ppso
About ppso
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Version: 0.9-99991
Result: WARNING Check time: 2021-09-08 05:57 * using log directory '' * using R Under development (unstable) (2021-09-06 r80865) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: ASCII * using option '--as-cran' * checking for file 'ppso/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ppso' version '0.9-99991' * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: 'Rmpi' * 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 serialization versions ... OK * checking whether package 'ppso' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... NOTE Non-standard files/directories found at top level: 'ppso.Rproj' 'readme.md' * 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 Found an obsolete/platform-specific call in the following functions: 'do_plot_function' 'plot_optimization_progress' Found the platform-specific device: 'x11' dev.new() is the preferred way to open a new device, in the unlikely event one is needed. .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 '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 'savePlot' 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.new points points3d quantile r randomLHS read.table rgl.pop rnorm runif savePlot slave.hostinfo surface3d terrain.colors topo.colors trans3d write.table x11 Consider adding importFrom("grDevices", "dev.cur", "dev.list", "dev.set", "palette", "savePlot", "terrain.colors", "topo.colors", "trans3d", "x11") importFrom("graphics", "hist", "legend", "lines", "par", "persp", "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 line widths ... NOTE Rd file 'optim_ppso.Rd': \usage lines wider than 90 characters: wait_complete_iteration = FALSE, parameter_bounds = cbind(rep(-1, number_of_parameters), rep(1, number_of_parameters)), projectfile = "ppso.pro", save_interval = ceiling(number_of_particles/4), load_projectfile = "try", wait_complete_iteration = FALSE, parameter_bounds = cbind(rep(-1, number_of_parameters), rep(1, number_of_parameters)), projectfile = "ppso.pro", save_interval = ceiling(number_of_particles/4), load_projectfile = "try", projectfile = "dds.pro", save_interval = ceiling(number_of_particles/4), load_projectfile = "try", projectfile = "dds.pro", save_interval = ceiling(number_of_particles/4), load_projectfile = "try", \examples lines wider than 100 characters: result = optim_pso(objective_function=rastrigin_function, projectfile=NULL, logfile=NULL, do_plot="rgl") result = optim_dds(objective_function=rastrigin_function, projectfile=NULL, logfile=NULL, do_plot="base") result = optim_pso(objective_function=rastrigin_function, projectfile=projectfile, logfile=NULL, load_projectfile="no") ... [TRUNCATED] result = optim_pso(objective_function=rastrigin_function, projectfile=projectfile, logfile=NULL, load_projectfile="yes") ... [TRUNCATED] result = optim_pso(objective_function=rastrigin_function, projectfile=projectfile, logfile=logfile, load_projectfile="no", plot ... [TRUNCATED] result = optim_ppso_robust(objective_function=rastrigin_function, nslaves=2, max_number_function_calls=200, projectfile=NULL, l ... [TRUNCATED] result = optim_pdds_robust(objective_function=rastrigin_function, nslaves=2, max_number_function_calls=200, projectfile=NULL, l ... [TRUNCATED] result = optim_pdds_robust(objective_function=rastrigin_function, nslaves=4, working_dir_list=working_dir_list) Rd file 'plot_optimization_progress.Rd': \usage lines wider than 90 characters: plot_optimization_progress (logfile="pso.log", projectfile="pso.pro", progress_plot_filename=NULL, goodness_plot_filename=NULL, cutoff_ ... [TRUNCATED] \examples lines wider than 100 characters: result = optim_pso(objective_function=rastrigin_function, projectfile=projectfile, logfile=logfile, load_projectfile="no") ... [TRUNCATED] Rd file 'push_object.Rd': \examples lines wider than 100 characters: result = optim_pdds_robust(objective_function=interact_function, projectfile=NULL, logfile=NULL, load_projectfile="no", Rd file 'request_object.Rd': \examples lines wider than 100 characters: result = optim_pdds_robust(objective_function=interact_function, projectfile=NULL, logfile=NULL, load_projectfile="no", Rd file 'sample_function.Rd': \examples lines wider than 100 characters: # cat("error in objective function simulated by slave ",mpi.comm.rank(), file=paste("slave",mpi.comm.rank(),".log",sep="")) These lines will be truncated in the PDF manual. * 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, verbose = FALSE, nslaves = -1, working_dir_list = NULL, execution_timeout = NULL, maxtries = 10, ...) 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, nslaves = -1, working_dir_list = NULL, execution_timeout = NULL, maxtries = 10, ...) 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: ... Codoc mismatches from documentation object 'plot_optimization_progress': plot_optimization_progress Code: function(logfile = "pso.log", projectfile = "pso.pro", progress_plot_filename = NULL, goodness_plot_filename = NULL, cutoff_quantile = 0.95, verbose = FALSE, plots = c("eval_vs_param", "param_vs_objfun")) Docs: function(logfile = "pso.log", projectfile = "pso.pro", progress_plot_filename = NULL, goodness_plot_filename = NULL, cutoff_quantile = 0.95, verbose = FALSE) Argument names in code not in docs: plots * 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 * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 WARNING, 7 NOTEs See '/00check.log' for details. Installation log: 00install.out
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) |