## CRAN Package Check Results for Maintainer ‘Karline Soetaert <Karline.Soetaert at nioz.nl>’

Last updated on 2020-05-31 00:47:37 CEST.

Package ERROR WARN NOTE OK
AquaEnv 12
bvpSolve 2 9
diagram 12
ecolMod 12
FME 12
LIM 12
limSolve 12
marelac 12
NetIndices 12
OceanView 1 11
plot3D 12
plot3Drgl 1 11
ReacTran 12
rootSolve 12
shape 12

### Package AquaEnv

Current CRAN status: OK: 12

### Package bvpSolve

Current CRAN status: ERROR: 2, OK: 9

Version: 1.4
Check: examples
Result: ERROR
Running examples in ‘bvpSolve-Ex.R’ failed
The error most likely occurred in:

> ### Name: bvpcol
> ### Title: Solves multipoint boundary value problems of ordinary
> ### differential equations or differential algebraic equations, using a
> ### collocation method.
> ### Aliases: bvpcol
> ### Keywords: math
>
> ### ** Examples
>
> ## =============================================================================
> ## Example 1: simple standard problem
> ## solve the BVP ODE:
> ## d2y/dt^2=-3py/(p+t^2)^2
> ## y(t= -0.1)=-0.1/sqrt(p+0.01)
> ## y(t= 0.1)= 0.1/sqrt(p+0.01)
> ## where p = 1e-5
> ##
> ## analytical solution y(t) = t/sqrt(p + t^2).
> ##
> ## The problem is rewritten as a system of 2 ODEs:
> ## dy=y2
> ## dy2=-3p*y/(p+t^2)^2
> ## =============================================================================
>
> #--------------------------------
> # Derivative function
> #--------------------------------
> fun <- function(t, y, pars) {
+ dy1 <- y[2]
+ dy2 <- - 3 * p * y[1] / (p+t*t)^2
+ return(list(c(dy1,
+ dy2))) }
>
> # parameter value
> p <- 1e-5
>
> # initial and final condition; second conditions unknown
> init <- c(-0.1 / sqrt(p+0.01), NA)
> end <- c( 0.1 / sqrt(p+0.01), NA)
>
> # Solve bvp
> sol <- bvpcol(yini = init, yend = end,
+ x = seq(-0.1, 0.1, by = 0.001), func = fun)

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
1: bvpsolver(2, yini, x, func, yend, parms, order, ynames, xguess, yguess, jacfunc, bound, jacbound, leftbc, posbound, islin, nmax, ncomp, atol, dllname, initfunc, rpar, ipar, nout, outnames, forcings, initforc, fcontrol, verbose, cond = FALSE, lobatto = FALSE, allpoints = TRUE, colp = colp, fullOut = fullOut, bspline = bspline, eps = NULL, epsini = NULL, dae = dae, ...)
2: bvpcol(yini = init, yend = end, x = seq(-0.1, 0.1, by = 0.001), func = fun)
An irrecoverable exception occurred. R is aborting now ...
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.4
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘bvpSolve.Rnw’
...
7: withVisible(eval(ei, envir))
8: source(output, echo = TRUE)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)})
13: tools:::.run_one_vignette("bvpSolve.Rnw", "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bvpSolve.Rcheck/00_pkg_src/bvpSolve/vignettes", encoding = "latin1", pkgdir = "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bvpSolve.Rcheck/00_pkg_src/bvpSolve")
An irrecoverable exception occurred. R is aborting now ...

... incomplete output. Crash?
when running code in ‘bvpTests.Rnw’
...
7: withVisible(eval(ei, envir))
8: source(output, echo = TRUE)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)})
13: tools:::.run_one_vignette("bvpTests.Rnw", "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bvpSolve.Rcheck/00_pkg_src/bvpSolve/vignettes", encoding = "latin1", pkgdir = "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bvpSolve.Rcheck/00_pkg_src/bvpSolve")
An irrecoverable exception occurred. R is aborting now ...

... incomplete output. Crash?

