5 packages fail checks after prohibiting duplicate key columns #7770

-* checking examples ... OK
+* checking examples ... ERROR
+Running examples in 'bridger2-Ex.R' failed
+The error most likely occurred in:
+
+> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+> ### Name: BridgeRCore
+> ### Title: BridgeR basic function for calculating RNA half-life from
+> ###   BRIC-seq data
+> ### Aliases: BridgeRCore
+> 
+> ### ** Examples
+> 
+> halflife_table <- BridgeRCore(RNA_halflife_comparison[1:30,],
++                               save = FALSE)
+> halflife_table <- BridgeRCore(RNA_halflife_comparison_HK[177:206],
++                               save = FALSE,
++                               normalization = "house_keeping_genes",
++                               method = "3models")
+Error in setkeyv(inputFile, inforHKGenesRow) : 
+  x has duplicated column names in the columns to key by: [symbol]
+Calls: BridgeRCore ... BridgeRNormalizationFactorsHK -> setkeyv -> stopf -> raise_condition -> signal
+Execution halted
 * checking for unstated dependencies in 'tests' ... OK
-* checking tests ... OK
+* checking tests ... ERROR
   Running 'testthat.R'
+Running the tests in 'tests/testthat.R' failed.
+Complete output:
+  > library(testthat)
+  > library(bridger2)
+  > 
+  > test_check("bridger2")
+  Saving _problems/test-RNA_halflife_comparison-53.R
+  Saving _problems/test-RNA_halflife_core-15.R
+  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 17 ]
+  
+  == Failed tests ================================================================
+  -- Error ('test-RNA_halflife_comparison.R:53:3'): Comparing RNA halflife -------
+  Error in `setkeyv(inputFile, searchRowName)`: x has duplicated column names in the columns to key by: [symbol]
+  Backtrace:
+      x
+   1. \-bridger2::BridgeReport(pvalue_table) at test-RNA_halflife_comparison.R:53:3
+   2.   \-data.table::setkeyv(inputFile, searchRowName)
+   3.     \-data.table:::stopf(...)
+   4.       \-data.table:::raise_condition(...)
+  -- Error ('test-RNA_halflife_core.R:12:3'): testing BridgeRCore 2 --------------
+  Error in `setkeyv(inputFile, inforHKGenesRow)`: x has duplicated column names in the columns to key by: [symbol]
+  Backtrace:
+      x
+   1. \-bridger2::BridgeRCore(...) at test-RNA_halflife_core.R:12:3
+   2.   \-bridger2::BridgeRNormalizationFactorsHK(...)
+   3.     \-data.table::setkeyv(inputFile, inforHKGenesRow)
+   4.       \-data.table:::stopf(...)
+   5.         \-data.table:::raise_condition(...)
+  
+  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 17 ]
+  Error:
+  ! Test failures.
+  Execution halted
 * checking PDF version of manual ... OK
 * DONE
-Status: OK
+Status: 2 ERRORs

-* checking tests ... OK
+* checking tests ... ERROR
   Running 'testthat.R'
+Running the tests in 'tests/testthat.R' failed.
+Complete output:
+  > # This file is part of the standard setup for testthat.
+  > # It is recommended that you do not modify it.
+  > #
+  > # Where should you do additional test configuration?
+  > # Learn more about the roles of various files in:
+  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+  > # * https://testthat.r-lib.org/articles/special-files.html
+  > 
+  > library(testthat)
+  > library(dbi.table)
+  > 
+  > test_check("dbi.table")
+  
+  Attaching package: 'data.table'
+  
+  The following object is masked from 'package:base':
+  
+      %notin%
+  
+  Saving _problems/test-merge-71.R
+  Saving _problems/test-merge-71.R
+  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 420 ]
+  
+  == Skipped tests (2) ===========================================================
+  * On CRAN (2): 'test-mariadb.R:10:3', 'test-postgres.R:11:3'
+  
+  == Failed tests ================================================================
+  -- Error ('test-merge.R:69:5'): self merge works with no.dups = FALSE [chinook_sqlite] --
+  Error in `setkeyv(x, key)`: x has duplicated column names in the columns to key by: [AlbumId]
+  Backtrace:
+       x
+    1. +-testthat::expect_warning(...) at test-merge.R:69:5
+    2. | \-testthat:::expect_condition_matching_(...)
+    3. |   \-testthat:::quasi_capture(...)
+    4. |     +-testthat (local) .capture(...)
+    5. |     | \-base::withCallingHandlers(...)
+    6. |     \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
+    7. \-dbi.table::reference.test(...)
+    8.   +-data.table::as.data.table(dbit_eval)
+    9.   \-dbi.table (local) as.data.table.dbi.table(dbit_eval)
+   10.     \-data.table::setDT(x, key = x_key)
+   11.       \-data.table::setkeyv(x, key)
+   12.         \-data.table:::stopf(...)
+   13.           \-data.table:::raise_condition(...)
+  -- Error ('test-merge.R:69:5'): self merge works with no.dups = FALSE [chinook_duckdb] --
+  Error in `setkeyv(x, key)`: x has duplicated column names in the columns to key by: [AlbumId]
+  Backtrace:
+       x
+    1. +-testthat::expect_warning(...) at test-merge.R:69:5
+    2. | \-testthat:::expect_condition_matching_(...)
+    3. |   \-testthat:::quasi_capture(...)
+    4. |     +-testthat (local) .capture(...)
+    5. |     | \-base::withCallingHandlers(...)
+    6. |     \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
+    7. \-dbi.table::reference.test(...)
+    8.   +-data.table::as.data.table(dbit_eval)
+    9.   \-dbi.table (local) as.data.table.dbi.table(dbit_eval)
+   10.     \-data.table::setDT(x, key = x_key)
+   11.       \-data.table::setkeyv(x, key)
+   12.         \-data.table:::stopf(...)
+   13.           \-data.table:::raise_condition(...)
+  
+  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 420 ]
+  Error:
+  ! Test failures.
+  Execution halted
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes ... OK
 * checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * DONE
-Status: OK
+Status: 1 ERROR

