• using R version 4.6.1 Patched (2026-06-28 r90199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.3.0-1) 15.3.0     GNU Fortran (Debian 15.3.0-1) 15.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-07-01 15:26:52 UTC
• checking for file ‘mets/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘mets’ version ‘1.3.10’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘mets’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-15 (Debian 15.3.0-1) 15.3.0’
• used Fortran compiler: ‘GNU Fortran (Debian 15.3.0-1) 15.3.0’
• used C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
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• checking loading without being on the library search path ... [2s/3s] OK
• checking whether startup messages can be suppressed ... [2s/3s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [130s/162s] OK
• checking Rd files ... [2s/3s] OK
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• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
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• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
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• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
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• checking compiled code ... OK
• checking usage of KIND in Fortran files ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [47s/64s] ERROR Running examples in ‘mets-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: test_marginalMean > ### Title: Pepe-Mori Test for Marginal Mean Comparison > ### Aliases: test_marginalMean > > ### ** Examples > > data(bmt,package="mets") > bmt$time <- bmt$time+runif(nrow(bmt))*0.01 > bmt$id <- 1:nrow(bmt) > dcut(bmt) <- age.f~age > > fg=cifregFG(Event(time,cause)~tcell,data=bmt,cause=1) > > ## computing tests for difference for CIF > pmt <- test_marginalMean(Event(time,cause)~strata(tcell)+cluster(id),data=bmt,cause=1, + death.code=1:2,death.code.prop=2,cens.code=0,time=40) Warning in check_ic_mean_zero(ic_theta) :   IC does not have mean zero (max |mean|/rms = 0.11). Using lava.options(check.ic = FALSE) disables the warning globally. Warning in estimate.default(NULL, ...) :   The 'null', 'contrast', 'type', 'back.transform', 'level' and 'var.adj' arguments of estimate.default() are deprecated and will be removed in version 1.9.3. Use summary(estimate(...), null=, contrast=, type=, transform=,level=, df=, var.adj=) instead. Warning in estimate.default(pepe.mori, null = 0) :   The 'null', 'contrast', 'type', 'back.transform', 'level' and 'var.adj' arguments of estimate.default() are deprecated and will be removed in version 1.9.3. Use summary(estimate(...), null=, contrast=, type=, transform=,level=, df=, var.adj=) instead. Warning in estimate.default(b, ...) :   The 'null', 'contrast', 'type', 'back.transform', 'level' and 'var.adj' arguments of estimate.default() are deprecated and will be removed in version 1.9.3. Use summary(estimate(...), null=, contrast=, type=, transform=,level=, df=, var.adj=) instead. > summary(pmt) Error in dimnames(x) <- dn :   length of 'dimnames' [1] not equal to array extent Calls: summary -> summary.marginalTest -> rownames<- Execution halted
• checking for unstated dependencies in ‘demo’ ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [19s/25s] OK   Running ‘tinytest.R’ [19s/25s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [192s/241s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘basic-dutils.Rmd’ using rmarkdown --- finished re-building ‘basic-dutils.Rmd’ --- re-building ‘binomial-family.Rmd’ using rmarkdown --- finished re-building ‘binomial-family.Rmd’ --- re-building ‘binomial-twin.Rmd’ using rmarkdown --- finished re-building ‘binomial-twin.Rmd’ --- re-building ‘binreg-TRS.Rmd’ using rmarkdown --- finished re-building ‘binreg-TRS.Rmd’ --- re-building ‘binreg-ate.Rmd’ using rmarkdown --- finished re-building ‘binreg-ate.Rmd’ --- re-building ‘binreg.Rmd’ using rmarkdown --- finished re-building ‘binreg.Rmd’ --- re-building ‘cifreg.Rmd’ using rmarkdown --- finished re-building ‘cifreg.Rmd’ --- re-building ‘cooking-survival-data.Rmd’ using rmarkdown --- finished re-building ‘cooking-survival-data.Rmd’ --- re-building ‘cumulative-cost.Rmd’ using rmarkdown --- finished re-building ‘cumulative-cost.Rmd’ --- re-building ‘glm-utility.Rmd’ using rmarkdown --- finished re-building ‘glm-utility.Rmd’ --- re-building ‘haplo-discrete-ttp.Rmd’ using rmarkdown --- finished re-building ‘haplo-discrete-ttp.Rmd’ --- re-building ‘interval-discrete-survival.Rmd’ using rmarkdown --- finished re-building ‘interval-discrete-survival.Rmd’ --- re-building ‘marginal-cox.Rmd’ using rmarkdown --- finished re-building ‘marginal-cox.Rmd’ --- re-building ‘mediation-survival.Rmd’ using rmarkdown --- finished re-building ‘mediation-survival.Rmd’ --- re-building ‘phreg_rct.Rmd’ using rmarkdown --- finished re-building ‘phreg_rct.Rmd’ --- re-building ‘quantitative-twin.Rmd’ using rmarkdown --- finished re-building ‘quantitative-twin.Rmd’ --- re-building ‘recurrent-events.Rmd’ using rmarkdown Quitting from recurrent-events.Rmd:281-289 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `dimnames(x) <- dn`: ! length of 'dimnames' [1] not equal to array extent --- Backtrace:      ▆   1. ├─base::withVisible(knit_print(x, ...))   2. ├─knitr::knit_print(x, ...)   3. └─knitr:::knit_print.default(x, ...)   4. └─knitr::normal_print(x)   5. ├─base::print(x)   6. └─mets:::print.marginalTest(x)   7. ├─base::print(summary(x), ...)   8. ├─base::summary(x)   9. └─mets:::summary.marginalTest(x)  10. └─base::`rownames<-`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'recurrent-events.Rmd' failed with diagnostics: length of 'dimnames' [1] not equal to array extent --- failed re-building ‘recurrent-events.Rmd’ --- re-building ‘rmst-ate.Rmd’ using rmarkdown --- finished re-building ‘rmst-ate.Rmd’ --- re-building ‘survival-ate.Rmd’ using rmarkdown --- finished re-building ‘survival-ate.Rmd’ --- re-building ‘time-to-event-family-studies-arev.Rmd’ using rmarkdown --- finished re-building ‘time-to-event-family-studies-arev.Rmd’ --- re-building ‘twostage-survival.Rmd’ using rmarkdown --- finished re-building ‘twostage-survival.Rmd’ --- re-building ‘while-alive.Rmd’ using rmarkdown --- finished re-building ‘while-alive.Rmd’ SUMMARY: processing the following file failed:   ‘recurrent-events.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [14s/21s] OK
• checking HTML version of manual ... [16s/23s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs