Last updated on 2026-05-26 03:51:32 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.8.232 | 3.59 | 94.54 | 98.13 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.8.232 | 2.94 | 62.10 | 65.04 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.8.232 | 7.00 | 162.32 | 169.32 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.12.120 | 8.00 | 205.64 | 213.64 | OK | |
| r-devel-windows-x86_64 | 2.8.232 | 5.00 | 115.00 | 120.00 | OK | |
| r-patched-linux-x86_64 | 2.8.232 | 6.27 | 90.70 | 96.97 | OK | |
| r-release-linux-x86_64 | 2.8.232 | 3.80 | 90.95 | 94.75 | OK | |
| r-release-macos-arm64 | 2.12.120 | 1.00 | 63.00 | 64.00 | ERROR | |
| r-release-macos-x86_64 | 2.12.120 | 3.00 | 188.00 | 191.00 | ERROR | |
| r-release-windows-x86_64 | 2.8.232 | 6.00 | 112.00 | 118.00 | OK | |
| r-oldrel-macos-arm64 | 2.12.120 | ERROR | ||||
| r-oldrel-macos-x86_64 | 2.12.120 | 3.00 | 179.00 | 182.00 | ERROR | |
| r-oldrel-windows-x86_64 | 2.8.232 | 6.00 | 104.00 | 110.00 | OK |
Version: 2.8.232
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Mark V. Bravington <mark.bravington@csiro.au>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = c("Mark", "V."),
family = "Bravington",
role = c("aut", "cre"),
email = "mark.bravington@csiro.au")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.12.120
Check: examples
Result: ERROR
Running examples in ‘mvbutils-Ex.R’ failed
The error most likely occurred in:
> ### Name: numvbderiv_parallel
> ### Title: Economy numerical derivatives
> ### Aliases: numvbderiv_parallel numvbderiv
> ### Keywords: misc
>
> ### ** Examples
>
> # Complex numbers are OK:
> numvbderiv( function( x) x*x, complex( real=1, imaginary=3))
[1] 2+6i
> # [1] 2+6i
> # Parallel example... the whole point is to show speed and generality
> # Works fine on my machine
> # But if testing under CRAN, which I normally never do,
> # then CRAN's ludicrous 2-core limit, and deliberate inability to
> # check CRANality (or even number of cores _allowed_) while running,
> # makes this completely ridiculous
> # Not for the first time
> # I have used the function 'get_ncores_CRANal' to try to get round this...
> if( require( 'doParallel')){ # auto loads foreach, iterators, parallel thx2 "Depends"
+ ncores <- detectCores( logical=FALSE)
+ scatn( '%i cores really found', ncores)
+ if( ncores > 2 ){ # pointless otherwise
+ # Need a slowish example. 1e5 is too small; 1e7 better,
+ # ... but hard on auto builders eg R-universe
+ BIGGOVAL <- 1e5
+ slowfun <- function( pars, BIGGO)
+ sum( sqr( 1+1/outer( seq_len( BIGGO), pars)))
+ parstart <- rep( 2, 8)
+ system.time(
+ dscalar <- numvbderiv( slowfun, parstart,
+ BIGGO=BIGGOVAL # named extra param (part of ...)
+ )
+ ) # scalar
+ # Make "doPar back end". I do not know what I am doing ...
+ # NB I like to leave some cores spare, hence "-1"--
+ # superstition, really
+ ncores_target <- min( ncores-1, length( parstart))
+ # Anti CRANky: ignore on your own machine:
+ # ncores_target should just work
+ ncores_avail <- get_ncores_CRANal( ncores_target)
+ scatn( 'Using %i cores eg cozza CRAN', ncores_avail)
+ CLUSTO <- makeCluster( ncores_avail)
+ registerDoParallel( CLUSTO, ncores_avail)
+ # Next bit ensures slaves can find packages... sigh.
