* using log directory 'd:/Rcompile/CRANpkg/local/4.6/EBASE.Rcheck'
* using R version 4.6.0 (2026-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-05-28 08:06:33 UTC
* checking for file 'EBASE/DESCRIPTION' ... OK
* this is package 'EBASE' version '1.1.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'EBASE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ebase_plot.R' 'ebase_prep.R'
* 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
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] 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 ... [4s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* 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] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [18s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [72s] OK
  Running 'testthat.R' [72s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [87s] ERROR
Error(s) in re-building vignettes:
--- re-building 'EBASE.Rmd' using rmarkdown

Quitting from EBASE.Rmd:203-210 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `{
    dat.sub <- dat[dat$grp == i, ]
    num.measurements <- nrow(dat.sub)
    DO_obs <- dat.sub$DO_obs
    PAR <- dat.sub$PAR
    DO_sat <- dat.sub$DO_sat
    sc <- dat.sub$sc
    Z <- dat.sub$Z
    U10 <- dat.sub$WSpd
    DO_start <- DO_obs[1]
    if (doave) DO_start <- mean(DO_obs)
    dat.list <- list("num.measurements", "nstepd", "interval", "aprior", "rprior",
      "bprior", "bmax", "DO_obs", "PAR", "DO_sat", "Z", "sc", "U10", "DO_start")
    params <- c("ats", "bts", "gppts", "erts", "gets", "nemts", "DO_mod")
    metabfit <- do.call(jags.parallel, list(data = dat.list, parameters.to.save = params,
      model.file = mod_in, n.chains = n.chains, n.iter = n.iter, n.burnin = n.burnin,
      n.thin = n.thin, n.cluster = n.chains, DIC = TRUE, jags.seed = 123, digits = 5))
    metabfit <- metab_update(metabfit, update.chains, n.iter)
    srf <- metabfit$BUGSoutput$summary[, 8]
    Rhat.test <- ifelse(any(srf > 1.1, na.rm = TRUE) == TRUE, "Check convergence",
    "Fine")
    cred <- data.frame(metabfit$BUGSoutput$summary)
    cred$var <- row.names(cred)
    cred$var <- gsub("\\[|\\]|\\d+", "", cred$var)
    result <- data.frame(Date = dat.sub$Date, grp = dat.sub$grp, Z = Z, DO_obs = dat.sub$
      DO_obs, DO_mod = metabfit$BUGSoutput$mean$DO_mod, DO_modlo = cred[cred$
    var == "DO_mod", "X2.5."], DO_modhi = cred[cred$var == "DO_mod", "X97.5."],
    DateTimeStamp = dat.sub$DateTimeStamp, ats = c(NA, metabfit$BUGSoutput$mean$
      ats), atslo = c(NA, cred[cred$var == "ats", "X2.5."]), atshi = c(NA, cred[
      cred$var == "ats", "X97.5."]), bts = c(NA, metabfit$BUGSoutput$mean$bts),
    btslo = c(NA, cred[cred$var == "bts", "X2.5."]), btshi = c(NA, cred[cred$
    var == "bts", "X97.5."]), gppts = c(NA, metabfit$BUGSoutput$mean$gppts),
    gpptslo = c(NA, cred[cred$var == "gppts", "X2.5."]), gpptshi = c(NA, cred[
      cred$var == "gppts", "X97.5."]), erts = c(NA, metabfit$BUGSoutput$mean$erts),
    ertslo = c(NA, cred[cred$var == "erts", "X2.5."]), ertshi = c(NA, cred[cred$
      var == "erts", "X97.5."]), nemts = c(NA, metabfit$BUGSoutput$mean$nemts),
    nemtslo = c(NA, cred[cred$var == "nemts", "X2.5."]), nemtshi = c(NA, cred[
      cred$var == "nemts", "X97.5."]), gets = c(NA, metabfit$BUGSoutput$mean$gets),
    getslo = c(NA, cred[cred$var == "gets", "X2.5."]), getshi = c(NA, cred[cred$
      var == "gets", "X97.5."]), dDO = c(NA, diff(metabfit$BUGSoutput$mean$DO_mod)),
    converge = Rhat.test)
    rsq <- lm(DO_mod ~ DO_obs, data = result) %>% summary() %>% .$r.squared
    result$rsq <- rsq
    return(result)
  }`:
! task 2 failed - "creation of server socket failed: port 11751 cannot be opened"
---
Backtrace:
    ▆
 1. └─EBASE::ebase(...)
 2.   └─... %dopar% ...
 3.     └─e$fun(obj, substitute(ex), parent.frame(), e$data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'EBASE.Rmd' failed with diagnostics:
task 2 failed - "creation of server socket failed: port 11751 cannot be opened"
--- failed re-building 'EBASE.Rmd'

SUMMARY: processing the following file failed:
  'EBASE.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [5s] OK
* DONE
Status: 1 ERROR, 1 NOTE