ppso - Particle Swarm Optimization and Dynamically Dimensioned Search, with parallel option - check results
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ppso

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Version: 0.9-9994
Result: WARNING
Check time: 2017-08-03 08:27
* using log directory ''
* using R version 3.3.3 Patched (2017-03-15 r72930)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* checking for file 'ppso/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ppso' version '0.9-9994'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'Rmpi' 'rgl' 'lhs'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ppso' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'Rmpi' 'lhs' 'rgl'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad: no visible global function definition for 'mpi.comm.size'
ackley_function: no visible global function definition for 'runif'
check_execution_timeout: no visible global function definition for
'flush.console'
close_mpi: no visible global function definition for 'mpi.iprobe'
close_mpi: no visible global function definition for 'mpi.any.source'
close_mpi: no visible global function definition for 'mpi.recv.Robj'
close_mpi: no visible global function definition for
'mpi.get.sourcetag'
close_mpi: no visible global function definition for 'mpi.send.Robj'
close_mpi: no visible global function definition for 'mpi.comm.size'
close_mpi: no visible global function definition for 'mpi.any.tag'
close_mpi: no visible global function definition for 'flush.console'
close_mpi: no visible global function definition for 'mpi.bcast.cmd'
do_plot_function: no visible global function definition for 'dev.list'
do_plot_function: no visible global function definition for 'dev.set'
do_plot_function: no visible global function definition for 'x11'
do_plot_function: no visible global function definition for 'dev.cur'
do_plot_function: no visible global function definition for 'persp'
do_plot_function: no visible global function definition for 'points'
do_plot_function: no visible global function definition for 'trans3d'
do_plot_function: no visible global function definition for 'lines'
do_plot_function: no visible global function definition for 'rgl.pop'
do_plot_function: no visible global function definition for 'points3d'
griewank_function: no visible global function definition for 'runif'
init_particles: no visible binding for global variable
'number_of_parameters'
init_particles: no visible global function definition for 'read.table'
init_particles: no visible global function definition for 'runif'
init_particles: no visible global function definition for
'installed.packages'
init_particles: no visible global function definition for 'randomLHS'
init_visualisation: no visible binding for global variable
'number_of_parameters'
init_visualisation: no visible global function definition for
'objective_function'
init_visualisation: no visible global function definition for 'par'
init_visualisation: no visible global function definition for 'open3d'
init_visualisation: no visible global function definition for
'terrain.colors'
init_visualisation: no visible global function definition for
'surface3d'
mpi_loop: no visible global function definition for 'flush.console'
mpi_loop: no visible global function definition for 'mpi.iprobe'
mpi_loop: no visible global function definition for 'mpi.any.source'
mpi_loop: no visible global function definition for 'mpi.any.tag'
mpi_loop: no visible global function definition for 'mpi.recv.Robj'
mpi_loop: no visible global function definition for 'mpi.get.sourcetag'
mpi_loop: no visible global function definition for 'write.table'
mpi_loop: no visible binding for global variable 'number_of_parameters'
mpi_loop: no visible global function definition for 'mpi.send.Robj'
optim_dds: no visible global function definition for 'flush.console'
optim_dds: no visible global function definition for 'write.table'
optim_pdds_robust: no visible global function definition for
'flush.console'
optim_pdds_robust: no visible global function definition for
'write.table'
optim_ppso_robust: no visible global function definition for
'flush.console'
optim_ppso_robust: no visible global function definition for
'write.table'
optim_pso: no visible global function definition for 'write.table'
plot_optimization_progress: no visible global function definition for
'read.table'
plot_optimization_progress: no visible global function definition for
'dev.list'
plot_optimization_progress: no visible global function definition for
'dev.set'
plot_optimization_progress: no visible global function definition for
'x11'
plot_optimization_progress: no visible global function definition for
'dev.cur'
plot_optimization_progress: no visible global function definition for
'par'
plot_optimization_progress: no visible global function definition for
'plot'
plot_optimization_progress: no visible global function definition for
'points'
plot_optimization_progress: no visible global function definition for
'quantile'
plot_optimization_progress: no visible global function definition for
'plot.new'
plot_optimization_progress: no visible global function definition for
'legend'
plot_optimization_progress: no visible global function definition for
'palette'
plot_optimization_progress: no visible global function definition for
'topo.colors'
plot_optimization_progress: no visible global function definition for
'hist'
plot_optimization_progress: no visible global function definition for
'median'
prepare_mpi_cluster: no visible global function definition for
'mpi.universe.size'
prepare_mpi_cluster: no visible global function definition for
'mpi.comm.size'
prepare_mpi_cluster: no visible global function definition for
'flush.console'
prepare_mpi_cluster: no visible global function definition for
'mpi.spawn.Rslaves'
prepare_mpi_cluster: no visible global function definition for
'mpi.iprobe'
prepare_mpi_cluster: no visible global function definition for
'mpi.any.source'
prepare_mpi_cluster: no visible global function definition for
'mpi.any.tag'
prepare_mpi_cluster: no visible global function definition for
'mpi.recv.Robj'
prepare_mpi_cluster : .Last: no visible global function definition for
'mpi.comm.size'
prepare_mpi_cluster : .Last: no visible global function definition for
'mpi.close.Rslaves'
prepare_mpi_cluster : perform_task: no visible global function
definition for 'mpi.comm.rank'
prepare_mpi_cluster : perform_task: no visible global function
definition for 'flush.console'
prepare_mpi_cluster : perform_task: no visible global function
definition for 'mpi.send.Robj'
