* 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 <yhuan39@uic.edu>'

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