CRAN Package Check Results for Package tramnet

Last updated on 2026-03-06 13:49:58 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.0-10	17.56	326.87	344.43	OK
r-devel-linux-x86_64-debian-gcc	0.0-10	13.65	206.81	220.46	OK
r-devel-linux-x86_64-fedora-clang	0.0-10	23.00	132.02	155.02	ERROR
r-devel-linux-x86_64-fedora-gcc	0.0-10	21.00	164.14	185.14	ERROR
r-devel-macos-arm64	0.0-10	5.00	88.00	93.00	OK
r-devel-windows-x86_64	0.0-10	20.00	314.00	334.00	OK
r-patched-linux-x86_64	0.0-10	17.24	310.95	328.19	OK
r-release-linux-x86_64	0.0-10	16.75	312.28	329.03	OK
r-release-macos-arm64	0.0-9	7.00	71.00	78.00	OK
r-release-macos-x86_64	0.0-10	13.00	335.00	348.00	OK
r-release-windows-x86_64	0.0-10	20.00	309.00	329.00	OK
r-oldrel-macos-arm64	0.0-10	5.00	77.00	82.00	WARN
r-oldrel-macos-x86_64	0.0-10	13.00	396.00	409.00	OK
r-oldrel-windows-x86_64	0.0-10	27.00	418.00	445.00	OK

Check Details

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. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.0-10
Check: tests
Result: ERROR Running ‘Colr-pen.R’ 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.0-10
Check: re-building of vignette outputs
Result: WARN Error(s) in re-building vignettes: --- re-building ‘tramnet.Rnw’ using knitr warning: solve(): system is singular (rcond: 3.22591e-19); attempting approx solution warning: solve(): system is singular (rcond: 3.22591e-19); attempting approx solution warning: solve(): system is singular (rcond: 3.22591e-19); attempting approx solution warning: solve(): system is singular (rcond: 3.22591e-19); attempting approx solution warning: solve(): system is singular (rcond: 3.22591e-19); attempting approx solution warning: solve(): system is singular (rcond: 7.74539e-19); attempting approx solution warning: solve(): system is singular (rcond: 7.74539e-19); attempting approx solution warning: solve(): system is singular (rcond: 7.74539e-19); attempting approx solution warning: solve(): system is singular (rcond: 7.74539e-19); attempting approx solution warning: solve(): system is singular (rcond: 7.74539e-19); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution warning: solve(): system is singular (rcond: 8.10808e-18); attempting approx solution Error: processing vignette 'tramnet.Rnw' failed with diagnostics: Running 'texi2dvi' on 'tramnet.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.46 ^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘tramnet.Rnw’ SUMMARY: processing the following file failed: ‘tramnet.Rnw’ Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-macos-arm64