+ # Necessary _here_ coz example, but you may not need it
+ # clusterCall does not work properly :/, so the "obvious" fails:
+ # clusterCall( CLUSTO, .libPaths, .libPaths())
+ # Instead, we are forced into this nonsense:
+ print( # for debuggery with as-CRAN
+ eval( substitute(
+ clusterEvalQ( CLUSTO, .libPaths( lb)),
+ list( lb=.libPaths())))
+ )
+ # Need 'mvbutils::sqr', hence '.packages' arg
+ scatn( 'Starting parallel time test')
+ print( system.time(
+ dpara <- numvbderiv_parallel( slowfun, parstart,
+ BIGGO=BIGGOVAL, # named extra parameter
+ FOREACH_ARGS=list( .packages= 'mvbutils')
+ )
+ )
+ )
+ scatn( 'Done')
+ print( rbind( dscalar, dpara))
+ # To refer to other data (ie beside params)
+ # best practice is to put it into function's environment
+ # (generally true, not just for numvbderiv)
+ e <- new.env()
+ e$paroffset <- c( 6, -3)
+ fun2 <- function( pars) { # not a speed test, can be smaller
+ sum( sqr( 1+1/outer( 1:1e3, pars+paroffset)))
+ }
+ environment( fun2) <- e
+ scatn( 'Scalar, using extra data via environment')
+ print( numvbderiv( fun2, parstart))
+ # Parallel version should still work, coz function's environment
+ # is also passed to slaves
+ scatn( 'Trying parallel version...')
+ print( try({
+ numvbderiv_parallel( fun2, parstart,
+ FOREACH_ARGS=list( .packages= 'mvbutils')
+ )
+ })
+ )
+ # Sometimes you do need to explicitly export stuff to the slave processes
+ # Here's a version that will get paroffset from datenv
+ # datenv must exist...
+ alt_fun2 <- function( pars){
+ environment( fun2) <- list2env( datenv)
+ fun2( pars)
+ }
+ scatn( 'With explicit data (in parallel)')
+ datenv <- as.list( e)
+ print( numvbderiv_parallel( alt_fun2, parstart,
+ FOREACH_ARGS=list(
+ .packages= 'mvbutils',
+ .export= cq( datenv, fun2) # stuff that alt_fun2 refers to
+ )
+ )
+ )
+ # Always tidy up your clusters once you have finished playing
+ stopImplicitCluster()
+ stopCluster( CLUSTO)
+ rm( CLUSTO)
+ } # if ncores>2
+ } # parallel
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
12 cores really found
Error in stopCluster(CLUSTO) : CRANtidote
Calls: get_ncores_CRANal -> stopCluster
Execution halted
Flavor: r-release-macos-arm64
Version: 2.12.120
Check: examples
Result: ERROR
Running examples in ‘mvbutils-Ex.R’ failed
The error most likely occurred in:
> ### Name: numvbderiv_parallel
> ### Title: Economy numerical derivatives
> ### Aliases: numvbderiv_parallel numvbderiv
> ### Keywords: misc
>
> ### ** Examples
>
> # Complex numbers are OK:
> numvbderiv( function( x) x*x, complex( real=1, imaginary=3))
[1] 2+6i
> # [1] 2+6i
> # Parallel example... the whole point is to show speed and generality
> # Works fine on my machine
> # But if testing under CRAN, which I normally never do,
> # then CRAN's ludicrous 2-core limit, and deliberate inability to
> # check CRANality (or even number of cores _allowed_) while running,
> # makes this completely ridiculous
> # Not for the first time
> # I have used the function 'get_ncores_CRANal' to try to get round this...
> if( require( 'doParallel')){ # auto loads foreach, iterators, parallel thx2 "Depends"
+ ncores <- detectCores( logical=FALSE)
+ scatn( '%i cores really found', ncores)
+ if( ncores > 2 ){ # pointless otherwise
+ # Need a slowish example. 1e5 is too small; 1e7 better,
+ # ... but hard on auto builders eg R-universe
+ BIGGOVAL <- 1e5
+ slowfun <- function( pars, BIGGO)
+ sum( sqr( 1+1/outer( seq_len( BIGGO), pars)))
+ parstart <- rep( 2, 8)
+ system.time(
+ dscalar <- numvbderiv( slowfun, parstart,
+ BIGGO=BIGGOVAL # named extra param (part of ...)
+ )
+ ) # scalar
+ # Make "doPar back end". I do not know what I am doing ...
