* using log directory 'd:/Rcompile/CRANpkg/local/4.5/glmMisrep.Rcheck'
* using R Under development (unstable) (2024-05-30 r86651 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 'glmMisrep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmMisrep' version '0.1.1'
* 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 'glmMisrep' can be installed ... OK
* checking installed package size ... OK
* checking package 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s] OK
* checking loading without being on the library search path ... [0s] 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 ... [10s] 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 examples ... [14s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [11s] ERROR
  Running 'LN-testing.R' [2s]
  Running 'NB-testing.R' [2s]
  Running 'Norm-testing.R' [1s]
  Running 'Pois-testing.R' [3s]
  Running 'gamma-testing.R' [4s]
Running the tests in 'tests/Pois-testing.R' failed.
Complete output:
  > require(glmMisrep)
  Loading required package: glmMisrep
  > 
  > data <- data.frame( Y = c(0,   0,   2,   0,   3,   0,  36,   0,   2,   1,   0,   2,   6,   9,   0,   0,   0,   0,   7,   1,   1,   2,  50,   4,   0,   0,   0,   1,
  +                           0,   0,   0,   3,   0,   0,   1,   0,   1,   3, 176,   0,   0,   0,   0,   0,   2, 286,   0,   0,   0,  18),
  +                     X1 = c(0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1),
  +                     X2 = c(1.71870212, -0.55840901,  1.22589915,  0.53000107,  0.62571132,  0.02873955,  0.30989954,  1.35514993,  0.15587503,
  +                              0.27987513,  0.48892178,  0.35218767,  0.52382778,  1.58126751, -0.07855081, -0.57128802, -0.92500953, -2.48543328,
  +                              0.03810910,  0.39929906, -0.54854763, -0.10505694,  0.45120734,  0.32295222, -0.68595918, -0.66892486,  1.72253431,
  +                             -0.28425276, -0.67719912, -0.39644260, -0.16843500,  0.90540261, -1.38574804,  0.14456841,  0.44142810, -1.89442541,
  +                             -0.65961894,  2.13148776,  1.72410805, -1.60207312, -1.09525034, -1.31327168, -0.43378445,  1.33644956,  1.28938359,
  +                              0.90232362, -0.94112768, -0.61851917,  0.37033085, -0.47019541),
  +                     X3 = c(0.6882029, 0.9934165, 0.9173388, 0.9406660, 0.5130041, 0.8590187, 0.4468488, 0.4186652, 0.5098278, 0.3339481, 0.6922477,
  +                             0.6793977, 0.4983724, 0.6079911, 0.7763041, 0.8529067, 0.8287771, 0.9125900, 0.4802076, 0.8981448, 0.3570093, 0.9209584,
  +                             0.4353817, 0.9426418, 0.9550002, 0.4869851, 0.9560156, 0.8247537, 0.1939687, 0.6103839, 0.7721900, 0.5980044, 0.8683831,
  +                             0.7004518, 0.8577210, 0.3576712, 0.9540088, 0.9880046, 0.4304899, 0.7416618, 0.6656063, 0.8920356, 0.6097593, 0.8008748,
  +                             0.8110432, 0.5967969, 0.6983106, 0.9471680, 0.9929186, 0.9059200),
  +                     Sex = c("Female", "Male",   "Male",   "Female", "Male",   "Female", "Male",   "Male",   "Female", "Female", "Male",   "Male",
  +                              "Male",   "Female", "Male",   "Male",   "Female", "Female", "Male",   "Female", "Female", "Male",   "Female", "Male",
  +                              "Male",   "Male",   "Male",   "Female", "Female", "Female", "Male",   "Male",   "Male",   "Male",   "Female", "Female",
  +                              "Female", "Female", "Male",   "Male",   "Male",   "Male",   "Male",   "Male",   "Female", "Male",   "Male",   "Female",
  +                              "Female", "Male"),
  +                     Race = c("Black", "White", "White", "White", "White", "White", "Black", "Black", "Black", "Black", "Black", "Black", "White", "Other",
  +                               "Black", "White", "Black", "White", "Other", "Black", "White", "Other", "Other", "White", "White", "White", "Black", "Other",
  +                               "White", "Other", "White", "Black", "Other", "Black", "Other", "Other", "Other", "Black", "Other", "Black", "White", "Other",
  +                               "Black", "White", "Black", "Other", "White", "Black", "Black", "Other"),
  +                     V_star = c(0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0))
  > 
  > data$Race <- as.factor(data$Race)
  > data$Sex <- as.factor(data$Sex)
  > 
