Last updated on 2026-03-10 21:53:59 CET.
| Package | ERROR | WARN | OK |
|---|---|---|---|
| comets | 14 | ||
| tramicp | 14 | ||
| tramnet | 2 | 12 | |
| tramvs | 2 | 2 | 10 |
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: ERROR: 2, OK: 12
Version: 0.0-99
Check: tests
Result: ERROR
Running ‘Colr-pen.R’ [14s/18s]
Running the tests in ‘tests/Colr-pen.R’ failed.
Complete output:
> # Tests for COLR models
>
> set.seed(0)
>
> ## Depencies
> ## IGNORE_RDIFF_BEGIN
> library("tramnet")
Loading required package: tram
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
Loading required package: CVXR
Attaching package: 'CVXR'
The following objects are masked from 'package:stats':
power, sd, var
The following objects are masked from 'package:base':
norm, outer
Loading required package: mlrMBO
Loading required package: mlr
Loading required package: ParamHelpers
Loading required package: smoof
Loading required package: checkmate
> library("sandwich")
>
> ## IGNORE_RDIFF_END
> old <- options(digits = 3)
>
> if (require("survival") & require("TH.data")) {
+ ## Exact and Right censored
+ data("GBSG2", package = "TH.data")
+ GBSG2$surv <- with(GBSG2, Surv(time, cens))
+ x <- matrix(1 * (GBSG2$horTh == "yes"), ncol = 1)
+ colnames(x) <- "horTh"
+
+ yCOLR <- Colr(surv ~ 1, data = GBSG2, log_first = TRUE, order = 10, support = c(1e-12, max(GBSG2$time)))
+ modCOLR <- tramnet(yCOLR, x, lambda = 0, alpha = 0)
+ yCOLRb <- Colr(surv ~ horTh, data = GBSG2, log_first = TRUE, order = 10)
+ print(max(abs(coef(yCOLRb, with_baseline = FALSE) -
+ coef(modCOLR, with_baseline = FALSE))))
+ print(logLik(yCOLRb))
+ print(logLik(modCOLR))
+ print(-modCOLR$result$value)
+ print(logLik(modCOLR, newdata = tramnet:::.get_tramnet_data(modCOLR)[1:10, ]))
+
+ ## methods
+ print(coef(modCOLR, tol = 0, with_baseline = TRUE))
+ print(logLik(modCOLR))
+ print(c(resid(modCOLR)[1:10]))
+ print(predict(modCOLR, type = "distribution", q = 1)[, 1:10])
+ print(predict(modCOLR, type = "quantile", prob = 0.5)[, 1:10])
+ print.default(head(simulate(modCOLR)))
+ print(as.data.frame(head(estfun(modCOLR))))
+ plot(modCOLR, type = "survivor")
+ plot(modCOLR, type = "density", K = 120)
+ print(modCOLR)
+ }
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:CVXR':
huber
Attaching package: 'TH.data'
The following object is masked from 'package:MASS':
geyser
Error in Rmosek::mosek(prob, opts) :
Unknown exported object to be built. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
Calls: tramnet ... method(solve_via_data, CVXR::Mosek_Solver) -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0-99
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘tramnet.Rnw’ using knitr
Quitting from tramnet.Rnw:936-941 [BH_Linear2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `Rmosek::mosek()`:
! Unknown exported object to be built. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
---
Backtrace:
x
1. \-tramnet::tramnet(m0, x = x, alpha = 0, lambda = 0)
2. \-CVXR::psolve(prob, ...)
3. \-CVXR::solve_via_data(...)
4. +-S7::S7_dispatch()
5. \-CVXR (local) `method(solve_via_data, CVXR::SolvingChain)`(...)
6. \-CVXR::solve_via_data(...)
7. +-S7::S7_dispatch()
8. \-CVXR (local) `method(solve_via_data, CVXR::Mosek_Solver)`(...)
9. \-Rmosek::mosek(prob, opts)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tramnet.Rnw' failed with diagnostics:
Unknown exported object to be built. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
--- failed re-building ‘tramnet.Rnw’
SUMMARY: processing the following file failed:
‘tramnet.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0-10
Check: Rd cross-references
Result: WARN
Missing link(s) in Rd file 'tramnet.Rd':
'[CVXR]{solve}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Flavor: r-release-windows-x86_64
Version: 0.0-10
Check: tests
Result: ERROR
Running 'Colr-pen.R' [4s]
Running the tests in 'tests/Colr-pen.R' failed.
