tram

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re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building ‘NAMI.Rnw’ using knitr
--- finished re-building ‘NAMI.Rnw’

--- re-building ‘mtram.Rnw’ using knitr
--- finished re-building ‘mtram.Rnw’

+-+mtram.pdf

 *** caught segfault ***
address 0x2070, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘survtram.Rnw’ using knitr
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  semi-transparency is not supported on this device: reported only once per page
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  semi-transparency is not supported on this device: reported only once per page
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘survtram.Rnw’

--- re-building ‘tram.Rnw’ using knitr
--- finished re-building ‘tram.Rnw’

SUMMARY: processing the following file failed:
  ‘mtram.Rnw’

Error: Vignette re-building failed.
Execution halted

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Rd files

prepare_Rd: ./man/Aareg.Rd:55: unknown macro '\bibcitet'
prepare_Rd: ./man/Aareg.Rd:56: unknown macro '\bibcitet'
checkRd: (-1) Aareg.Rd:55: Lost braces
    55 | can be found in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017} and
       |                          ^
checkRd: (-1) Aareg.Rd:56: Lost braces
    56 | \bibcitet{tram::Hothorn:2018}.
       |          ^
prepare_Rd: ./man/BoxCox.Rd:46: unknown macro '\bibcitep'
prepare_Rd: ./man/BoxCox.Rd:54: unknown macro '\bibcitet'
prepare_Rd: ./man/BoxCox.Rd:55: unknown macro '\bibcitet'
checkRd: (-1) BoxCox.Rd:46: Lost braces
    46 | This is similar to a Box-Cox transformation \bibcitep{tram::BoxCox:1964}, but the technical details
       |                                                      ^
checkRd: (-1) BoxCox.Rd:54: Lost braces
    54 | can be found in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017} and
       |                          ^
checkRd: (-1) BoxCox.Rd:55: Lost braces
    55 | \bibcitet{tram::Hothorn:2018}.
       |          ^
prepare_Rd: ./man/Colr.Rd:58: unknown macro '\bibcitet'
prepare_Rd: ./man/Colr.Rd:59: unknown macro '\bibcitet'
checkRd: (-1) Colr.Rd:58: Lost braces
    58 | \bibcitet{tram::Lohse:Rohrmann:Faeh:2017} and
       |          ^
checkRd: (-1) Colr.Rd:59: Lost braces
    59 | \bibcitet{tram::Hothorn:Moest:Buehlmann:2017}.
       |          ^
prepare_Rd: ./man/Compris.Rd:77: unknown macro '\bibcitet'
prepare_Rd: ./man/Compris.Rd:78: unknown macro '\bibcitet'
prepare_Rd: ./man/Compris.Rd:79: unknown macro '\bibcitet'
checkRd: (-1) Compris.Rd:77: Lost braces
    77 | regression framework described by \bibcitet{tram::Czado:Keilegom:2022} and 
       |                                            ^
checkRd: (-1) Compris.Rd:78: Lost braces
    78 | \bibcitet{tram::Deresa:Keilegom:2023}, the implementation here is discussed
       |          ^
checkRd: (-1) Compris.Rd:79: Lost braces
    79 | in \bibcitet{tram::Siegfried:Tamasi:Hothorn:2026}.
       |             ^
prepare_Rd: ./man/Coxph.Rd:52: unknown macro '\bibcitet'
prepare_Rd: ./man/Coxph.Rd:62: unknown macro '\bibcitet'
prepare_Rd: ./man/Coxph.Rd:63: unknown macro '\bibcitet'
prepare_Rd: ./man/Coxph.Rd:64: unknown macro '\bibcitet'
checkRd: (-1) Coxph.Rd:52: Lost braces
    52 | \bibcitet{tram::McLain:Ghosh:2013}.
       |          ^
checkRd: (-1) Coxph.Rd:62: Lost braces
    62 | can be found in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017},
       |                          ^
checkRd: (-1) Coxph.Rd:63: Lost braces
    63 | \bibcitet{tram::Siegfried:Tamasi:Hothorn:2026}, and
       |          ^
checkRd: (-1) Coxph.Rd:64: Lost braces
    64 | \bibcitet{tram::Hothorn:2018}.
       |          ^
prepare_Rd: ./man/Lehmann.Rd:44: unknown macro '\bibcitet'
