revdeps fail after setDT shallow copy earlier  #6575

* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(DTwrappers)
  > 
  > test_check("DTwrappers")
  [ FAIL 4 | WARN 3 | SKIP 0 | PASS 0 ]
  
  == Failed tests ================================================================
  -- Failure ('test-dtwrappers.R:15:3'): select first 3 rows of dataset ----------
  `firstthree_dtwrappers` not equal to `chosefirstthree`.
  Attributes: < Names: 2 string mismatches >
  Attributes: < Length mismatch: comparison on first 2 components >
  Attributes: < Component 1: Modes: character, externalptr >
  Attributes: < Component 1: target is character, current is externalptr >
  Attributes: < Component 2: Modes: numeric, character >
  Attributes: < Component 2: Lengths: 3, 2 >
  Attributes: < Component 2: target is numeric, current is character >
  -- Failure ('test-dtwrappers.R:25:3'): select first 5 entries of dataset with all columns --
  `chose_first_5_allcolumns` not equal to `chose_first5_dtwrappers`.
  target is data.table, current is data.frame
  -- Failure ('test-dtwrappers.R:34:3'): count rows in dataset -------------------
  `countrows` not equal to `countrows_dtwrappers`.
  Types not compatible: integer is not list
  -- Error ('test-dtwrappers.R:41:1'): (code run outside of `test_that()`) -------
  Error in `.(variable = "Sepal.Length", mean = mean(Sepal.Length))`: could not find function "."
  Backtrace:
      x
   1. +-DTwrappers::dt.calculate(...) at test-dtwrappers.R:41:1
   2. | \-DTwrappers:::eval.dt.statement(...)
   3. |   \-base::eval(...)
   4. |     \-base::eval(...)
   5. +-iris[, .(variable = "Sepal.Length", mean = mean(Sepal.Length))]
   6. \-base::`[.data.frame`(iris, , .(variable = "Sepal.Length", mean = mean(Sepal.Length)))
  
  [ FAIL 4 | WARN 3 | SKIP 0 | PASS 0 ]

* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction_to_DTwrappers2.Rmd' using knitr

Quitting from lines 81-82 [unnamed-chunk-4] (Introduction_to_DTwrappers2.Rmd)
Error: processing vignette 'Introduction_to_DTwrappers2.Rmd' failed with diagnostics:
could not find function "."
--- failed re-building 'Introduction_to_DTwrappers2.Rmd'

SUMMARY: processing the following file failed:
  'Introduction_to_DTwrappers2.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR

* checking examples ... ERROR
Running examples in 'marginaleffects-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: comparisons
> ### Title: Comparisons Between Predictions Made With Different Regressor
> ###   Values
> ### Aliases: comparisons avg_comparisons
> 
> ### ** Examples
> 
> ## Don't show: 
> if (interactive() || isTRUE(Sys.getenv("R_DOC_BUILD") == "true")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ ## Don't show: 
+ }) # examplesIf
> ## End(Don't show)
> library(marginaleffects)
> 
> # Linear model
> tmp <- mtcars
> tmp$am <- as.logical(tmp$am)
> mod <- lm(mpg ~ am + factor(cyl), tmp)
> avg_comparisons(mod, variables = list(cyl = "reference"))
Warning: The `cyl` variable is treated as a categorical (factor) variable, but
  the original data is of class numeric. It is safer and faster to convert
  such variables to factor before fitting the model and calling a
  `marginaleffects` function.
  
  This warning appears once per session.
  FALSE

          Contrast Estimate Std. Error     z Pr(>|z|)    S  2.5 % 97.5 %
 mean(6) - mean(4)    -6.16       1.54 -4.01   <0.001 14.0  -9.17  -3.15
 mean(8) - mean(4)   -10.07       1.45 -6.93   <0.001 37.8 -12.91  -7.22

Term: cyl
Type:  response 
Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, predicted_lo, predicted_hi, predicted 

> avg_comparisons(mod, variables = list(cyl = "sequential"))

          Contrast Estimate Std. Error     z Pr(>|z|)    S 2.5 % 97.5 %
 mean(6) - mean(4)    -6.16       1.54 -4.01  < 0.001 14.0 -9.17  -3.15
 mean(8) - mean(6)    -3.91       1.47 -2.66  0.00781  7.0 -6.79  -1.03

Term: cyl
Type:  response 
Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, predicted_lo, predicted_hi, predicted 

> avg_comparisons(mod, variables = list(cyl = "pairwise"))

          Contrast Estimate Std. Error     z Pr(>|z|)    S  2.5 % 97.5 %
 mean(6) - mean(4)    -6.16       1.54 -4.01  < 0.001 14.0  -9.17  -3.15
 mean(8) - mean(4)   -10.07       1.45 -6.93  < 0.001 37.8 -12.91  -7.22
 mean(8) - mean(6)    -3.91       1.47 -2.66  0.00781  7.0  -6.79  -1.03