-* checking examples ... OK
+* checking examples ... ERROR
+Running examples in 'formulaic-Ex.R' failed
+The error most likely occurred in:
+
+> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+> ### Name: reduce.existing.formula
+> ### Title: Reduce Existing Formula
+> ### Aliases: reduce.existing.formula
+> 
+> ### ** Examples
+> 
+> data('snack.dat')
+> the.initial.formula <- 'Income ~ .'
+> 
+> reduce.existing.formula(the.initial.formula = the.initial.formula,dat = snack.dat,
++   max.input.categories = 30)$formula
+Error in setnames(x = num.unique.tab, old = "V1", new = outcome.name) : 
+  The new names would result in duplicated key columns: [Income]
+Calls: reduce.existing.formula ... create.formula -> setnames -> stopf -> raise_condition -> signal
+Execution halted
 * checking for unstated dependencies in 'tests' ... OK
-* checking tests ... OK
+* checking tests ... ERROR
   Running 'testthat.R'
+Running the tests in 'tests/testthat.R' failed.
+Complete output:
+  > testthat::test_check("formulaic")
+  Loading required package: formulaic
+  Saving _problems/test-reduce-formula-10.R
+  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
+  
+  == Failed tests ================================================================
+  -- Error ('test-reduce-formula.R:6:1'): (code run outside of `test_that()`) ----
+  Error in `setnames(x = num.unique.tab, old = "V1", new = outcome.name)`: The new names would result in duplicated key columns: [Awareness]
+  Backtrace:
+      x
+   1. \-formulaic::reduce.existing.formula(...) at test-reduce-formula.R:6:1
+   2.   \-formulaic::create.formula(...)
+   3.     \-data.table::setnames(x = num.unique.tab, old = "V1", new = outcome.name)
+   4.       \-data.table:::stopf(...)
+   5.         \-data.table:::raise_condition(...)
+  
+  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
+  Error:
+  ! Test failures.
+  Execution halted
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes ... OK
-* checking re-building of vignette outputs ... OK
+* checking re-building of vignette outputs ... ERROR
+Error(s) in re-building vignettes:
+--- re-building 'Introduction-to-formulaic.Rmd' using rmarkdown
+
+Quitting from Introduction-to-formulaic.Rmd:557-566 [create.formula large volume of categorical variables]
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+<error/rlang_error>
+Error in `setnames()`:
+! The new names would result in duplicated key columns: [Income]
+---
+Backtrace:
+    x
+ 1. \-formulaic::create.formula(...)
+ 2.   \-data.table::setnames(x = num.unique.tab, old = "V1", new = outcome.name)
+ 3.     \-data.table:::stopf(...)
+ 4.       \-data.table:::raise_condition(...)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
+The new names would result in duplicated key columns: [Income]
+--- failed re-building 'Introduction-to-formulaic.Rmd'
+
+SUMMARY: processing the following file failed:
+  'Introduction-to-formulaic.Rmd'
+
+Error: Vignette re-building failed.
+Execution halted
+
 * checking PDF version of manual ... OK
 * DONE
-Status: OK
+Status: 3 ERRORs

-* checking examples ... OK
-Examples with CPU (user + system) or elapsed time > 5s
-           user system elapsed
-multiFAMM 9.478  0.291  10.097
+* checking examples ... ERROR
+Running examples in 'multifamm-Ex.R' failed
+The error most likely occurred in:
+
+> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+> ### Name: multiFAMM
+> ### Title: Multivariate Functional Additive Mixed Model Regression
+> ### Aliases: multiFAMM
+> 
+> ### ** Examples
+> 
+> 
+> # subset of the phonetic data (very small subset, no meaningful results can
+> # be expected and no random effects other than the random smooth should be
+> # included in the model)
+> 
+> data(phonetic_subset)
+> 
+> m <- multiFAMM(data = phonetic_subset, covariate = TRUE, num_covariates = 2,
++                covariate_form = c("by", "by"), interaction = TRUE,
++                which_interaction = matrix(c(FALSE, TRUE, TRUE, FALSE),
++                nrow = 2, ncol = 2), bf_covs = c(5), m_covs = list(c(2, 3)),
++                mfpc_cut_method = "total_var", final_method = "w_bam")
+--------------------------------------
+sparseFLMM for Dimension aco 
+--------------------------------------
+Warning in sparseFLMM::sparseFLMM(curve_info = data, use_RI = use_RI, use_simple = use_simple,  :
+  as use_famm == FALSE, no confidence bands for mean and covariate effects are given out
+mean estimation; time: Fri May 29 03:11:57
+get cross products; time: Fri May 29 03:11:57
+Error in setnames(crosstable, old = c("id", "y_tilde", "t", "subj1", "subj2"),  : 
+  The new names would result in duplicated key columns: [id2]
+Calls: multiFAMM ... make_crossprod_dt -> setnames -> stopf -> raise_condition -> signal
+Execution halted
 * checking PDF version of manual ... OK
 * DONE
-Status: OK
+Status: 1 ERROR