checkRd: (-1) Lehmann.Rd:44: Lost braces
    44 | This transformation model, introduced by \bibcitet{tram::Lehmann:1953}, uses the cumulative distribution function for the
       |                                                   ^
prepare_Rd: ./man/Lm.Rd:60: unknown macro '\bibcitet'
prepare_Rd: ./man/Lm.Rd:61: unknown macro '\bibcitet'
checkRd: (-1) Lm.Rd:60: Lost braces
    60 | can be found in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017} and
       |                          ^
checkRd: (-1) Lm.Rd:61: Lost braces
    61 | \bibcitet{tram::Hothorn:2018}.
       |          ^
prepare_Rd: ./man/Polr.Rd:60: unknown macro '\bibcitet'
prepare_Rd: ./man/Polr.Rd:61: unknown macro '\bibcitet'
checkRd: (-1) Polr.Rd:60: Lost braces
    60 | can be found in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017} and
       |                          ^
checkRd: (-1) Polr.Rd:61: Lost braces
    61 | \bibcitet{tram::Hothorn:2018}.
       |          ^
prepare_Rd: ./man/Survreg.Rd:66: unknown macro '\bibcitet'
prepare_Rd: ./man/Survreg.Rd:67: unknown macro '\bibcitet'
prepare_Rd: ./man/Survreg.Rd:68: unknown macro '\bibcitet'
checkRd: (-1) Survreg.Rd:66: Lost braces
    66 | can be found in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017},
       |                          ^
checkRd: (-1) Survreg.Rd:67: Lost braces
    67 | \bibcitet{tram::Siegfried:Tamasi:Hothorn:2026}, and
       |          ^
checkRd: (-1) Survreg.Rd:68: Lost braces
    68 | \bibcitet{tram::Hothorn:2018}.
       |          ^
prepare_Rd: ./man/mmlt.Rd:29: unknown macro '\bibcitet'
prepare_Rd: ./man/mmlt.Rd:31: unknown macro '\bibcitet'
prepare_Rd: ./man/mmlt.Rd:59: unknown macro '\bibcitet'
checkRd: (-1) mmlt.Rd:29: Lost braces
    29 | described by \bibcitet{tram::Klein:Hothorn:Barbanti:2020}. If \code{FALSE}, parameters can be
       |                       ^
checkRd: (-1) mmlt.Rd:31: Lost braces
    31 | \bibcitet{tram::Klein:Hothorn:Barbanti:2020}. Using \code{conditional = FALSE} with probit-only models
       |          ^
checkRd: (-1) mmlt.Rd:59: Lost braces
    59 |   as described by \bibcitet{tram::Klein:Hothorn:Barbanti:2020}. 
       |                            ^
prepare_Rd: ./man/mtram.Rd:43: unknown macro '\bibcitet'
checkRd: (-1) mtram.Rd:43: Lost braces
    43 |   \bibcitet{tram::Barbanti:Hothorn:2023} and examples are given in the \code{mtram} package vignette.
       |            ^
prepare_Rd: ./man/robust_score_test.Rd:60: unknown macro '\bibcitet'
checkRd: (-1) robust_score_test.Rd:60: Lost braces
    60 | see \bibcitet{tram::Kook:Saengkyongam:Lundborg:2024}.
       |              ^
prepare_Rd: ./man/score_test.Rd:45: unknown macro '\bibcitet'
checkRd: (-1) score_test.Rd:45: Lost braces
    45 |   Model scores are available from \bibcitet{tram::Hothorn:Moest:Buehlmann:2017}.
       |                                            ^
prepare_Rd: ./man/tram-methods.Rd:161: unknown macro '\bibcitet'
checkRd: (-1) tram-methods.Rd:161: Lost braces
   161 |   \bibcitet{tram::Sewak:Hothorn:2023}.
       |            ^
prepare_Rd: ./man/tram.Rd:156: unknown macro '\bibcitet'
prepare_Rd: ./man/tram.Rd:158: unknown macro '\bibcitet'
prepare_Rd: ./man/tram.Rd:159: unknown macro '\bibcitet'
checkRd: (-1) tram.Rd:156: Lost braces
   156 | is presented in \bibcitet{tram::Hothorn:Moest:Buehlmann:2017}, computational
       |                          ^
checkRd: (-1) tram.Rd:158: Lost braces
   158 | are discussed by \bibcitet{Hothorn:2018}. Location-scale transformation 
       |                           ^
checkRd: (-1) tram.Rd:159: Lost braces
   159 | models have been introduced by \bibcitet{tram::Siegfried:Kook:Hothorn:2023}.
       |                                         ^

