Error(s) in re-building vignettes:
--- re-building 'create_run_read.Rmd' using rmarkdown
trying URL 'https://github.com/osmose-model/osmose/raw/master/data-raw/gog.zip'
Content type 'application/zip' length 3912708 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

trying URL 'https://github.com/osmose-model/osmose/raw/master/inst/java/lib.zip'
Quitting from lines 103-105 (create_run_read.Rmd) 
Error: processing vignette 'create_run_read.Rmd' failed with diagnostics:
cannot open URL 'https://github.com/osmose-model/osmose/raw/master/inst/java/lib.zip'
--- failed re-building 'create_run_read.Rmd'

--- re-building 'plot_method.Rmd' using rmarkdown
trying URL 'https://github.com/osmose-model/osmose/raw/master/data-raw/gog.zip'
Content type 'application/zip' length 3912708 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

trying URL 'https://github.com/osmose-model/osmose/raw/master/inst/java/lib.zip'
Content type 'application/zip' length 26000983 bytes (24.8 MB)
==================================================
downloaded 24.8 MB

trying URL 'https://github.com/osmose-model/osmose/raw/master/inst/java/osmose_3.3.3.zip'
Content type 'application/zip' length 194319 bytes (189 KB)
==================================================
downloaded 189 KB

Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in plot.window(xlim, ylim, log = log, ...) :
  "ci" is not a graphical parameter
Warning in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty = axis.lty,  :
  "ci" is not a graphical parameter
Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  "ci" is not a graphical parameter
--- finished re-building 'plot_method.Rmd'

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

Error: Vignette re-building failed.
Execution halted