Complete output:
> # Tests for COLR models
>
> set.seed(0)
>
> ## Depencies
> ## IGNORE_RDIFF_BEGIN
> library("tramnet")
Loading required package: tram
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
Loading required package: CVXR
Attaching package: 'CVXR'
The following objects are masked from 'package:stats':
power, sd, var
The following objects are masked from 'package:base':
norm, outer
Loading required package: mlrMBO
Loading required package: mlr
Loading required package: ParamHelpers
Loading required package: smoof
Loading required package: checkmate
> library("sandwich")
>
> ## IGNORE_RDIFF_END
> old <- options(digits = 3)
>
> if (require("survival") & require("TH.data")) {
+ ## Exact and Right censored
+ data("GBSG2", package = "TH.data")
+ GBSG2$surv <- with(GBSG2, Surv(time, cens))
+ x <- matrix(1 * (GBSG2$horTh == "yes"), ncol = 1)
+ colnames(x) <- "horTh"
+
+ yCOLR <- Colr(surv ~ 1, data = GBSG2, log_first = TRUE, order = 10, support = c(1e-12, max(GBSG2$time)))
+ modCOLR <- tramnet(yCOLR, x, lambda = 0, alpha = 0)
+ yCOLRb <- Colr(surv ~ horTh, data = GBSG2, log_first = TRUE, order = 10)
+ print(max(abs(coef(yCOLRb, with_baseline = FALSE) -
+ coef(modCOLR, with_baseline = FALSE))))
+ print(logLik(yCOLRb))
+ print(logLik(modCOLR))
+ print(-modCOLR$result$value)
+ print(logLik(modCOLR, newdata = tramnet:::.get_tramnet_data(modCOLR)[1:10, ]))
+
+ ## methods
+ print(coef(modCOLR, tol = 0, with_baseline = TRUE))
+ print(logLik(modCOLR))
+ print(c(resid(modCOLR)[1:10]))
+ print(predict(modCOLR, type = "distribution", q = 1)[, 1:10])
+ print(predict(modCOLR, type = "quantile", prob = 0.5)[, 1:10])
+ print.default(head(simulate(modCOLR)))
+ print(as.data.frame(head(estfun(modCOLR))))
+ plot(modCOLR, type = "survivor")
+ plot(modCOLR, type = "density", K = 120)
+ print(modCOLR)
+ }
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:CVXR':
huber
Attaching package: 'TH.data'
The following object is masked from 'package:MASS':
geyser
Error in as.vector(x, mode) :
cannot coerce type 'object' to vector of type 'any'
Calls: tramnet ... <Anonymous> -> as.matrix.default -> array -> as.vector
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.0-10
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'tramnet.Rnw' using knitr
Quitting from tramnet.Rnw:936-941 [BH_Linear2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `as.vector()`:
! cannot coerce type 'object' to vector of type 'any'
---
Backtrace:
x
1. \-tramnet::tramnet(m0, x = x, alpha = 0, lambda = 0)
2. \-tramnet:::.tramnet_objective(...)
3. +-trdat$const$ui %*% theta
4. \-trdat$const$ui %*% theta
5. +-(if (length(dim(y)) == 2L) as.matrix else as.vector)(y)
6. +-(if (length(dim(y)) == 2L) as.matrix else as.vector)(y)
7. \-base::as.matrix.default(y)
8. \-base::array(...)
9. \-base::as.vector(data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tramnet.Rnw' failed with diagnostics:
cannot coerce type 'object' to vector of type 'any'
--- failed re-building 'tramnet.Rnw'
SUMMARY: processing the following file failed:
'tramnet.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Current CRAN status: ERROR: 2, WARN: 2, OK: 10
Version: 0.0-8
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘tramvs.Rnw’ using knitr
Quitting from tramvs.Rnw:385-390 [profile]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `Rmosek::mosek()`:
! Unknown exported object to be built. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
---
Backtrace:
x
1. \-tramnet::tramnet(m0, X, lambda = 0, alpha = 1)
2. \-CVXR::psolve(prob, ...)
3. \-CVXR::solve_via_data(...)
4. +-S7::S7_dispatch()
5. \-CVXR (local) `method(solve_via_data, CVXR::SolvingChain)`(...)
6. \-CVXR::solve_via_data(...)
7. +-S7::S7_dispatch()
8. \-CVXR (local) `method(solve_via_data, CVXR::Mosek_Solver)`(...)
9. \-Rmosek::mosek(prob, opts)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tramvs.Rnw' failed with diagnostics:
Unknown exported object to be built. Please use 'Rmosek::mosek_attachbuilder' to complete the installation of Rmosek.
--- failed re-building ‘tramvs.Rnw’
SUMMARY: processing the following file failed:
‘tramvs.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0-8
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘tramvs.Rnw’ using knitr
Error: processing vignette 'tramvs.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tramvs.tex' failed.
LaTeX errors:
! LaTeX Error: File `accents.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.3 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘tramvs.Rnw’
SUMMARY: processing the following file failed:
‘tramvs.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64
Version: 0.0-8
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'tramvs.Rnw' using knitr
Quitting from tramvs.Rnw:385-390 [profile]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `as.vector()`:
! cannot coerce type 'object' to vector of type 'any'
---
Backtrace:
x
1. \-tramnet::tramnet(m0, X, lambda = 0, alpha = 1)
2. \-tramnet:::.tramnet_objective(...)
3. +-trdat$const$ui %*% theta
4. \-trdat$const$ui %*% theta
5. +-(if (length(dim(y)) == 2L) as.matrix else as.vector)(y)
6. +-(if (length(dim(y)) == 2L) as.matrix else as.vector)(y)
7. \-base::as.matrix.default(y)
8. \-base::array(...)
9. \-base::as.vector(data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tramvs.Rnw' failed with diagnostics:
cannot coerce type 'object' to vector of type 'any'
--- failed re-building 'tramvs.Rnw'
SUMMARY: processing the following file failed:
'tramvs.Rnw'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.