Error(s) in re-building vignettes:
  ...
--- re-building ‘EBASE.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EBASE.Rcheck/vign_test/EBASE/vignettes/EBASE_files/figure-html/unnamed-chunk-5-1.png
864x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 59280 bytes
Input file size = 59442 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 46509
  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 = 46509

Output IDAT size = 46509 bytes (12771 bytes decrease)
Output file size = 46587 bytes (12855 bytes = 21.63% decrease)

** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EBASE.Rcheck/vign_test/EBASE/vignettes/EBASE_files/figure-html/unnamed-chunk-6-1.png
864x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21603 bytes
Input file size = 21705 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 17735
  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 = 17735

Output IDAT size = 17735 bytes (3868 bytes decrease)
Output file size = 17813 bytes (3892 bytes = 17.93% decrease)

** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/EBASE.Rcheck/vign_test/EBASE/vignettes/EBASE_files/figure-html/unnamed-chunk-7-1.png
864x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 56003 bytes
Input file size = 56153 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 43799
  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 = 43799

Output IDAT size = 43799 bytes (12204 bytes decrease)
Output file size = 43877 bytes (12276 bytes = 21.86% decrease)


Quitting from EBASE.Rmd:107-116 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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$rsq <- rsq
    return(result)
  }`:
! task 2 failed - "creation of server socket failed: port 11301 cannot be opened"
---
Backtrace:
    ▆
 1. └─EBASE::ebase(dat, interval = 900, Z = 1.85, n.chains = 2)
 2.   └─... %dopar% ...
 3.     └─e$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 11301 cannot be opened"
--- failed re-building ‘EBASE.Rmd’

SUMMARY: processing the following file failed:
  ‘EBASE.Rmd’

Error: Vignette re-building failed.
Execution halted