+ # NB I like to leave some cores spare, hence "-1"--
+ # superstition, really
+ ncores_target <- min( ncores-1, length( parstart))
+ # Anti CRANky: ignore on your own machine:
+ # ncores_target should just work
+ ncores_avail <- get_ncores_CRANal( ncores_target)
+ scatn( 'Using %i cores eg cozza CRAN', ncores_avail)
+ CLUSTO <- makeCluster( ncores_avail)
+ registerDoParallel( CLUSTO, ncores_avail)
+ # Next bit ensures slaves can find packages... sigh.
+ # Necessary _here_ coz example, but you may not need it
+ # clusterCall does not work properly :/, so the "obvious" fails:
+ # clusterCall( CLUSTO, .libPaths, .libPaths())
+ # Instead, we are forced into this nonsense:
+ print( # for debuggery with as-CRAN
+ eval( substitute(
+ clusterEvalQ( CLUSTO, .libPaths( lb)),
+ list( lb=.libPaths())))
+ )
+ # Need 'mvbutils::sqr', hence '.packages' arg
+ scatn( 'Starting parallel time test')
+ print( system.time(
+ dpara <- numvbderiv_parallel( slowfun, parstart,
+ BIGGO=BIGGOVAL, # named extra parameter
+ FOREACH_ARGS=list( .packages= 'mvbutils')
+ )
+ )
+ )
+ scatn( 'Done')
+ print( rbind( dscalar, dpara))
+ # To refer to other data (ie beside params)
+ # best practice is to put it into function's environment
+ # (generally true, not just for numvbderiv)
+ e <- new.env()
+ e$paroffset <- c( 6, -3)
+ fun2 <- function( pars) { # not a speed test, can be smaller
+ sum( sqr( 1+1/outer( 1:1e3, pars+paroffset)))
+ }
+ environment( fun2) <- e
+ scatn( 'Scalar, using extra data via environment')
+ print( numvbderiv( fun2, parstart))
+ # Parallel version should still work, coz function's environment
+ # is also passed to slaves
+ scatn( 'Trying parallel version...')
+ print( try({
+ numvbderiv_parallel( fun2, parstart,
+ FOREACH_ARGS=list( .packages= 'mvbutils')
+ )
+ })
+ )
+ # Sometimes you do need to explicitly export stuff to the slave processes
+ # Here's a version that will get paroffset from datenv
+ # datenv must exist...
+ alt_fun2 <- function( pars){
+ environment( fun2) <- list2env( datenv)
+ fun2( pars)
+ }
+ scatn( 'With explicit data (in parallel)')
+ datenv <- as.list( e)
+ print( numvbderiv_parallel( alt_fun2, parstart,
+ FOREACH_ARGS=list(
+ .packages= 'mvbutils',
+ .export= cq( datenv, fun2) # stuff that alt_fun2 refers to
+ )
+ )
+ )
+ # Always tidy up your clusters once you have finished playing
+ stopImplicitCluster()
+ stopCluster( CLUSTO)
+ rm( CLUSTO)
+ } # if ncores>2
+ } # parallel
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
6 cores really found
Error in stopCluster(CLUSTO) : CRANtidote
Calls: get_ncores_CRANal -> stopCluster
Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 2.12.120
Check: R code for possible problems
Result: NOTE
cd.load: possible error in mget("tasks", pos = 2, ifnotfound =
list(character(0))): unused argument (pos = 2)
get.cd.from.menu: possible error in mget("tasks", pos = 1, ifnotfound =
list(structure(character(0), names = character(0)))): unused argument
(pos = 1)
make.new.cd.task: possible error in mget("tasks", pos = 2, ifnotfound =
list(character(0))): unused argument (pos = 2)
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.12.120
Check: examples
Result: ERROR
Running examples in ‘mvbutils-Ex.R’ failed
The error most likely occurred in:
> ### Name: numvbderiv_parallel
> ### Title: Economy numerical derivatives
> ### Aliases: numvbderiv_parallel numvbderiv
> ### Keywords: misc
>
> ### ** Examples
>
> # Complex numbers are OK:
> numvbderiv( function( x) x*x, complex( real=1, imaginary=3))
[1] 2+6i
> # [1] 2+6i
> # Parallel example... the whole point is to show speed and generality
> # Works fine on my machine
> # But if testing under CRAN, which I normally never do,
> # then CRAN's ludicrous 2-core limit, and deliberate inability to
> # check CRANality (or even number of cores _allowed_) while running,
> # makes this completely ridiculous
> # Not for the first time
> # I have used the function 'get_ncores_CRANal' to try to get round this...
