* using log directory 'd:/Rcompile/CRANpkg/local/4.7/glmMisrep.Rcheck'
* using R Under development (unstable) (2026-08-24 r90445 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* current time: 2026-08-25 16:41:38 UTC
* checking for file 'glmMisrep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glmMisrep' version '0.1.2'
* 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 ... [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 ... [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 ... [12s] 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 ... [1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [16s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [20s] ERROR
  Running 'LN-testing.R' [5s]
  Running 'NB-testing.R' [4s]
  Running 'Norm-testing.R' [2s]
  Running 'Pois-testing.R' [7s]
  Running 'gamma-testing.R' [1s]
Running the tests in 'tests/gamma-testing.R' failed.
Complete output:
  > require(glmMisrep)
  Loading required package: glmMisrep
  > 
  > data <- data.frame( Y = c(45.857704, 26.966636, 1058.634073, 623.319053, 1087.177701, 19.323827, 86.047383, 606.742023,
  +                       1647.937035, 266.180140, 157.192319, 281.382229, 648.672212, 140.771360, 102.904828, 380.052888,
  +                         22.064627, 208.741717, 67.074619, 174.856091, 31.569650, 626.408259, 993.658540, 189.571355,
  +                        374.603446, 1802.252002, 543.301728, 158.015234, 104.378652, 582.149021, 52.249839, 45.702009,
  +                      11806.824361, 10053.322011,  1.087628, 55.884707, 271.186925, 178.080733, 563.668826, 1596.744067,
  +                          8.947570, 398.868445, 39.580796, 1293.273355, 23.025039, 184.609120, 238.859666, 169.540935,
  +                       775.025538, 4.616906),
  +                     X1 = c(1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1,
  +                            0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0),
  +                     X2 = c(-1.072049676,  0.727369558,  1.420449831,  0.919953091,  0.274830496,  0.546589583,  0.766522073,  0.102791747,
  +                              0.326183969,  1.929334793, -0.843138417, -0.064225873,  0.256683194,  0.625580034,  0.469241089,  0.255148171,
  +                             -0.235947534,  1.816474277, -1.692768826, -1.068503018, -0.137072147,  0.772976621, -0.719329599, -1.581414358,
  +                              0.049968814,  0.184292275, -1.321527190,  0.593936587, -1.441344834,  0.493651003, -0.468055987, -0.312559805,
  +                             -0.196035448, -0.541855456,  1.913445157,  0.403104413, -1.503943713,  0.401514018,  1.613023384, -1.063038013,
  +                              0.414808888,  0.417654550,  0.410841245,  0.218083137, -0.462372658, -0.908533492,  0.157572760,  0.750073708,
  +                              0.005803132,  0.152076943),
  +                     X3 = c(0.48973164, 0.69612108, 0.81936453, 0.83451060, 0.97515909, 0.88015868, 0.88890374, 0.37991780, 0.89681143, 0.99601041,
  +                             0.67524620, 0.92379599, 0.85120739, 0.41159392, 0.53689827, 0.77538594, 0.19803702, 0.95549912, 0.14601890, 0.80506128,
  +                             0.12918729, 0.89932864, 0.74272902, 0.47642162, 0.29003290, 0.61241891, 0.62205612, 0.77209866, 0.83853287, 0.80933236,
  +                             0.42349111, 0.81845100, 0.95771341, 0.73298222, 0.02518371, 0.63923492, 0.54736138, 0.57766185, 0.64674272, 0.54556027,
  +                             0.76556145, 0.74711758, 0.74089894, 0.99431826, 0.49083626, 0.27663899, 0.85629864, 0.71527708, 0.62011519, 0.25683099),
  +                     Sex = c("Female", "Female", "Male",   "Male",   "Female", "Female", "Female", "Female", "Female", "Female", "Female", "Male",
  +                             "Female", "Male",   "Male",   "Female", "Female", "Male",   "Male",   "Female", "Female", "Female", "Male",   "Male",
  +                             "Male",   "Female", "Male",   "Female", "Male",   "Female", "Male",   "Male",   "Male",   "Male",   "Female", "Female",
  +                             "Female", "Female", "Male",   "Male",   "Female", "Female", "Male",   "Female", "Male",   "Male",   "Male",   "Female",
  +                             "Male",   "Female"),
  +                     Race = c("Other", "White", "Black", "White", "White", "Other", "White", "White", "Other", "Other", "Other", "Black", "White", "Other",
  +                               "Black", "Black", "Black", "Black", "White", "Black", "White", "White", "Black", "White", "Black", "Black", "Black", "Other",
  +                               "Other", "Black", "White", "Other", "Black", "White", "Other", "White", "White", "Black", "Black", "White", "Other", "White",
  +                               "Black", "Other", "White", "White", "White", "White", "Black", "Black"),
  +                     V_star = c(0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0) )
  > 
  > data$Race <- as.factor(data$Race)
  > data$Sex <- as.factor(data$Sex)
  > 
  > t1 <- tryCatch(gammaRegMisrepEM(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 (should be Y, not y)
  > stopifnot(
  +   t1$message == "object 'y' not found"
  + )
  > 
  > 
  > t2 <- tryCatch(gammaRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_Star",
  +                                 data = data,
  +                                 lambda = c(0.6,0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Argument to 'v_star' is misspelled
  > stopifnot(
  +   t2$message == "variable V_Star not present in dataframe"
  + )
  > 
  > 
  > data$V_star <- ifelse(data$V_star == 1, yes = "yes", no = "no")
  > 
  > t3 <- tryCatch(gammaRegMisrepEM(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(gammaRegMisrepEM(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(gammaRegMisrepEM(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$V_star == 1, yes = 1, no = 0)
  > 
  > t6 <- tryCatch(gammaRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.49, 0.52),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Inappropriately specified lambda argument
  > stopifnot(
  +   t6$message == "Lambda vector must sum to one"
  + )
  > 
  > 
  > t7 <- tryCatch(gammaRegMisrepEM(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$X2*0.3
  > 
  > t8 <- tryCatch(gammaRegMisrepEM(formula = Y ~ X1 + X2 + X3 + X4 + Sex + Race + V_star,
  +                                 v_star = "V_star",
  +                                 data = data,
  +                                 lambda = c(0.6, 0.4),
  +                                 epsilon = 1e-08,
  +                                 maxit = 10000,
  +                                 maxrestarts = 20),
  +                error = function(x) x )
  > 
  > # Linearly dependent covariates/degenerate design matrix
  > stopifnot(
  +   t8$message == "Linear dependencies exist in the covariates"
  + )
  > 
  > t9 <- tryCatch(gammaRegMisrepEM(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 is not present in formula argument
  > stopifnot(
  +   t9$message == "v_star variable must be specified in 'formula'"
  + )
  > 
  > # EM algorithm should fail to converge within the specified number of attempts
  > t10 <- tryCatch(
  +   capture.output(gammaRegMisrepEM(formula = Y ~ X1 + X2 + X3 + Sex + Race + V_star,
  +                                     v_star = "V_star",
  +                                     data = data,
  +                                     lambda = c(0.6, 0.4),
  +                                     epsilon = 1e-08,
  +                                     maxit = 3,
  +                                     maxrestarts = 4)),
  +   error = function(x) x
  + )
  number of iterations = 2
  > 
  > stopifnot(
  +   t10$message == "NOT CONVERGENT! Failed to converge after 4 attempts"
  + )
  Error in t10$message : $ operator is invalid for atomic vectors
  Calls: stopifnot
  Execution halted
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [1s] OK
* DONE
Status: 1 ERROR