CRAN Package Check Results for Maintainer Torsten Hothorn <Torsten.Hothorn at R-project.org>

CRAN Package Check Results for Maintainer ‘Torsten Hothorn <Torsten.Hothorn at R-project.org>’

Last updated on 2024-05-28 12:57:02 CEST.

Package	ERROR	WARN	NOTE	OK
ATR				12
basefun				12
coin				12
exactRankTests				12
HSAUR				12
HSAUR2				12
HSAUR3				12
inum				12
ipred				12
libcoin				12
maxstat				12
mboost				13
mlt				13
mlt.docreg	1			12
modeltools				12
multcomp				12
MVA				12
mvtnorm				13
party				13
partykit				12
tbm				13
TH.data		1	7	4
tram				13
trtf				12
variables				12

Package ATR

Current CRAN status: OK: 12

Package basefun

Current CRAN status: OK: 12

Package coin

Current CRAN status: OK: 12

Package HSAUR

Current CRAN status: OK: 12

Package HSAUR2

Current CRAN status: OK: 12

Package HSAUR3

Current CRAN status: OK: 12

Package inum

Current CRAN status: OK: 12

Package ipred

Current CRAN status: OK: 12

Package libcoin

Current CRAN status: OK: 12

Package maxstat

Current CRAN status: OK: 12

Package mboost

Current CRAN status: OK: 13

Package mlt

Current CRAN status: OK: 13

Version: 1.1-8
Check: tests
Result: ERROR Running ‘AFT-Ex.R’ [5s/8s] Comparing ‘AFT-Ex.Rout’ to ‘AFT-Ex.Rout.save’ ... OK Running ‘GBSG2.R’ [3s/5s] Running ‘KM-Ex.R’ [3s/5s] Comparing ‘KM-Ex.Rout’ to ‘KM-Ex.Rout.save’ ... OK Running ‘faithful.R’ [7s/8s] Comparing ‘faithful.Rout’ to ‘faithful.Rout.save’ ... OK Running ‘orm-Ex.R’ [16s/23s] Comparing ‘orm-Ex.Rout’ to ‘orm-Ex.Rout.save’ ... OK Running ‘timedep_covar.R’ [11s/16s] Running ‘truncreg-Ex.R’ [4s/5s] Comparing ‘truncreg-Ex.Rout’ to ‘truncreg-Ex.Rout.save’ ... OK Running the tests in ‘tests/timedep_covar.R’ failed. Complete output: > > library("mlt") Loading required package: basefun Loading required package: variables > library("survival") > library("flexsurv") > > chk <- function(x, y, ...) { + + ret <- all.equal(x, y, ...) + if (isTRUE(ret)) return(ret) + print(ret) + return(TRUE) + } > tol <- .001 > > ### right-censored veteran data > ### exponential model > fit1 <- coxph(Surv(time, status) ~ karno + age + trt, veteran) > fit2 <- survreg(Surv(time, status) ~ karno + age + trt, veteran, dist = "exponential") > fit3 <- flexsurvreg(Surv(time, status) ~ karno + age + trt, data= veteran, dist = "exponential") > > veteran$ytime <- with(veteran, Surv(time, status)) > dy <- numeric_var("ytime", support = c(0.1, 1000)) > by <- log_basis(dy, ui = "increasing") > m <- mlt(ctm(by, shift = ~ karno + age + trt, data = veteran, todistr = "MinExtr"), + data = veteran, fixed = c("log(ytime)" = 1)) > > stopifnot(chk(fit3$logliki, m$logliki(coef(m)[-2], weights(m)), + tol = tol, check.attributes = FALSE)) > > stopifnot(chk(logLik(fit2), logLik(m), tol = tol)) > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, + check.attributes = FALSE)) > > ### Weibull model > fit2 <- survreg(Surv(time, status) ~ karno + age + trt, veteran, dist = "weibull") > fit3 <- flexsurvreg(Surv(time, status) ~ karno + age + trt, data= veteran, dist = "weibull") > > veteran$ytime <- with(veteran, Surv(time, status)) > dy <- numeric_var("ytime", support = c(0.1, 1000)) > # by <- Bernstein_basis(dy, order = 10, ui = "increasing") > by <- log_basis(dy, ui = "increasing") > m <- mlt(ctm(by, shift = ~ karno + age + trt, data = veteran, todistr = "MinExtr"), + data = veteran) > > stopifnot(chk(fit3$logliki, m$logliki(coef(m), weights(m)), + tol = tol, check.attributes = FALSE)) > > stopifnot(chk(logLik(fit2), logLik(m), tol = tol)) > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, + check.attributes = FALSE)) > > ### now with time-dependent covariates > vet2 <- survSplit(Surv(time, status) ~., veteran, + cut=c(60, 120), episode ="timegroup") > vet2$timegroup <- factor(vet2$timegroup) > vet2$ytime <- with(vet2, Surv(tstart, time, status)) > > ## exponential model > suppressWarnings(fit3 <- flexsurvreg(Surv(tstart, time, status) ~ + karno + karno:timegroup + age + trt, data= vet2, dist = "exponential")) > m <- mlt(ctm(by, shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"), + data = vet2, fixed = c("log(ytime)" = 1)) > > stopifnot(chk(fit3$logliki, m$logliki(coef(m)[-2], weights(m)), + tol = tol, check.attributes = FALSE)) > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, check.attributes = FALSE)) > > ### Weibull model > fit3 <- flexsurvreg(Surv(tstart, time, status) ~ karno + karno:timegroup + + age + trt, data= vet2, dist = "weibull") > m <- mlt(ctm(by, shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"), + data = vet2, scale = TRUE) > > stopifnot(chk(fit3$logliki, m$logliki(coef(m), weights(m)), + tol = tol, check.attributes = FALSE)) > stopifnot(chk(logLik(fit3), logLik(m), tol = tol, check.attributes = FALSE)) > > ## Cox model, see ?survival::survSplit > fit1 <- coxph(Surv(tstart, time, status) ~ karno + karno:strata(timegroup) + + age + trt, data= vet2) > > ### refit this model using mlt > btg <- as.basis(vet2$timegroup) > by <- Bernstein_basis(dy, order = 3, ui = "increasing") > m <- mlt(ctm(by, interacting = btg, + shift = ~ karno + karno:timegroup + age + trt, data = vet2, todistr = "MinExtr"), + data = vet2, scale = TRUE) Error in optim(par = par, fn = fun, gr = gradient, control = control.optim, : non-finite value supplied by optim Error in ret$convergence : $ operator is invalid for atomic vectors Error in ret$par : $ operator is invalid for atomic vectors Calls: mlt -> do.call -> .mlt_fit -> <Anonymous> Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Package modeltools