  > t1 <- tryCatch(poisRegMisrepEM(formula = y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.6,0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # The response above is inappropriately specified (y, not Y)
  > stopifnot(
  +   t1$message == "object 'y' not found"
  + )
  > 
  > 
  > t2 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_Star",
  +                                 data = data,
  +                                 lambda = c(0.6,0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Argument to 'v_star' is misspelled
  > stopifnot(
  +   t2$message == "variable V_Star not present in dataframe"
  + )
  > 
  > 
  > data$V_star <- ifelse(data$V_star == 1, yes = "yes", no = "no")
  > 
  > t3 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.6,0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > 
  > # v* variable is type character (yes and no)
  > stopifnot(
  +   t3$message == "v_star variable must be of class 'factor' or 'numeric'"
  + )
  > 
  > data$V_star <- ifelse(data$V_star == "yes", yes = 1, no = 0)
  > 
  > 
  > data$V_star[10] <- -1
  > 
  > 
  > t4 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.6,0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # v* variable must be binary
  > stopifnot(
  +   t4$message == "v_star variable must contain two unique values"
  + )
  > 
  > data$V_star[10] <- 0
  > 
  > 
  > data$V_star <- ifelse(data$V_star == 1, yes = 1, no = 2)
  > 
  > t5 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.6,0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # v* must be binary, but more specifically 0/1;
  > stopifnot(
  +   t5$message == "v_star variable must be coded with ones and zeroes"
  + )
  > 
  > 
  > 
  > data$V_star <- ifelse(data$V_star == 1, yes = 1, no = 0)
  > 
  > t6 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.49, 0.52),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Inappropriately specified lambda argument
  > stopifnot(
  +   t6$message == "Lambda vector must sum to one"
  + )
  > 
  > 
  > t7 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(1/3, 1/3, 1/3),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Inappropriately specified lambda argument
  > stopifnot(
  +   t7$message == "Lambda vector must contain two elements"
  + )
  > 
  > 
  > 
  > data$X4 <- data$X2*0.3
  > 
  > t8 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + X4 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.6, 0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Linearly dependent covariates/degenerate design matrix
  > stopifnot(
  +   t8$message == "Linear dependencies exist in the covariates"
  + )
  > 
  > 
  > t9 <- tryCatch(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race,
  +                                v_star = "V_star",
  +                                data = data,
  +                                lambda = c(0.6, 0.4),
  +                                epsilon = 1e-08,
  +                                maxit = 10000,
  +                                maxrestarts = 20),
  +                error = function(x) x )
  > 
  > #V_star variable absent from formula
  > stopifnot(
  +   t9$message == "v_star variable must be specified in 'formula'"
  + )
  > 
  > 
  > 
  > # EM algorithm should fail to converge within the specified number of attempts
  > t10 <- tryCatch(
  +   capture.output(poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                   v_star = "V_star",
  +                                   data = data,
  +                                   lambda = c(0.6, 0.4),
  +                                   epsilon = 1e-08,
  +                                   maxit = 2,
  +                                   maxrestarts = 1)),
  +   error = function(x) x
  + )
  > 
  > stopifnot(
  +   t10$message == "NOT CONVERGENT! Failed to converge after 1 attempts"
  + )
  > 
  > 
  > # On the first attempt, fails to converge, and restarts with new mixing props.
  > # Succeeds on the second attempt.
  > msg <- capture.output(
  +   t11 <-  poisRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                            v_star = "V_star",
  +                            data = data,
  +                            lambda = c(0.6, 0.4),
  +                            epsilon = 1e-08,
  +                            maxit = 16,
  +                            maxrestarts = 4, verb = TRUE),
  +   type = "message"
  + )
  Execution halted
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 1 ERROR