prepare_mpi_cluster: no visible global function definition for
'mpi.bcast.Robj2slave'
prepare_mpi_cluster: no visible global function definition for
'mpi.bcast.cmd'
prepare_mpi_cluster: no visible global function definition for
'mpi.comm.rank'
prepare_mpi_cluster: no visible global function definition for
'capture.output'
prepare_mpi_cluster: no visible global function definition for
'slave.hostinfo'
prepare_mpi_cluster: no visible global function definition for
'mpi.remote.exec'
prepare_mpi_cluster : mpi_receive_loop: no visible global function
definition for 'mpi.recv.Robj'
prepare_mpi_cluster : mpi_receive_loop: no visible global function
definition for 'mpi.any.tag'
prepare_mpi_cluster : mpi_receive_loop: no visible global function
definition for 'mpi.get.sourcetag'
prepare_mpi_cluster : mpi_receive_loop: no visible global function
definition for 'mpi.comm.rank'
prepare_mpi_cluster : mpi_receive_loop: no visible global function
definition for 'mpi.send.Robj'
push_object: no visible global function definition for 'mpi.comm.rank'
push_object: no visible binding for global variable 'object_names'
push_object: no visible global function definition for 'mpi.send.Robj'
rastrigin_function: no visible global function definition for 'runif'
request_object: no visible global function definition for
'mpi.comm.rank'
request_object: no visible global function definition for
'mpi.send.Robj'
request_object: no visible global function definition for
'mpi.recv.Robj'
request_object: no visible global function definition for 'mpi.any.tag'
request_object: no visible global function definition for
'mpi.get.sourcetag'
send_task: no visible global function definition for 'mpi.remote.exec'
send_task: no visible binding for global variable 'perform_task'
send_task: no visible global function definition for 'mpi.send.Robj'
set_object: no visible binding for global variable 'flush.console'
update_tasklist_dds: no visible global function definition for
'write.table'
update_tasklist_dds: no visible binding for global variable
'number_of_parameters'
update_tasklist_dds: no visible binding for global variable
'part_xchange'
update_tasklist_dds: no visible binding for global variable 'r'
update_tasklist_dds: no visible global function definition for 'runif'
update_tasklist_dds: no visible global function definition for 'rnorm'
update_tasklist_pso: no visible global function definition for
'write.table'
update_tasklist_pso: no visible global function definition for
'flush.console'
update_tasklist_pso: no visible binding for global variable
'number_of_parameters'
update_tasklist_pso: no visible global function definition for 'runif'
Undefined global functions or variables:
capture.output dev.cur dev.list dev.set flush.console hist
installed.packages legend lines median mpi.any.source mpi.any.tag
mpi.bcast.Robj2slave mpi.bcast.cmd mpi.close.Rslaves mpi.comm.rank
mpi.comm.size mpi.get.sourcetag mpi.iprobe mpi.recv.Robj
mpi.remote.exec mpi.send.Robj mpi.spawn.Rslaves mpi.universe.size
number_of_parameters object_names objective_function open3d palette
par part_xchange perform_task persp plot plot.new points points3d
quantile r randomLHS read.table rgl.pop rnorm runif slave.hostinfo
surface3d terrain.colors topo.colors trans3d write.table x11
Consider adding
importFrom("grDevices", "dev.cur", "dev.list", "dev.set", "palette",
"terrain.colors", "topo.colors", "trans3d", "x11")
importFrom("graphics", "hist", "legend", "lines", "par", "persp",
"plot", "plot.new", "points")
importFrom("stats", "median", "quantile", "rnorm", "runif")
importFrom("utils", "capture.output", "flush.console",
"installed.packages", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: pkg-internal.Rd:25-27: Dropping empty section \arguments
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'optim_pso':
optim_dds
Code: function(objective_function = sample_function,
number_of_parameters = 2, number_of_particles = 1,
max_number_function_calls = 500, r = 0.2, abstol =
-Inf, reltol = -Inf, max_wait_iterations = 50,
parameter_bounds = cbind(rep(-1,
number_of_parameters), rep(1, number_of_parameters)),
initial_estimates = NULL, lhc_init = FALSE,
part_xchange = 2, do_plot = NULL, wait_for_keystroke =
FALSE, logfile = "dds.log", projectfile = "dds.pro",
save_interval = ceiling(number_of_particles/4),
load_projectfile = "try", break_file = NULL,
plot_progress = FALSE, tryCall = FALSE, verbose =
FALSE, ...)
Docs: function(objective_function = sample_function,
number_of_parameters = 2, number_of_particles = 1,
max_number_function_calls = 500, r = 0.2, abstol =
-Inf, reltol = -Inf, max_wait_iterations = 50,
parameter_bounds = cbind(rep(-1,
number_of_parameters), rep(1, number_of_parameters)),
initial_estimates = NULL, part_xchange = 2, lhc_init =
FALSE, do_plot = NULL, wait_for_keystroke = FALSE,
logfile = "dds.log", projectfile = "dds.pro",
save_interval = ceiling(number_of_particles/4),
load_projectfile = "try", break_file = NULL,
plot_progress = FALSE, tryCall = FALSE, verbose =
FALSE, ...)
Mismatches in argument names:
Position: 11 Code: lhc_init Docs: part_xchange
Position: 12 Code: part_xchange Docs: lhc_init
optim_pdds_robust
Code: function(objective_function = sample_function,
number_of_parameters = 2, number_of_particles = 1,
max_number_function_calls = 500, r = 0.2, abstol =
-Inf, reltol = -Inf, max_wait_iterations = 50,
parameter_bounds = cbind(rep(-1,
number_of_parameters), rep(1, number_of_parameters)),
initial_estimates = NULL, lhc_init = FALSE,
part_xchange = 2, do_plot = NULL, wait_for_keystroke =
FALSE, logfile = "dds.log", projectfile = "dds.pro",
save_interval = ceiling(number_of_particles/4),
load_projectfile = "try", break_file = NULL,
plot_progress = FALSE, tryCall = FALSE, nslaves = -1,
working_dir_list = NULL, execution_timeout = NULL,
maxtries = 10, verbose = FALSE, ...)
Docs: function(objective_function = sample_function,
number_of_parameters = 2, number_of_particles = 1,
max_number_function_calls = 500, r = 0.2, abstol =
-Inf, reltol = -Inf, max_wait_iterations = 50,
parameter_bounds = cbind(rep(-1,
number_of_parameters), rep(1, number_of_parameters)),
initial_estimates = NULL, part_xchange = 2, lhc_init =
FALSE, do_plot = NULL, wait_for_keystroke = FALSE,
logfile = "dds.log", projectfile = "dds.pro",
save_interval = ceiling(number_of_particles/4),
load_projectfile = "try", break_file = NULL,
plot_progress = FALSE, tryCall = FALSE, nslaves = -1,
working_dir_list = NULL, execution_timeout = NULL,
maxtries = 10, verbose = FALSE, ...)
Mismatches in argument names:
Position: 11 Code: lhc_init Docs: part_xchange
Position: 12 Code: part_xchange Docs: lhc_init

