Running examples in 'lipidomeR-Ex.R' failed
The error most likely occurred in:

> ### Name: liverlipidome
> ### Title: Levels of lipids in the human liver with or without
> ###   non-alcoholic liver disease (NAFLD).
> ### Aliases: liverlipidome
> ### Keywords: NASH data datasets diagnosis disease human lipidome
> ###   lipidomics lipids liver molecule non-alcoholic steatohepatitis tissue
> 
> ### ** Examples
> 
> # Load the data set.
> data( liverlipidome )
> # Convert the data into wide format, where each lipid is one column and
> # each sample is one row.
> liverlipidome.wide <-
+    tidyr::pivot_wider(
+        data = liverlipidome,
+        names_from = Lipid_Name,
+        values_from = Lipid_Level
+    )
> # Create a mapping of the lipid names.
> names.mapping <-
+    map_lipid_names( x = unique( liverlipidome$"Lipid_Name" ) )
> # Compute the regression models.
> result.limma <-
+    compute_models_with_limma(
+        x = liverlipidome.wide,
+        dependent.variables = names.mapping$"Name",
+        independent.variables = c( "Diagnosis" ),
+        F.test = TRUE # Compute an F-test for a factor variable.
+    )
Fitting models: ~ Diagnosis
> # Compute the F-test.
> result.limma <- compute_F_test_with_limma( x = result.limma )
> # Print a figure of the F-test.
> # Compute pairwise post-hoc comparisons between the factor levels for
> # the dependent variables (i.e., lipids) with a significant F-test result.
> result.limma <-
+    compute_post_hoc_test_with_limma(
+        x = result.limma,
+        remap.level.names = TRUE
+    )
Warning in limma::makeContrasts(contrasts = contrasts.posthoc, levels = x$data$design) :
  Renaming (Intercept) to Intercept
Warning in limma::contrasts.fit(fit = rEbFit, contrasts = contrasts.posthoc) :
  row names of contrasts don't match col names of coefficients
> # Print a figure of all post-hoc comparisons.
> # Specify the contrasts of the post-hoc comparison that will be included
> # in the figure.
> contrasts.included <-
+    c( "DiagnosisSteatosis", "DiagnosisNASH", "DiagnosisCirrhosis" )
> # Get the omitted contrasts based on the above definition.
> contrasts.omitted <-
+    colnames( result.limma$"result.post.hoc.test"$"p.value" )[
+        !(
+            colnames( result.limma$"result.post.hoc.test"$"p.value" ) %in%
+            contrasts.included
+        )
+    ]
> # Find dependent variables (i.e., lipids) that have any significant
> # difference.
> has.any.significant <-
+    apply(
+        X =
+            result.limma$"result.post.hoc.test"$"p.value"[
+                ,
+                contrasts.included
+            ],
+        MAR = 2,
+        FUN = p.adjust,
+        method = "BH"
+    )
> has.any.significant <-
+    rownames(
+        has.any.significant[
+            apply(
+                X = has.any.significant < 0.05,
+                MAR = 1,
+                FUN = any
+            ),
+        ]
+    )
> # Include in the figure only lipid classes that have at least four
> # significant differences.
> classes.included <-
+    names(
+        which(
+            table(
+                names.mapping[
+                    make.names( has.any.significant ), "Class"
+                ]
+            ) > 4
+        )
+    )
> classes.omitted <- unique( names.mapping$"Class" )
> classes.omitted <-
+    classes.omitted[ !( classes.omitted ) %in% classes.included ]
> # Print a figure of the selected post-hoc-comparisons.
> figure.output <-
+    heatmap_lipidome_from_limma(
+        x = result.limma$"result.post.hoc.test",
+        names.mapping = names.mapping,
+        axis.x.carbons = FALSE,
+        omit.class = classes.omitted,
+        omit.factor = contrasts.omitted,
+        plot.all = TRUE,
+        plot.individual = FALSE,
+        scales = "free",
+        space = "free"
+    )
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: Removed 119 rows containing missing values (geom_point).
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()