Check results for 'glmMisrep'

using R Under development (unstable) (2026-08-25 r90448)
using platform: x86_64-pc-linux-gnu
R was compiled by Debian clang version 22.1.8 (1+b2) Debian flang version 22.1.8 (1+b2)
running under: Debian GNU/Linux forky/sid
using session charset: UTF-8 * current time: 2026-08-28 02:19:13 UTC
checking for file ‘glmMisrep/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘glmMisrep’ version ‘0.1.2’
package encoding: UTF-8
checking CRAN incoming feasibility ... [1s/2s] OK
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checking package dependencies ... OK
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checking if there is a namespace ... OK
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checking for sufficient/correct file permissions ... OK
checking whether package ‘glmMisrep’ can be installed ... OK See the install log for details.
checking package directory ... OK
checking for future file timestamps ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
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checking examples ... [7s/9s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [8s/11s] ERROR Running ‘LN-testing.R’ [2s/3s] Running ‘NB-testing.R’ [2s/2s] Running ‘Norm-testing.R’ [1s/1s] Running ‘Pois-testing.R’ [2s/3s] Running ‘gamma-testing.R’ [1s/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 ... [5s/7s] OK
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DONE

Status: 1 ERROR