Codoc mismatches from documentation object 'check_execution_timeout':
check_execution_timeout
Code: function(verbose_master)
Docs: function(maxtries = 10)
Argument names in code not in docs:
verbose_master
Argument names in docs not in code:
maxtries
Mismatches in argument names:
Position: 1 Code: verbose_master Docs: maxtries
prepare_mpi_cluster
Code: function(nslaves, working_dir_list = NULL, verbose_slave =
FALSE, ...)
Docs: function(nslaves, working_dir_list = NULL, verbose_slave =
FALSE)
Argument names in code not in docs:
...

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
'/00check.log'
for details.



Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Windows (R 2.11.x)

* checking for file 'ppso/DESCRIPTION' ... OK
* preparing 'ppso':
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
WTFPL
Standardizable: FALSE
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'ppso' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** MD5 sums
** testing if installed package can be loaded
packaged installation of 'ppso' as ppso_0.9-934.zip

* DONE (ppso)


Build log for Windows 64-bit (R 2.11.x)

* checking for file 'ppso/DESCRIPTION' ... OK
* preparing 'ppso':
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
WTFPL
Standardizable: FALSE
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'ppso' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** MD5 sums
** testing if installed package can be loaded
packaged installation of 'ppso' as ppso_0.9-934.zip

* DONE (ppso)


Build log for Mac OS X 10.5 (R 2.16.x)

* installing *source* package 'ppso' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - ppc
*** arch - x86_64
packaged installation of 'ppso' as 'ppso_0.9-948.tgz'

* DONE (ppso)

Build log for Windows 7 (R 3.0.x)

(ppso 0.9-986)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'ppso' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'ppso' as ppso_0.9-986.zip
* DONE (ppso)