Merge pull request #54 from omnideconv/bugFix

Bug Fixes
omnideconv · Dec 1, 2023 · 97576ad · 97576ad
2 parents 0449e31 + b7e19a6
commit 97576ad
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -57,6 +57,7 @@ Suggests:
     knitr,
     rmarkdown,
     bookdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0), 
+    markdown
 VignetteBuilder: knitr
 Config/testthat/edition: 3
diff --git a/R/SignatureExplorationPlots.R b/R/SignatureExplorationPlots.R
@@ -44,7 +44,7 @@ plot_signatureGenesPerMethod <- function(signature_list,
       vjust = -1, family = "Helvetica",
       color = "black"
     ) +
-    geom_hline(yintercept = 0, size = 1, colour = "#333333") +
+    geom_hline(yintercept = 0, linewidth = 1, colour = "#333333") +
     theme_minimal() +
     theme(legend.position = "none") +
     ggplot2::scale_fill_manual(values = RColorBrewer::brewer.pal(8, color_palette)[1:length(names(signature_list))]) +
@@ -93,7 +93,7 @@ plot_conditionNumberPerMethod <- function(signature_list,
       fontface = "bold", vjust = -1,
       color = "black", size = 7, family = "Helvetica"
     ) +
-    geom_hline(yintercept = 0, size = 1, colour = "#333333") +
+    geom_hline(yintercept = 0, linewidth = 1, colour = "#333333") +
     theme_minimal() +
     labs(x = "Method", y = "Kappa") +
     theme(legend.position = "none") +
@@ -142,7 +142,7 @@ plot_meanEntropyPerMethod <- function(signature_list,
       fontface = "bold", vjust = -1,
       color = "black", size = 7, family = "Helvetica"
     ) +
-    geom_hline(yintercept = 0, size = 1, colour = "#333333") +
+    geom_hline(yintercept = 0, linewidth = 1, colour = "#333333") +
     theme_minimal() +
     labs(x = "Method", y = "Entropy") +
     theme(legend.position = "none") +

diff --git a/inst/webserver_setup/app/Dockerfile b/inst/webserver_setup/app/Dockerfile
@@ -8,6 +8,7 @@ ARG GITHUB_PAT
 RUN apt-get update && apt-get install -y \
     sudo \
     pandoc \
+    apt-utils \
     #pandoc-citeproc \
     libcurl4-gnutls-dev \
     libcairo2-dev \
@@ -32,7 +33,7 @@ RUN R -e "pak::pkg_install('omnideconv/omnideconv', dependencies=TRUE)"
 #RUN R -e "remotes::install_github('omnideconv/DeconvExplorer', dependencies=TRUE)"
 RUN R -e "pak::pkg_install('omnideconv/DeconvExplorer', dependencies=TRUE)"
 
-RUN R -e "reticulate::install_miniconda()" # will not install automatically
+RUN R -e "reticulate::install_miniconda(force=TRUE)" # will not install automatically
 
 RUN R -e "omnideconv::install_all_python()"
 

diff --git a/tests/testthat/test-DeconvExplorer.R b/tests/testthat/test-DeconvExplorer.R
@@ -4,6 +4,7 @@ test_that("Shiny app is generated", {
   )
 })
 
+
 test_that("Helper funcs", {
   internal_list <- returnSelectedDeconvolutions(c("momf"), deconv_list)
   expect_true(
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,7 @@ test_that("Shiny app is generated", { @@
       )
     })
     test_that("Helper funcs", {
       internal_list <- returnSelectedDeconvolutions(c("momf"), deconv_list)
       expect_true(
@@ Expand Down @@