> if( require( 'doParallel')){ # auto loads foreach, iterators, parallel thx2 "Depends"
+ ncores <- detectCores( logical=FALSE)
+ scatn( '%i cores really found', ncores)
+ if( ncores > 2 ){ # pointless otherwise
+ # Need a slowish example. 1e5 is too small; 1e7 better,
+ # ... but hard on auto builders eg R-universe
+ BIGGOVAL <- 1e5
+ slowfun <- function( pars, BIGGO)
+ sum( sqr( 1+1/outer( seq_len( BIGGO), pars)))
+ parstart <- rep( 2, 8)
+ system.time(
+ dscalar <- numvbderiv( slowfun, parstart,
+ BIGGO=BIGGOVAL # named extra param (part of ...)
+ )
+ ) # scalar
+ # Make "doPar back end". I do not know what I am doing ...
+ # NB I like to leave some cores spare, hence "-1"--
+ # superstition, really
+ ncores_target <- min( ncores-1, length( parstart))
+ # Anti CRANky: ignore on your own machine:
+ # ncores_target should just work
+ ncores_avail <- get_ncores_CRANal( ncores_target)
+ scatn( 'Using %i cores eg cozza CRAN', ncores_avail)
+ CLUSTO <- makeCluster( ncores_avail)
+ registerDoParallel( CLUSTO, ncores_avail)
+ # Next bit ensures slaves can find packages... sigh.
+ # Necessary _here_ coz example, but you may not need it
+ # clusterCall does not work properly :/, so the "obvious" fails:
+ # clusterCall( CLUSTO, .libPaths, .libPaths())
+ # Instead, we are forced into this nonsense:
+ print( # for debuggery with as-CRAN
+ eval( substitute(
+ clusterEvalQ( CLUSTO, .libPaths( lb)),
+ list( lb=.libPaths())))
+ )
+ # Need 'mvbutils::sqr', hence '.packages' arg
+ scatn( 'Starting parallel time test')
+ print( system.time(
+ dpara <- numvbderiv_parallel( slowfun, parstart,
+ BIGGO=BIGGOVAL, # named extra parameter
+ FOREACH_ARGS=list( .packages= 'mvbutils')
+ )
+ )
+ )
+ scatn( 'Done')
+ print( rbind( dscalar, dpara))
+ # To refer to other data (ie beside params)
+ # best practice is to put it into function's environment
+ # (generally true, not just for numvbderiv)
+ e <- new.env()
+ e$paroffset <- c( 6, -3)
+ fun2 <- function( pars) { # not a speed test, can be smaller
+ sum( sqr( 1+1/outer( 1:1e3, pars+paroffset)))
+ }
+ environment( fun2) <- e
+ scatn( 'Scalar, using extra data via environment')
+ print( numvbderiv( fun2, parstart))
+ # Parallel version should still work, coz function's environment
+ # is also passed to slaves
+ scatn( 'Trying parallel version...')
+ print( try({
+ numvbderiv_parallel( fun2, parstart,
+ FOREACH_ARGS=list( .packages= 'mvbutils')
+ )
+ })
+ )
+ # Sometimes you do need to explicitly export stuff to the slave processes
+ # Here's a version that will get paroffset from datenv
+ # datenv must exist...
+ alt_fun2 <- function( pars){
+ environment( fun2) <- list2env( datenv)
+ fun2( pars)
+ }
+ scatn( 'With explicit data (in parallel)')
+ datenv <- as.list( e)
+ print( numvbderiv_parallel( alt_fun2, parstart,
+ FOREACH_ARGS=list(
+ .packages= 'mvbutils',
+ .export= cq( datenv, fun2) # stuff that alt_fun2 refers to
+ )
+ )
+ )
+ # Always tidy up your clusters once you have finished playing
+ stopImplicitCluster()
+ stopCluster( CLUSTO)
+ rm( CLUSTO)
+ } # if ncores>2
+ } # parallel
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
16 cores really found
Error in stopCluster(CLUSTO) : CRANtidote
Calls: get_ncores_CRANal -> stopCluster
Execution halted
Flavor: r-oldrel-macos-arm64