Term: cyl
Type:  response 
Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, predicted_lo, predicted_hi, predicted 

> 
> # GLM with different scale types
> mod <- glm(am ~ factor(gear), data = mtcars)
> avg_comparisons(mod, type = "response")

          Contrast Estimate Std. Error    z Pr(>|z|)    S 2.5 % 97.5 %
 mean(4) - mean(3)    0.667      0.117 5.68   <0.001 26.1 0.436  0.897
 mean(5) - mean(3)    1.000      0.157 6.39   <0.001 32.5 0.693  1.307

Term: gear
Type:  response 
Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, predicted_lo, predicted_hi, predicted 

> avg_comparisons(mod, type = "link")

          Contrast Estimate Std. Error    z Pr(>|z|)    S 2.5 % 97.5 %
 mean(4) - mean(3)    0.667      0.117 5.68   <0.001 26.1 0.436  0.897
 mean(5) - mean(3)    1.000      0.157 6.39   <0.001 32.5 0.693  1.307

Term: gear
Type:  link 
Columns: term, contrast, estimate, std.error, statistic, p.value, s.value, conf.low, conf.high, predicted_lo, predicted_hi, predicted 

> 
> # Contrasts at the mean
> comparisons(mod, newdata = "mean")
Error in comparisons(mod, newdata = "mean") : object '..idx' not found
Calls: comparisons -> [ -> [.data.frame

-* checking examples ... OK
+* checking examples ... ERROR
+Running examples in 'snpsettest-Ex.R' failed
+The error most likely occurred in:
+
+> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+> ### Name: harmonize_sumstats
+> ### Title: Harmonizing GWAS summary to reference data
+> ### Aliases: harmonize_sumstats
+> 
+> ### ** Examples
+> 
+> ## Don't show: 
+> data.table::setDTthreads(1)
+> ## End(Don't show)
+> ## GWAS summary statistics
+> head(exGWAS)
+     id chr   pos A1 A2      pvalue
+1 SNP_0   1 50215  G  C 0.196935302
+2 SNP_2   1 50768  A  G 0.662046499
+3 SNP_3   1 50833  T  G 0.582259626
+4 SNP_4   1 50848  C  T 0.232650995
+5 SNP_5   1 51330  A  G 0.081534282
+6 SNP_6   1 51696  T  C 0.002349804
+> 
+> ## Load reference genotype data
+> bfile <- system.file("extdata", "example.bed", package = "snpsettest")
+> x <- read_reference_bed(path = bfile)
+Reading /tmp/th798/13300208/R-devel/1303/snpsettest.Rcheck/snpsettest/extdata/example.fam 
+Reading /tmp/th798/13300208/R-devel/1303/snpsettest.Rcheck/snpsettest/extdata/example.bim 
+Reading /tmp/th798/13300208/R-devel/1303/snpsettest.Rcheck/snpsettest/extdata/example.bed 
+ped stats and snps stats have been set. 
+'p' has been set. 
+'mu' and 'sigma' have been set.
+Created a bed.matrix with 300 individuals and 2,942 markers.
+> 
+> ## Harmonize by SNP IDs
+> hsumstats1 <- harmonize_sumstats(exGWAS, x)
+-----
+Checking the reference data for harmonization...
+Found 0 monomoprhic SNPs in the reference data.
+Found 0 duplicate SNP IDs in the reference data.
+Excluded 0 SNPs from the harmonization.
+-----
+Checking the GWAS summary statistics...
+2,753 variants to be matched.
+Error in `[.data.frame`(x@snps[ref_keep_ind, ], sumstats[, .(id, pvalue)],  : 
+  unused arguments (on = .(id), nomatch = NULL)
+Calls: harmonize_sumstats -> [
+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 'reference_1000Genomes.Rmd' using rmarkdown
+--- finished re-building 'reference_1000Genomes.Rmd'
+
+--- re-building 'snpsettest_intro.Rmd' using rmarkdown
+
+Quitting from lines 68-78 [harmonization] (snpsettest_intro.Rmd)
+Error: processing vignette 'snpsettest_intro.Rmd' failed with diagnostics:
+unused arguments (on = .(id), nomatch = NULL)
+--- failed re-building 'snpsettest_intro.Rmd'
+
+--- re-building 'snpsettest_model.Rmd' using rmarkdown
+--- finished re-building 'snpsettest_model.Rmd'
+
+SUMMARY: processing the following file failed:
+  'snpsettest_intro.Rmd'
+
+Error: Vignette re-building failed.