* using log directory 'd:/Rcompile/CRANpkg/local/4.3/geex.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'geex/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geex' version '1.1.1'
* package encoding: UTF-8
* 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 whether package 'geex' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [0s] 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 ... [18s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [65s] OK
  Running 'testthat.R' [65s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [177s] ERROR
Error(s) in re-building vignettes:
--- re-building 'v00_geex_intro.Rmd' using rmarkdown


  |   SB1_estfun <- function(data){
  |     Y1 <- data$Y1
  |     function(theta){
  |         c(Y1 - theta[1],
  |          (Y1 - theta[1])^2 - theta[2])
  |     }
  |   } 


  |   library(geex)
  |   results <- m_estimate(
  |       estFUN = SB1_estfun, 
  |       data   = geexex,
  |       root_control = setup_root_control(start = c(1,1))) 


  |   n <- nrow(geexex)
  |   A <- diag(1, nrow = 2)
  |   
  |   B <- with(geexex, {
  |     Ybar <- mean(Y1)
  |     B11 <- mean( (Y1 - Ybar)^2 )
  |     B12 <- mean( (Y1 - Ybar) * ((Y1 - Ybar)^2 - B11) )
  |     B22 <- mean( ((Y1 - Ybar)^2 - B11)^2 )
  |     matrix(
  |       c(B11, B12,
  |         B12, B22), nrow = 2
  |     )
  |   })
  |   
  |   # closed form roots
  |   theta_cls <- c(mean(geexex$Y1),
  |                  # since var() divides by n - 1, not n
  |                  var(geexex$Y1) * (n - 1)/ n ) 
  |   
  |   # closed form sigma
  |   Sigma_cls <- (solve(A) %*% B %*% t(solve(A))) / n
  |   
  |   comparison <- list(geex = list(estimates = coef(results), vcov = vcov(results)), 
  |                      cls  = list(estimates = theta_cls, vcov = Sigma_cls)) 

  |  format(max(abs(comparison$geex$estimates - comparison$cls$estimates), abs(comparison$geex$vcov - comparison$cls$vcov)), digits = 1)  #757:891

  |   comparison 


  |   SB2_estfun <- function(data){
  |     Y1 <- data$Y1; Y2 <- data$Y2
  |     function(theta){
  |         c(Y1 - theta[1],
  |           Y2 - theta[2],
  |           theta[1] - (theta[3] * theta[2]) 
  |       )
  |     }
  |   } 


  |   results <- m_estimate(
  |       estFUN = SB2_estfun, 
  |       data  = geexex, 
  |       root_control = setup_root_control(start = c(1, 1, 1))) 


  |   # Comparison to an analytically derived sanwich estimator
  |   A <- with(geexex, {
  |    matrix(
  |     c(1 , 0, 0,
  |       0 , 1, 0,
  |       -1, mean(Y1)/mean(Y2), mean(Y2)),
  |     byrow = TRUE, nrow = 3)
  |   })
  |   
  |   B <- with(geexex, {
  |     matrix(
  |       c(var(Y1)   , cov(Y1, Y2), 0,
  |         cov(Y1, Y2), var(Y2)   , 0,
  |         0, 0, 0),
  |       byrow = TRUE, nrow = 3)
  |   })
  |   
  |   ## closed form roots
  |   theta_cls <- c(mean(geexex$Y1), mean(geexex$Y2))
  |   theta_cls[3] <- theta_cls[1]/theta_cls[2]
  |   ## closed form covariance
  |   Sigma_cls <- (solve(A) %*% B %*% t(solve(A))) / nrow(geexex)
  |   comparison <- list(geex = list(estimates = coef(results), vcov = vcov(results)), 
  |                      cls  = list(estimates = theta_cls, vcov = Sigma_cls)) 

  |  format(max(abs(comparison$geex$estimates - comparison$cls$estimates)), digits = 2)  #261:346
  |  format(max(abs(comparison$geex$vcov - comparison$cls$vcov)), scientific = TRUE, digits = 2)  #438:532

  |   comparison 


  |   SB3_estfun <- function(data){
  |     Y1 <- data$Y1
  |     function(theta){
  |         c(Y1 - theta[1],
  |          (Y1 - theta[1])^2 - theta[2],
  |          sqrt(theta[2]) - theta[3],
  |          log(theta[2]) - theta[4])
  |     }
  |   } 


  |   results <- m_estimate(
  |      estFUN= SB3_estfun, 
  |      data  = geexex,
  |      root_control = setup_root_control(start = rep(2, 4, 4, 4))) 


  |   ## closed form roots
  |   theta_cls <- numeric(4)
  |   theta_cls[1] <- mean(geexex$Y1)
  |   theta_cls[2] <- sum((geexex$Y1 - theta_cls[1])^2)/nrow(geexex)
  |   theta_cls[3] <- sqrt(theta_cls[2])
  |   theta_cls[4] <- log(theta_cls[2])
  |   
  |   ## Compare to closed form ##
  |   theta2 <- theta_cls[2]
  |   mu3 <- moments::moment(geexex$Y1, order = 3, central = TRUE)
  |   mu4 <- moments::moment(geexex$Y1, order = 4, central = TRUE)
  |   ## closed form covariance
  |   Sigma_cls <- matrix(
  |     c(theta2, mu3, mu3/(2*sqrt(theta2)), mu3/theta2,
  |       mu3, mu4 - theta2^2, (mu4 - theta2^2)/(2*sqrt(theta2)), (mu4 - theta2^2)/theta2,
  |       mu3/(2 * sqrt(theta2)), (mu4 - theta2^2)/(2*sqrt(theta2)), (mu4 - theta2^2)/(4*theta2), (mu4 - theta2^2)/(2*theta2^(3/2)),
  |       mu3/theta2, (mu4 - theta2^2)/theta2, (mu4 - theta2^2)/(2*theta2^(3/2)), (mu4/theta2^2) - 1) ,
  |     nrow = 4, byrow = TRUE) / nrow(geexex)
  |   ## closed form covariance
  |   # Sigma_cls <- (solve(A) %*% B %*% t(solve(A))) / n
  |   comparison <- list(geex = list(estimates = coef(results), vcov = vcov(results)), 
  |                      cls  = list(estimates = theta_cls, vcov = Sigma_cls)) 

  |  format(max(abs(comparison$geex$estimates - comparison$cls$estimates), abs(comparison$geex$vcov - comparison$cls$vcov)), digits = 2)  #234:368

  |   comparison 

--- finished re-building 'v00_geex_intro.Rmd'

--- re-building 'v01_additional_examples.Rmd' using rmarkdown
--- finished re-building 'v01_additional_examples.Rmd'

--- re-building 'v02_sandwich_comparison.Rmd' using rmarkdown
--- finished re-building 'v02_sandwich_comparison.Rmd'

--- re-building 'v03_root_solvers.Rmd' using rmarkdown
--- finished re-building 'v03_root_solvers.Rmd'

--- re-building 'v04_weights.Rmd' using rmarkdown
--- finished re-building 'v04_weights.Rmd'

--- re-building 'v05_finite_sample_corrections.Rmd' using rmarkdown
--- finished re-building 'v05_finite_sample_corrections.Rmd'

--- re-building 'v06_causal_example.Rmd' using rmarkdown
--- finished re-building 'v06_causal_example.Rmd'

--- re-building 'v07_geex_design.Rmd' using rmarkdown
--- finished re-building 'v07_geex_design.Rmd'

+-+v07_geex_design.html
SUMMARY: processing the following file failed:
  'v07_geex_design.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [9s] OK
* DONE
Status: 1 ERROR