Last updated on 2025-05-22 15:51:52 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 6.53 | 134.08 | 140.61 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 4.53 | 89.91 | 94.44 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 219.79 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 224.53 | NOTE | |||
| r-devel-windows-x86_64 | 1.1.0 | 9.00 | 263.00 | 272.00 | NOTE | |
| r-patched-linux-x86_64 | 1.1.0 | 5.98 | 113.96 | 119.94 | ERROR | |
| r-release-linux-x86_64 | 1.1.0 | 5.89 | 127.56 | 133.45 | NOTE | |
| r-release-macos-arm64 | 1.1.0 | 130.00 | NOTE | |||
| r-release-macos-x86_64 | 1.1.0 | 349.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.0 | 9.00 | 261.00 | 270.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.1.0 | 133.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.1.0 | 244.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 11.00 | 383.00 | 394.00 | OK |
Version: 1.1.0
Check: DESCRIPTION meta-information
Result: 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’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
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
Flavor: r-patched-linux-x86_64