CRAN Package Check Results for Package tern.gee

Last updated on 2024-08-24 12:50:22 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.4	12.02	116.19	128.21	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.4	7.23	82.43	89.66	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.5			124.36	OK
r-devel-linux-x86_64-fedora-gcc	0.1.5			113.24	OK
r-devel-windows-x86_64	0.1.4	14.00	120.00	134.00	ERROR
r-patched-linux-x86_64	0.1.4	10.57	108.53	119.10	ERROR
r-release-linux-x86_64	0.1.4	11.65	109.39	121.04	ERROR
r-release-macos-arm64	0.1.5			73.00	OK
r-release-macos-x86_64	0.1.5			166.00	OK
r-release-windows-x86_64	0.1.5	15.00	123.00	138.00	OK
r-oldrel-macos-arm64	0.1.5			17.00	ERROR
r-oldrel-macos-x86_64	0.1.5			11.00	ERROR
r-oldrel-windows-x86_64	0.1.4	18.00	143.00	161.00	ERROR

Check Details

Version: 0.1.4
Check: examples
Result: ERROR Running examples in ‘tern.gee-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: lsmeans > ### Title: Extract Least Square Means from a GEE Model > ### Aliases: lsmeans lsmeans.tern_gee_logistic > > ### ** Examples > > df <- fev_data > df$AVAL <- rbinom(n = nrow(df), size = 1, prob = 0.5) > fit <- fit_gee(vars = vars_gee(arm = "ARMCD"), data = df) > > lsmeans(fit) Error in `[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, : undefined columns selected Calls: lsmeans ... lsmeans.tern_gee_logistic -> cbind -> [ -> [.data.frame Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [10s/13s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tabulate_gee.R:32:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ────────────── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3 2. └─tern.gee:::lsmeans.tern_gee_logistic(model) 3. ├─base::cbind(...) 4. ├─...[] 5. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘tern-gee.Rmd’ using rmarkdown Quitting from lines 106-108 [unnamed-chunk-4] (tern-gee.Rmd) Error: processing vignette 'tern-gee.Rmd' failed with diagnostics: undefined columns selected --- failed re-building ‘tern-gee.Rmd’ SUMMARY: processing the following file failed: ‘tern-gee.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [6s/8s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tabulate_gee.R:32:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ────────────── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3 2. └─tern.gee:::lsmeans.tern_gee_logistic(model) 3. ├─base::cbind(...) 4. ├─...[] 5. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.4
Check: examples
Result: ERROR Running examples in 'tern.gee-Ex.R' failed The error most likely occurred in: > ### Name: lsmeans > ### Title: Extract Least Square Means from a GEE Model > ### Aliases: lsmeans lsmeans.tern_gee_logistic > > ### ** Examples > > df <- fev_data > df$AVAL <- rbinom(n = nrow(df), size = 1, prob = 0.5) > fit <- fit_gee(vars = vars_gee(arm = "ARMCD"), data = df) > > lsmeans(fit) Error in `[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, : undefined columns selected Calls: lsmeans ... lsmeans.tern_gee_logistic -> cbind -> [ -> [.data.frame Execution halted Flavors: r-devel-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.1.4
Check: tests
Result: ERROR Running 'testthat.R' [8s] Running the tests in 'tests/testthat.R' failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tabulate_gee.R:32:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ────────────── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3 2. └─tern.gee:::lsmeans.tern_gee_logistic(model) 3. ├─base::cbind(...) 4. ├─...[] 5. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

Version: 0.1.4
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'tern-gee.Rmd' using rmarkdown Quitting from lines 106-108 [unnamed-chunk-4] (tern-gee.Rmd) Error: processing vignette 'tern-gee.Rmd' failed with diagnostics: undefined columns selected --- failed re-building 'tern-gee.Rmd' SUMMARY: processing the following file failed: 'tern-gee.Rmd' Error: Vignette re-building failed. Execution halted Flavors: r-devel-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/11s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tabulate_gee.R:32:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ────────────── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3 2. └─tern.gee:::lsmeans.tern_gee_logistic(model) 3. ├─base::cbind(...) 4. ├─...[] 5. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 0.1.4
Check: tests
Result: ERROR Running ‘testthat.R’ [9s/12s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Attaching package: 'formatters' The following object is masked from 'package:base': %||% Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tabulate_gee.R:32:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ────────────── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3 2. └─tern.gee:::lsmeans.tern_gee_logistic(model) 3. ├─base::cbind(...) 4. ├─...[] 5. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 0.1.5
Check: package dependencies
Result: ERROR Package required and available but unsuitable version: ‘emmeans’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 0.1.4
Check: tests
Result: ERROR Running 'testthat.R' [11s] Running the tests in 'tests/testthat.R' failed. Complete output: > pkg_name <- "tern.gee" > library(pkg_name, character.only = TRUE) Loading required package: tern Loading required package: rtables Loading required package: formatters Loading required package: magrittr Attaching package: 'rtables' The following object is masked from 'package:utils': str > testthat::test_check(pkg_name) Attaching package: 'testthat' The following objects are masked from 'package:magrittr': equals, is_less_than, not [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-tabulate_gee.R:32:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-lsmeans.R:9:3'): lsmeans works for logistic model ────────────── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::lsmeans(model) at test-lsmeans.R:9:3 2. └─tern.gee:::lsmeans.tern_gee_logistic(model) 3. ├─base::cbind(...) 4. ├─...[] 5. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:36:3'): s_lsmeans_logistic works as expected when not in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[2, ], FALSE) at test-tabulate_gee.R:36:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:50:3'): s_mmrm_lsmeans works as expected when in reference column ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─tern.gee::s_lsmeans_logistic(lsmeans(model)[1, ], TRUE) at test-tabulate_gee.R:50:3 2. ├─tern.gee::lsmeans(model) 3. └─tern.gee:::lsmeans.tern_gee_logistic(model) 4. ├─base::cbind(...) 5. ├─...[] 6. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:64:3'): summarize_gee_logistic works as expected with covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:64:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) ── Error ('test-tabulate_gee.R:89:3'): summarize_gee_logistic works as expected with no covariates in the model ── Error in ``[.data.frame`(data.frame(stats::confint(prop_emm)), , c(object$vars$arm, "prob", "SE", "asymp.LCL", "asymp.UCL"))`: undefined columns selected Backtrace: ▆ 1. ├─... %>% ... at test-tabulate_gee.R:89:3 2. ├─rtables::build_table(., df = lsmeans(model), alt_counts_df = dat_adsl) 3. │ ├─rtables:::set_def_child_ord(lyt, df) 4. │ └─rtables:::set_def_child_ord(lyt, df) 5. │ ├─rtables:::set_def_child_ord(clayout(lyt), df) 6. │ └─rtables:::set_def_child_ord(clayout(lyt), df) 7. │ └─base::lapply(lyt, set_def_child_ord, df = df) 8. │ ├─rtables (local) FUN(X[[i]], ...) 9. │ └─rtables (local) FUN(X[[i]], ...) 10. │ └─base::lapply(lyt, set_def_child_ord, df = df) 11. │ ├─rtables (local) FUN(X[[i]], ...) 12. │ └─rtables (local) FUN(X[[i]], ...) 13. ├─tern.gee::lsmeans(model) 14. └─tern.gee:::lsmeans.tern_gee_logistic(model) 15. ├─base::cbind(...) 16. ├─...[] 17. └─base::`[.data.frame`(...) [ FAIL 5 | WARN 0 | SKIP 1 | PASS 37 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64