‘bvpSolve.Rnw’ using ‘latin1’... failed to complete the test
‘bvpTests.Rnw’ using ‘latin1’... failed to complete the test
Flavor: r-release-osx-x86_64

Version: 1.4
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
sh: line 1: 72701 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpuzF94d/file11b3b1d784842' 2>&1 < '/Volumes/Temp/tmp/RtmpuzF94d/file11b3b43cff42b'
--- re-building ‘bvpSolve.Rnw’ using Sweave
Loading required package: deSolve

Attaching package: ‘bvpSolve’

The following object is masked from ‘package:stats’:

approx

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
1: bvpsolver(1, yini, x, func, yend, parms, order, ynames, xguess, yguess, jacfunc, bound, jacbound, leftbc, posbound, islin, nmax, ncomp, atol, dllname, initfunc, rpar, ipar, nout, outnames, forcings, initforc, fcontrol, verbose, cond, lobatto, allpoints, colp = NULL, fullOut = TRUE, bspline = TRUE, eps = NULL, epsini = NULL, dae = NULL, ...)
2: bvptwp(yini = c(-1, NA), yend = c(1, NA), x = x, func = fun)
3: system.time(sol2 <- bvptwp(yini = c(-1, NA), yend = c(1, NA), x = x, func = fun))
4: print(system.time(sol2 <- bvptwp(yini = c(-1, NA), yend = c(1, NA), x = x, func = fun)))
5: eval(expr, .GlobalEnv)
6: eval(expr, .GlobalEnv)
7: withVisible(eval(expr, .GlobalEnv))
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
13: evalFunc(ce, options)
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
16: driver\$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(...)
18: engine\$weave(file, quiet = quiet, encoding = enc)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ engine\$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
23: tools:::.buildOneVignette("bvpSolve.Rnw", "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bvpSolve.Rcheck/vign_test/bvpSolve", TRUE, FALSE, "bvpSolve", "latin1", "/Volumes/Temp/tmp/RtmpuzF94d/file11b3b6e0fecd.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 72887 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpuzF94d/file11b3b48f417e6' 2>&1 < '/Volumes/Temp/tmp/RtmpuzF94d/file11b3b114d2275'
--- re-building ‘bvpTests.Rnw’ using Sweave
Loading required package: deSolve

Attaching package: ‘bvpSolve’

The following object is masked from ‘package:stats’:

approx

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
1: bvpsolver(1, yini, x, func, yend, parms, order, ynames, xguess, yguess, jacfunc, bound, jacbound, leftbc, posbound, islin, nmax, ncomp, atol, dllname, initfunc, rpar, ipar, nout, outnames, forcings, initforc, fcontrol, verbose, cond, lobatto, allpoints, colp = NULL, fullOut = TRUE, bspline = TRUE, eps = NULL, epsini = NULL, dae = NULL, ...)
2: bvptwp(yini = c(1, NA), yend = c(0, NA), x = seq(0, 1, by = 0.01), func = Prob1)
3: system.time(mod1 <- bvptwp(yini = c(1, NA), yend = c(0, NA), x = seq(0, 1, by = 0.01), func = Prob1))
4: print(system.time(mod1 <- bvptwp(yini = c(1, NA), yend = c(0, NA), x = seq(0, 1, by = 0.01), func = Prob1)))
5: eval(expr, .GlobalEnv)
6: eval(expr, .GlobalEnv)
7: withVisible(eval(expr, .GlobalEnv))
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
13: evalFunc(ce, options)
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
16: driver\$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(...)
18: engine\$weave(file, quiet = quiet, encoding = enc)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ engine\$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
23: tools:::.buildOneVignette("bvpTests.Rnw", "/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/bvpSolve.Rcheck/vign_test/bvpSolve", TRUE, FALSE, "bvpTests", "latin1", "/Volumes/Temp/tmp/RtmpuzF94d/file11b3b9a755d5.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following files failed:
‘bvpSolve.Rnw’ ‘bvpTests.Rnw’

Error: Vignette re-building failed.
Execution halted
Flavor: r-release-osx-x86_64

Version: 1.4
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘bvpSolve.Rnw’
...
7: withVisible(eval(ei, envir))
8: source(output, echo = TRUE)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)})
13: tools:::.run_one_vignette("bvpSolve.Rnw", "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bvpSolve.Rcheck/00_pkg_src/bvpSolve/vignettes", encoding = "latin1", pkgdir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bvpSolve.Rcheck/00_pkg_src/bvpSolve")
An irrecoverable exception occurred. R is aborting now ...

