <- m3$logliki(coef(as.mlt(m3)), rep(1, nrow(d)))
> stopifnot(cor(l1, l3) > .96)
>
> ### 0.3-0
> data("GBSG2", package = "TH.data")
> ### this model included an additional intercept
> m1 <- Coxph(Surv(time, cens) | menostat:tgrade ~ horTh, data = GBSG2)
> m2 <- Coxph(Surv(time, cens) | 0 + menostat:tgrade ~ horTh, data = GBSG2)
> stopifnot(max(abs(coef(as.mlt(m1)) - coef(as.mlt(m2)))) <
+ sqrt(.Machine$double.eps))
> ### interaction term with stratum
> m3 <- Coxph(Surv(time, cens) | horTh ~ menostat + menostat:horTh,
+ data = GBSG2)
> ci <- confint(m3)["menostatPre:horThyes",]
> stopifnot(all(!is.finite(ci)))
Error: all(!is.finite(ci)) is not TRUE
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2-3
Check: DESCRIPTION meta-information
Result: NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘Stat2Data’
A package should be listed in only one of these fields.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2-3
Check: package subdirectories
Result: WARN
Subdirectory 'demo' contains invalid file names:
‘NAMI.Rout.save’ ‘SCI_ePolr.Rout.save’ ‘hcc.Rout.save’
‘mtram.Rout.save’ ‘npb.Rout.save’ ‘npn.Rout.save’ ‘stram.Rout.save’
‘survtram.Rout.save’ ‘tram.Rout.save’ ‘undernutrition.Rout.save’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64