* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/glmMisrep.Rcheck’ * using R Under development (unstable) (2025-11-17 r89032) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘glmMisrep’ can be installed ... [12s/12s] 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 ... 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 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 ... [22s/22s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking examples with --run-donttest ... [30m/31m] ERROR Running examples in ‘glmMisrep-Ex.R’ failed The error most likely occurred in: > ### Name: MEPS14 > ### Title: MEPS 2014 Full Year Consolidated Data File > ### Aliases: MEPS14 > ### Keywords: datasets > > ### ** Examples > > ## No test: > > # Reproducing table 4 in Xia et. al., (2023). > > data(MEPS14) > > colMeans(MEPS14) TOTEXP14 OBTOTV14 UNINS14 SEX AGE14X ADSMOK42 5042.4647771 6.2260732 0.1242012 0.4153071 41.6628825 0.1670551 RTHLTH53 2.4319224 > # TOTEXP14 OBTOTV14 UNINS14 SEX AGE14X ADSMOK42 RTHLTH53 > #5042.4647771 6.2260732 0.1242012 0.4153071 41.6628825 0.1670551 2.4319224 > > apply(MEPS14, 2, sd) TOTEXP14 OBTOTV14 UNINS14 SEX AGE14X ADSMOK42 1.358567e+04 1.272065e+01 3.298233e-01 4.927934e-01 1.332746e+01 3.730391e-01 RTHLTH53 1.074713e+00 > # TOTEXP14 OBTOTV14 UNINS14 SEX AGE14X ADSMOK42 RTHLTH53 > #1.358567e+04 1.272065e+01 3.298233e-01 4.927934e-01 1.332746e+01 3.730391e-01 1.074713e+00 > > sum(MEPS14$OBTOTV14 == 0 ) / nrow(MEPS14) [1] 0.1595369 > # [1] 0.1595369 > > sd(MEPS14$OBTOTV14 == 0) [1] 0.3661898 > # [1] 0.3661898 > > # Fit Gamma regression model with insured status as > # the misrepresented variable. > MEPS14$RTHLTH53 <- as.factor(MEPS14$RTHLTH53) > > gamma_fit <- gammaRegMisrepEM(formula = TOTEXP14 ~ UNINS14 + + SEX + AGE14X + ADSMOK42 + RTHLTH53, + v_star = "UNINS14", data = MEPS14) number of iterations = 130 > > # summary returns a table of summary statistics, including > # goodness of fits (AIC, AICc, BIC), as well as the > # estimated prevalence of misrepresentation. > summary(gamma_fit) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 8.03468 0.05343 150.38692 <2e-16 *** UNINS14 -1.98160 0.03171 -62.48375 <2e-16 *** SEX -0.20468 0.02669 -7.66796 <2e-16 *** AGE14X 0.02763 0.00099 27.81962 <2e-16 *** ADSMOK42 -0.08819 0.03653 -2.41383 0.0158 * RTHLTH532 0.24940 0.03533 7.05894 <2e-16 *** RTHLTH533 0.53894 0.03656 14.74324 <2e-16 *** RTHLTH534 1.00666 0.04838 20.80884 <2e-16 *** RTHLTH535 1.87890 0.08105 23.18236 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --- AIC AICc BIC 241083.9 241083.9 241166.3 --- Log-Likelihood -120530.9 --- Lambda: 0.7735458 std.err: 0.00962798> > # Coefficients: > # Estimate Std. Error t value Pr(>|t|) > # (Intercept) 8.03379 0.05341 150.41937 <2e-16 *** > # UNINS14 -1.98132 0.03170 -62.49292 <2e-16 *** > # SEX -0.20427 0.02669 -7.65320 <2e-16 *** > # AGE14X 0.02764 0.00099 27.83485 <2e-16 *** > # ADSMOK42 -0.08868 0.03653 -2.42776 0.01521 * > # RTHLTH532 0.24923 0.03533 7.05469 <2e-16 *** > # RTHLTH533 0.53860 0.03655 14.73488 <2e-16 *** > # RTHLTH534 1.00615 0.04837 20.80026 <2e-16 *** > # RTHLTH535 1.87845 0.08104 23.17833 <2e-16 *** > # --- > # Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > # --- > # AIC AICc BIC > # 241083.9 241083.9 241166.3 > # --- > # Log-Likelihood > # -120530.9 > # --- > # Lambda: 0.7734337 std.err: 0.009628053 > > > # Fit Lognormal regression model with insured status as > # the misrepresented variable. > LN_fit <- LnRegMisrepEM(formula = log(TOTEXP14) ~ UNINS14 + + SEX + AGE14X + ADSMOK42 + RTHLTH53, + v_star = "UNINS14", data = MEPS14) number of iterations = 972 > > summary(LN_fit) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 7.28974 0.05648 129.05986 <2e-16 *** UNINS14 -1.29503 0.05496 -23.56317 <2e-16 *** SEX -0.29590 0.02808 -10.53844 <2e-16 *** AGE14X 0.02460 0.00107 23.10180 <2e-16 *** ADSMOK42 -0.07008 0.03756 -1.86591 0.06208 . RTHLTH532 0.26349 0.03831 6.87786 <2e-16 *** RTHLTH533 0.47184 0.03942 11.97017 <2e-16 *** RTHLTH534 1.05065 0.04990 21.05580 <2e-16 *** RTHLTH535 1.94978 0.08067 24.16987 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --- AIC AICc BIC 239726.4 239726.4 239808.8 --- Log-Likelihood -119852.2 --- Lambda: 0.1110631 std.err: 0.02548188> > # Coefficients: > # Estimate Std. Error t value Pr(>|t|) > # (Intercept) 7.28974 0.05648 129.05986 <2e-16 *** > # UNINS14 -1.29503 0.05496 -23.56317 <2e-16 *** > # SEX -0.29590 0.02808 -10.53844 <2e-16 *** > # AGE14X 0.02460 0.00107 23.10180 <2e-16 *** > # ADSMOK42 -0.07008 0.03756 -1.86591 0.06208 . > # RTHLTH532 0.26349 0.03831 6.87786 <2e-16 *** > # RTHLTH533 0.47184 0.03942 11.97017 <2e-16 *** > # RTHLTH534 1.05065 0.04990 21.05580 <2e-16 *** > # RTHLTH535 1.94978 0.08067 24.16987 <2e-16 *** > # --- > # Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > # --- > # AIC AICc BIC > # 239726.4 239726.4 239808.8 > # --- > # Log-Likelihood > # -119852.2 > # --- > # Lambda: 0.1110631 std.err: 0.02548188 > > > # Fit Negative Binomial regression model with insured status as > # the misrepresented variable. > NB_fit <- nbRegMisrepEM(formula = OBTOTV14 ~ UNINS14 + + SEX + AGE14X + ADSMOK42 + RTHLTH53, + v_star = "UNINS14", data = MEPS14) * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘LN-testing.R’ Running ‘NB-testing.R’ Running ‘Norm-testing.R’ Running ‘Pois-testing.R’ Running ‘gamma-testing.R’ [13s/13s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/glmMisrep.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 32:08.65, 1874.05 + 19.68