* using log directory 'd:/RCompile/CRANincoming/R-devel/CDsampling.Rcheck' * using R Under development (unstable) (2024-09-21 r87186 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 'CDsampling/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CDsampling' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Yifei Huang ' New submission License components with restrictions and base license permitting such: MIT + file LICENSE Possibly misspelled words in DESCRIPTION: CDsampling (8:199) EW (3:36) multinomial (8:753) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "Yifei", family = "Huang", role = c("aut", "cre"), email = "yhuan39@uic.edu"), person(given = "Liping", family = "Tong", role = "aut"), person(given = "Jie", family = "Yang", role = "aut")) as necessary. The Title field should be in title case. Current version is: 'locally D-optimal sampling, EW D-optimal sampling and uniform sampling for paid research studies with or without constraints' In title case that is: 'Locally D-Optimal Sampling, EW D-Optimal Sampling and Uniform Sampling for Paid Research Studies with or without Constraints' * 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 'CDsampling' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... WARNING Invalid license file pointers: LICENSE Packages listed in more than one of Depends, Imports, Suggests, Enhances: 'lpSolve' 'Rglpk' A package should be listed in only one of these fields. * 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 ... NOTE Packages in Depends field not imported from: 'Rglpk' 'lpSolve' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE W_func_GLM: no visible global function definition for 'dnorm' W_func_GLM: no visible global function definition for 'pnorm' liftone_GLM: no visible global function definition for 'rexp' liftone_MLM: no visible global function definition for 'rexp' liftone_MLM: no visible global function definition for 'optim' liftone_constrained_GLM: no visible global function definition for 'rexp' liftone_constrained_GLM: no visible global function definition for 'uniroot' liftone_constrained_GLM: no visible global function definition for 'runif' liftone_constrained_MLM: no visible global function definition for 'rnorm' liftone_constrained_MLM: no visible global function definition for 'Rglpk_solve_LP' liftone_constrained_MLM: no visible global function definition for 'rexp' liftone_constrained_MLM: no visible global function definition for 'optim' liftone_constrained_MLM: no visible global function definition for 'lp' liftone_constrained_MLM: no visible global function definition for 'uniroot' Undefined global functions or variables: Rglpk_solve_LP dnorm lp optim pnorm rexp rnorm runif uniroot Consider adding importFrom("stats", "dnorm", "optim", "pnorm", "rexp", "rnorm", "runif", "uniroot") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'F_func_MLM.Rd': \examples lines wider than 100 characters: bvec_temp = c(-4.047, -2.225, -0.302, 1.386, 4.214, 3.519, 2.420, 1.284, -0.131, -0.376, -0.237, -0.120) Rd file 'Fdet_func_MLM.Rd': \examples lines wider than 100 characters: bvec_temp = c(-4.047, -2.225, -0.302, 1.386, 4.214, 3.519, 2.420, 1.284, -0.131, -0.376, -0.237, -0.120) Rd file 'Fi_func_MLM.Rd': \examples lines wider than 100 characters: Example reference: Section 5 in Yifei, H., Liping, T., Yang, J. (2023) Constrained D-optimal design for paid research study bvec_temp = c(-4.047, -2.225, -0.302, 1.386, 4.214, 3.519, 2.420, 1.284, -0.131, -0.376, -0.237, -0.120) Rd file 'W_func_GLM.Rd': \examples lines wider than 100 characters: Example 6 the clinical trial example in Yifei, H., Liping, T., Yang, J. (2023) Constrained D-optimal design for paid research study X.liftone=matrix(data=c(1,0,0,0,1,0,1,0,1,0,0,1,1,1,0,0,1,1,1,0,1,1,0,1), ncol=4, byrow=T) #gives the 6 categories (0,0,0), (0,1,0),(0, ... [TRUNCATED] W=W_func_GLM(X= X.liftone, beta=beta, link="logit") #calculate diagonal elements of W based on beta's under logit link Rd file 'approxtoexact_constrained_func.Rd': \examples lines wider than 100 characters: exact_design = approxtoexact_constrained_func(n=200, w=c(0.25, 0.20, 0.05, 0.50, 0.00, 0.00), m=6, beta=beta, link='logit', X=X.liftone ... [TRUNCATED] Rd file 'approxtoexact_func.Rd': \examples lines wider than 100 characters: exact_design = approxtoexact_func(n=600, w=c(0.2593526, 0.0000000, 0.0000000, 0.1565024, 0.2891565, 0.0000000, 0.0000000, 0.2949885)) Rd file 'liftone_GLM.Rd': \examples lines wider than 100 characters: approximate_design = liftoneDoptimal.self(X=X, W=W_matrix, reltol=1e-10, maxit=100, random=F, nram=3, w00=w00) Rd file 'liftone_MLM.Rd': \examples lines wider than 100 characters: thetavec = c(-4.047, -0.131, 4.214, -2.225, -0.376, 3.519, -0.302, -0.237, 2.420, 1.386, -0.120, 1.284) liftone_MLM(m=m, p=p, Xi=Xi, J=J, beta=thetavec, link = "cumulative", Fi.func=Fi_func_MLM, reltol=1e-5, maxit=500, w00=NULL, random=T, ... [TRUNCATED] Rd file 'liftone_constrained_GLM.Rd': \examples lines wider than 100 characters: Example 11 the clinical trial example in Supplementary Material of Yifei, H., Liping, T., Yang, J. (2023) Constrained D-optimal design ... [TRUNCATED] X.liftone=matrix(data=c(1,0,0,0,1,0,1,0,1,0,0,1,1,1,0,0,1,1,1,0,1,1,0,1), ncol=4, byrow=T) #gives the 6 categories (0,0,0), (0,1,0),(0, ... [TRUNCATED] approximate_design = liftone_constrained_GLM(X=X.liftone, W=W_matrix, g.con=g.con, g.dir=g.dir, g.rhs=g.rhs, lower.bound=lower.bound, u ... [TRUNCATED] Rd file 'liftone_constrained_MLM.Rd': \examples lines wider than 100 characters: Example 8 of Trauma data example in Yifei, H., Liping, T., Yang, J. (2023) Constrained D-optimal design for paid research study thetavec = c(-4.3050, -0.0744, 4.3053, -2.3334, -0.3290, 3.4773, -0.1675, -0.3609, 2.7358, 1.2935, -0.1612, 1.4899) approx_design = liftone_constrained_MLM(m, ni, p, Xi, J, beta=thetavec, lower.bound=lower.bound, upper.bound=upper.bound, g.con=g.con, ... [TRUNCATED] 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 Data codoc mismatches from Rd file 'trauma_data.Rd': Variables in data frame 'trauma_data' Code: Dose ID Label Outcome Severity Docs: Dose ID Outcome Severity label * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'approxtoexact_constrained_func.Rd' 'm' 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 ... ERROR Warning: parse error in file 'lines': 9: unexpected ',' 20: 21: w = (1/3, ^ ** will not attempt to run examples * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 4 NOTEs