-* checking tests ... OK
+* checking tests ... ERROR
   Running 'testthat.R'
+Running the tests in 'tests/testthat.R' failed.
+Complete output:
+  > 
+  > if (requireNamespace("testthat")) {
+  +   library("testthat")
+  +   library("popEpi")
+  +   library("data.table")
+  + 
+  +   using_r_devel <- grepl(pattern = "devel", x = R.version$status)
+  +   if (using_r_devel) {
+  +     ## memory leak problem in data.table 1.11.2 in R-devel (3.6.0 atm)
+  +     requireNamespace("data.table")
+  +     data.table::setDTthreads(threads = 1L)
+  +   }
+  + 
+  +   testthat::test_check("popEpi")
+  + }
+  Loading required namespace: testthat
+  
+  Attaching package: 'data.table'
+  
+  The following object is masked from 'package:base':
+  
+      %notin%
+  
+  Saving _problems/test_aggre-71.R
+  NOTE: entry.status has been set to "DM" for all.
+     first.bad.surv.int last.bad.surv.int surv.obs
+                  <int>             <int>    <num>
+  1:                 61               120      NaN
+     first.bad.surv.int last.bad.surv.int surv.obs
+                  <int>             <int>    <num>
+  1:                 61               120      NaN
+  Key: <agegr>
+     agegr first.bad.surv.int last.bad.surv.int surv.obs
+     <int>              <int>             <int>    <num>
+  1:     3                 61               120      NaN
+  Key: <agegr>
+     agegr first.bad.surv.int last.bad.surv.int surv.obs
+     <int>              <int>             <int>    <num>
+  1:     3                 61               120      NaN
+  [ FAIL 1 | WARN 0 | SKIP 41 | PASS 258 ]
+  
+  == Skipped tests (41) ==========================================================
+  * Unit tests skipped normally (41): 'test_aggre.R:162:3', 'test_aggre.R:199:3',
+    'test_expo.R:4:3', 'test_lexpand.R:5:3', 'test_lexpand.R:29:3',
+    'test_lexpand.R:59:3', 'test_lexpand.R:78:3', 'test_lexpand.R:99:3',
+    'test_lexpand.R:137:3', 'test_lexpand.R:213:3', 'test_lexpand.R:249:3',
+    'test_lexpand.R:342:3', 'test_relpois_mean_curve.R:4:3', 'test_sir.R:221:5',
+    'test_sir.R:257:3', 'test_splitLexisDT.R:4:3', 'test_splitMulti.R:9:3',
+    'test_splitting_breaks.R:5:3', 'test_splitting_breaks.R:39:3',
+    'test_splitting_randomly_on_fixed_data.R:9:3',
+    'test_splitting_randomly_on_random_data.R:9:3', 'test_survmean.R:6:3',
+    'test_survmean.R:76:3', 'test_survmean.R:117:3', 'test_survmean.R:166:3',
+    'test_survmean.R:265:3', 'test_survtab_adjusted.R:4:3',
+    'test_survtab_observed.R:67:3', 'test_survtab_relative.R:81:5',
+    'test_survtab_usage.R:6:3', 'test_survtab_usage.R:121:3',
+    'test_survtab_usage.R:198:3', 'test_survtab_usage.R:432:3',
+    'test_utils.R:4:3', 'test_utils.R:27:3', 'test_utils.R:138:3',
+    'test_utils.R:179:3', 'test_weighter.R:5:3', 'test_weighter.R:47:3',
+    'test_weighter.R:99:3', 'test_weighter.R:122:3'
+  
+  == Failed tests ================================================================
+  -- Error ('test_aggre.R:71:3'): aggre and lexpand produce the same results -----
+  Error in `setkeyv(x, v)`: cols contains duplicate column names: [sex]
+  Backtrace:
+      x
+   1. \-data.table::setkeyv(x, v) at test_aggre.R:71:3
+   2.   \-data.table:::stopf(...)
+   3.     \-data.table:::raise_condition(...)
+  
+  [ FAIL 1 | WARN 0 | SKIP 41 | PASS 258 ]
+  Error:
+  ! Test failures.
+  Execution halted
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes ... OK
 * checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * DONE
-Status: OK
+Status: 1 ERROR