tests

  Running ‘Coxph-Ex.R’ [10s/13s]
  Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
  Running ‘KaplanMeier-Ex.R’ [2s/3s]
  Running ‘PI_OVL-Ex.R’ [4s/5s]
  Running ‘Polr-Ex.R’ [10s/12s]
  Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
  Running ‘Survreg-Ex.R’ [4s/5s]
  Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
  Running ‘bugfixes.R’ [71s/87s]
  Running ‘intercepts-Ex.R’ [4s/5s]
  Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
  Running ‘mmlt-Ex.R’ [144s/191s]
  Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ...931c931
< [1] "Mean relative difference: 3.3"
---
> [1] TRUE
  Running ‘mmlt-interface.R’ [9s/12s]
  Running ‘mtram-Ex.R’ [10s/12s]
  Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ...63,64d62
< attr(,"class")
< [1] "vcmat_us" "matrix"   "array"   
  Running ‘stram-Ex.R’ [27s/35s]
  Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
Running the tests in ‘tests/mmlt-interface.R’ failed.
Complete output:
  > 
  > library("tram")
  Loading required package: mlt
  Loading required package: basefun
  Loading required package: variables
  Loading required package: mvtnorm
  > library("survival")
  > library("sandwich")
  > library("numDeriv")
  > library("mvtnorm")
  > 
  > ### check mmlt for wild model combinations and weights
  > 
  > set.seed(290875)
  > 
  > chk <- function(x, y, tol = 1e-2) stopifnot(all.equal(x, y, tol = tol))
  > 
  > N <- 100
  > J <- 3
  > 
  > ### weights
  > w <- as.double(sample(0:5, size = N, replace = TRUE))
  > ### X1, X2, X3 correlated
  > z <- matrix(rnorm(N * J), nrow = J)
  > L <- ltMatrices(runif(J * (J - 1) / 2))
  > y <- t(solve(standardize(L), z))
  > ### uncorrelated ordered
  > x <- sample(gl(5, N / 5, ordered = TRUE))
  > ### X3 right censored
  > e <- sample(c(TRUE, FALSE), size = N, replace = TRUE)
  > X3 <- exp(y[,3])
  > X3 <- Surv(X3, event = e)
  > d <- data.frame(y[,1:2], X3, x, e)
  > dw <- d[rep(1:nrow(d), w),,drop = FALSE]
  > idx <- sample(1:N, size = N / 2)
  > 
  > ### global options (speed-up estimation)
  > M <- 200
  > args <- list(type = "ghalton", M = M)
  > op <- mltoptim()	### no hessian
  > 
  > ### marginal models (use Lm to reduce number of parameters)
  > m1 <- Lm(X1 ~ 1, data = d)
  > m2 <- Lm(X2 ~ 1, data = d)
  > m3 <- Lm(X3 ~ 1, data = d)
  > m4 <- Polr(x ~ 1, data = d, method = "probit")
  > 
  > ### joint distribution of X1, X2 (continuous), X3 (continuous and
  > ### right-censored) and x (discrete)
  > m <- mmlt(m1, m2, m3, m4, data = d, args = args, optim = op)
  > l1 <- logLik(m)
  > ## check gradient
  > s1 <- -colSums(estfun(m))
  > s2 <- grad(function(parm) logLik(m, parm = parm), coef(m))
  > chk(s2, unname(s1))
  > L1 <- aperm(coef(m, type = "Lambda"), perm = c("X1", "X2", "X3", "x"))
  Error in aperm.ltMatrices(coef(m, type = "Lambda"), perm = c("X1", "X2",  : 
    Cannot permute objects of class ltMatrices, 
            consider calling as.chol() or as.invchol() first
  Calls: aperm -> aperm.ltMatrices
  Execution halted

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