... incomplete output. Crash?
when running code in ‘bvpTests.Rnw’
...
7: withVisible(eval(ei, envir))
8: source(output, echo = TRUE)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ source(output, echo = TRUE)}, error = function(e) { cat("\n When sourcing ", sQuote(output), ":\n", sep = "") stop(conditionMessage(e), call. = FALSE, domain = NA)})
13: tools:::.run_one_vignette("bvpTests.Rnw", "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bvpSolve.Rcheck/00_pkg_src/bvpSolve/vignettes", encoding = "latin1", pkgdir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bvpSolve.Rcheck/00_pkg_src/bvpSolve")
An irrecoverable exception occurred. R is aborting now ...

... incomplete output. Crash?

‘bvpSolve.Rnw’using ‘latin1’... failed to complete the test
‘bvpTests.Rnw’using ‘latin1’... failed to complete the test
Flavor: r-oldrel-osx-x86_64

Version: 1.4
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
sh: line 1: 59495 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --slave > '/tmp/RtmpSxkpou/filee8625855a7bf' 2>&1 < '/tmp/RtmpSxkpou/filee8625f7819e7'
--- re-building ‘bvpSolve.Rnw’ using Sweave
Loading required package: deSolve

Attaching package: ‘bvpSolve’

The following object is masked from ‘package:stats’:

approx

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
1: bvpsolver(1, yini, x, func, yend, parms, order, ynames, xguess, yguess, jacfunc, bound, jacbound, leftbc, posbound, islin, nmax, ncomp, atol, dllname, initfunc, rpar, ipar, nout, outnames, forcings, initforc, fcontrol, verbose, cond, lobatto, allpoints, colp = NULL, fullOut = TRUE, bspline = TRUE, eps = NULL, epsini = NULL, dae = NULL, ...)
2: bvptwp(yini = c(-1, NA), yend = c(1, NA), x = x, func = fun)
3: system.time(sol2 <- bvptwp(yini = c(-1, NA), yend = c(1, NA), x = x, func = fun))
4: print(system.time(sol2 <- bvptwp(yini = c(-1, NA), yend = c(1, NA), x = x, func = fun)))
5: eval(expr, .GlobalEnv)
6: eval(expr, .GlobalEnv)
7: withVisible(eval(expr, .GlobalEnv))
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
13: evalFunc(ce, options)
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
16: driver\$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(...)
18: engine\$weave(file, quiet = quiet, encoding = enc)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ engine\$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
23: tools:::.buildOneVignette("bvpSolve.Rnw", "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bvpSolve.Rcheck/vign_test/bvpSolve", TRUE, FALSE, "bvpSolve", "latin1", "/tmp/RtmpSxkpou/filee86210a7ff1.rds")
An irrecoverable exception occurred. R is aborting now ...
sh: line 1: 59501 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --slave > '/tmp/RtmpSxkpou/filee86239978475' 2>&1 < '/tmp/RtmpSxkpou/filee862a793add'
--- re-building ‘bvpTests.Rnw’ using Sweave
Loading required package: deSolve

Attaching package: ‘bvpSolve’

The following object is masked from ‘package:stats’:

approx

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
1: bvpsolver(1, yini, x, func, yend, parms, order, ynames, xguess, yguess, jacfunc, bound, jacbound, leftbc, posbound, islin, nmax, ncomp, atol, dllname, initfunc, rpar, ipar, nout, outnames, forcings, initforc, fcontrol, verbose, cond, lobatto, allpoints, colp = NULL, fullOut = TRUE, bspline = TRUE, eps = NULL, epsini = NULL, dae = NULL, ...)
2: bvptwp(yini = c(1, NA), yend = c(0, NA), x = seq(0, 1, by = 0.01), func = Prob1)
3: system.time(mod1 <- bvptwp(yini = c(1, NA), yend = c(0, NA), x = seq(0, 1, by = 0.01), func = Prob1))
4: print(system.time(mod1 <- bvptwp(yini = c(1, NA), yend = c(0, NA), x = seq(0, 1, by = 0.01), func = Prob1)))
5: eval(expr, .GlobalEnv)
6: eval(expr, .GlobalEnv)
7: withVisible(eval(expr, .GlobalEnv))
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
13: evalFunc(ce, options)
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(evalFunc(ce, options), finally = { cat("\n") sink()})
16: driver\$runcode(drobj, chunk, chunkopts)
17: utils::Sweave(...)
18: engine\$weave(file, quiet = quiet, encoding = enc)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch({ engine\$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
23: tools:::.buildOneVignette("bvpTests.Rnw", "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bvpSolve.Rcheck/vign_test/bvpSolve", TRUE, FALSE, "bvpTests", "latin1", "/tmp/RtmpSxkpou/filee86245ecbda8.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following files failed:
‘bvpSolve.Rnw’ ‘bvpTests.Rnw’

Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-osx-x86_64

### Package diagram

Current CRAN status: OK: 12

### Package ecolMod

Current CRAN status: NOTE: 12

Version: 1.2.6
Check: R code for possible problems
Result: NOTE
dilution: no visible global function definition for 'grey'
dilution: no visible global function definition for 'lines'
dilution: no visible global function definition for 'rect'
dilution: no visible global function definition for 'segments'
dilution: no visible global function definition for 'text'
dilution: no visible global function definition for 'arrows'
pricefit: no visible global function definition for 'runif'
Undefined global functions or variables:
arrows grey lines rect runif segments text
Consider adding
importFrom("grDevices", "grey")
importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
importFrom("stats", "runif")
to your NAMESPACE file.
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-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.2.6
Check: compiled code
Result: NOTE
File ‘ecolMod/libs/ecolMod.so’:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

### Package FME

Current CRAN status: OK: 12

### Package LIM

Current CRAN status: NOTE: 12

Version: 1.4.6
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Title field: should not end in a period.
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-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4.6
Check: R code for possible problems
Result: NOTE
Plotranges.double: no visible global function definition for 'strwidth'
Plotranges.double: no visible global function definition for
'strheight'
Plotranges.double: no visible global function definition for 'plot.new'
Plotranges.double: no visible global function definition for 'par'
Plotranges.double: no visible global function definition for
'plot.window'
Plotranges.double: no visible global function definition for 'mtext'
Plotranges.double: no visible global function definition for 'abline'
Plotranges.double: no visible global function definition for 'points'
Plotranges.double: no visible global function definition for 'segments'
Plotranges.double: no visible global function definition for 'text'
Plotranges.double: no visible global function definition for 'axis'
Plotranges.double: no visible global function definition for 'box'
Plotranges.double: no visible global function definition for 'title'
Undefined global functions or variables:
abline axis box mtext par plot.new plot.window points segments
strheight strwidth text title
Consider adding
importFrom("graphics", "abline", "axis", "box", "mtext", "par",
"plot.new", "plot.window", "points", "segments",
"strheight", "strwidth", "text", "title")
to your NAMESPACE file.
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-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64, r-oldrel-windows-ix86+x86_64

### Package limSolve

Current CRAN status: OK: 12

### Package marelac

Current CRAN status: OK: 12

### Package NetIndices

Current CRAN status: NOTE: 12

Version: 1.4.4
Check: R code for possible problems
Result: NOTE
EnvInd: no visible global function definition for 'sd'
Undefined global functions or variables:
sd
Consider adding
importFrom("stats", "sd")
to your NAMESPACE file.
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-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64, r-oldrel-windows-ix86+x86_64

### Package OceanView

Current CRAN status: WARN: 1, OK: 11

Version: 1.0.5
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: dependencies in R code
Result: NOTE
No protocol specified
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: S3 generic/method consistency
Result: WARN
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: replacement functions
Result: WARN
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: foreign function calls
Result: NOTE
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: R code for possible problems
Result: NOTE
No protocol specified
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: for missing documentation entries
Result: WARN
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: for code/documentation mismatches
Result: WARN
No protocol specified
No protocol specified
No protocol specified
Flavor: r-oldrel-osx-x86_64

Version: 1.0.5
Check: Rd \usage sections
Result: NOTE
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

### Package plot3D

Current CRAN status: OK: 12

### Package plot3Drgl

Current CRAN status: WARN: 1, OK: 11

Version: 1.0.1
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-oldrel-osx-x86_64

### Package ReacTran

Current CRAN status: OK: 12

### Package rootSolve

Current CRAN status: OK: 12

### Package shape

Current CRAN status: OK: 12