* using log directory 'd:/RCompile/CRANincoming/R-devel/octopus.Rcheck' * using R Under development (unstable) (2024-07-10 r86888 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'octopus/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'octopus' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... WARNING Maintainer: 'The package maintainer ' Insufficient package version (submitted: 0.1.0, existing: 0.4.2) New maintainer: The package maintainer Old maintainer(s): Marcus Codrescu Possibly misspelled words in DESCRIPTION: clusterings (7:308) The Description field should not start with the package name, 'This package' or similar. DESCRIPTION fields with placeholder content: Maintainer: The package maintainer * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking serialization versions ... OK * checking whether package 'octopus' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING plot: function(x, ...) plot.octopus: function(M2, cex, lab.pos, n, distance, method, prop, Name, ylim, xlim, verbose, orientation) text: function(x, ...) text.octopus: function(M2, support, sep.lab, disp, verbose, orientation) See section 'Generic functions and methods' in the 'Writing R Extensions' manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [15s] NOTE IDscluster2: no visible binding for global variable 'LIST_HCLUST' plot.octopus: no visible binding for global variable 'LIST_HCLUST' text.octopus: no visible binding for global variable 'LIST_HCLUST' Undefined global functions or variables: LIST_HCLUST * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Functions or methods with usage in Rd file 'plot.octopus.Rd' but not in code: 'plot' Functions or methods with usage in Rd file 'text.octopus.Rd' but not in code: 'text' Codoc mismatches from Rd file 'F1.Rd': compsim2 Code: function(M) Docs: function(A, B) Argument names in code not in docs: M Argument names in docs not in code: A B Mismatches in argument names: Position: 1 Code: M Docs: A Codoc mismatches from Rd file 'IDscluster2.Rd': IDscluster2 Code: function(M2 = LIST_HCLUST[[length(LIST_HCLUST)]]) Docs: function(M2 = M2) Mismatches in argument default values: Name: 'M2' Code: LIST_HCLUST[[length(LIST_HCLUST)]] Docs: M2 Codoc mismatches from Rd file 'glzcluster.Rd': glzcluster Code: function(data, n = NULL, prop = NULL, distance = NULL, method = NULL, Name = NULL) Docs: function(data = data, n = 1000, prop = 0.8, distance = "bray", method = "average") Argument names in code not in docs: Name Mismatches in argument default values (first 3): Name: 'data' Code: Docs: data Name: 'n' Code: NULL Docs: 1000 Name: 'prop' Code: NULL Docs: 0.8 Codoc mismatches from Rd file 'glzcluster2.Rd': glzcluster2 Code: function(data = data, n = NULL, prop = NULL, distance = NULL, method = NULL, Name = NULL) Docs: function(data = data, n = 1000, prop = 0.8, distance = "bray", method = "average") Argument names in code not in docs: Name Mismatches in argument default values (first 3): Name: 'n' Code: NULL Docs: 1000 Name: 'prop' Code: NULL Docs: 0.8 Name: 'distance' Code: NULL Docs: "bray" Codoc mismatches from Rd file 'glzcs.Rd': glzcs Code: function(GRPs = GRPs, M2 = M2) Docs: function(GRPs = GRPs, LIST_HCLUST = LIST_HCLUST) Argument names in code not in docs: M2 Argument names in docs not in code: LIST_HCLUST Mismatches in argument names: Position: 2 Code: M2 Docs: LIST_HCLUST Codoc mismatches from Rd file 'octopus.Rd': octopus Code: function(data, n = NULL, prop = NULL, resample = TRUE, distance = NULL, method = NULL, orientation = NULL, disp = NULL, lab.pos = NULL, sep.lab = NULL, xlim = NULL, ylim = NULL, verbose = NULL) Docs: function(data, n = 1000, prop = 0.8, resample = TRUE, distance = "bray", method = "average", orientation = "r", disp = "sig", lab.pos = 0.09, sep.lab = 0.6, xlim = NULL, ylim = NULL, verbose = TRUE) Mismatches in argument default values (first 3): Name: 'n' Code: NULL Docs: 1000 Name: 'prop' Code: NULL Docs: 0.8 Name: 'distance' Code: NULL Docs: "bray" * checking Rd \usage sections ... WARNING Objects in \usage without \alias in Rd file 'F1.Rd': 'compsim2' Documented arguments not in \usage in Rd file 'glzcluster.Rd': 'Name' Documented arguments not in \usage in Rd file 'glzcluster2.Rd': 'Name' Objects in \usage without \alias in Rd file 'plot.octopus.Rd': 'plot' Objects in \usage without \alias in Rd file 'text.octopus.Rd': 'text' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... [26s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed octopus 15.4 0.16 16.49 * checking PDF version of manual ... [20s] OK * checking HTML version of manual ... OK * DONE Status: 4 WARNINGs, 2 NOTEs