Current CRAN status: OK: 12

Package multcomp

Current CRAN status: OK: 12

Package MVA

Current CRAN status: OK: 12

Package mvtnorm

Current CRAN status: OK: 13

Package party

Current CRAN status: OK: 13

Package partykit

Current CRAN status: OK: 12

Package tbm

Current CRAN status: OK: 13

Package TH.data

Current CRAN status: WARN: 1, NOTE: 7, OK: 4

Version: 1.1-2
Check: re-building of vignette outputs
Result: WARN Error(s) in re-building vignettes: ... --- re-building ‘blood_loss_report.Rnw’ using knitr ** Processing: figure/MBL-Colr-pre-1.png 1800x1500 pixels, 4x8 bits/pixel, RGB+alpha Input IDAT size = 66117 bytes Input file size = 66291 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 58657 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 58657 Output IDAT size = 58657 bytes (7460 bytes decrease) Output file size = 58735 bytes (7556 bytes = 11.40% decrease) warning: solve(): system is singular (rcond: 3.13991e-19); attempting approx solution ** Processing: figure/dr-plot-1.png 2100x2100 pixels, 4x8 bits/pixel, RGB+alpha Input IDAT size = 146629 bytes Input file size = 146911 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 132252 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 132252 Output IDAT size = 132252 bytes (14377 bytes decrease) Output file size = 132330 bytes (14581 bytes = 9.93% decrease) ** Processing: figure/MBL-xtree-1.png 3675x1350 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 83262 bytes Input file size = 84240 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 72531 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 72125 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 72125 Output IDAT size = 72125 bytes (11137 bytes decrease) Output file size = 72203 bytes (12037 bytes = 14.29% decrease) ** Processing: figure/F13-trt-1.png 2100x2100 pixels, 3x8 bits/pixel, RGB Input IDAT size = 186358 bytes Input file size = 186700 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 181068 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 181068 Output IDAT size = 181068 bytes (5290 bytes decrease) Output file size = 181146 bytes (5554 bytes = 2.97% decrease) ** Processing: figure/MBL-ztree-1.png 3750x1350 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 61052 bytes Input file size = 61994 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 53589 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 53160 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 53160 Output IDAT size = 53160 bytes (7892 bytes decrease) Output file size = 53238 bytes (8756 bytes = 14.12% decrease) Error: processing vignette 'blood_loss_report.Rnw' failed with diagnostics: Running 'texi2dvi' on 'blood_loss_report.tex' failed. LaTeX errors: ! Undefined control sequence. l.96 \hlkwd{library}\hldef {(}\hlsng{"knitr"}\hldef{)} ? ! Emergency stop. ! Emergency stop. l.96 End of file on the terminal! ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘blood_loss_report.Rnw’ SUMMARY: processing the following file failed: ‘blood_loss_report.Rnw’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1-2
Check: installed package size
Result: NOTE installed size is 9.0Mb sub-directories of 1Mb or more: data 1.1Mb rda 7.1Mb Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package tram

Current CRAN status: OK: 13

Package trtf

Current CRAN status: OK: 12

Package variables

Current CRAN status: OK: 12