Merge pull request #170 from shwilks/master

Update to 1.2.9
acorg · Dec 7, 2023 · abe5b3b · abe5b3b
2 parents 53b4f99 + c9899e5
commit abe5b3b
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Showing 11 changed files with 213 additions and 199 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.2.8
-Date: 2023-11-22 18:14:09 UTC
-SHA: f738ce3c333d12ada310f0c6aef4c01f9ab464cd
+Version: 1.2.9
+Date: 2023-11-30 11:13:00 UTC
+SHA: c52195bcd9da3469170ba38e65de34840b0e34d1
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Racmacs
 Type: Package
 Title: Antigenic Cartography Macros
-Version: 1.2.8
-Date: 2023-11-22
+Version: 1.2.9
+Date: 2023-11-30
 Authors@R: 
   c(person(given = "Sam",
            family = "Wilks",

diff --git a/NEWS.md b/NEWS.md
diff --git a/cran-comments.md b/cran-comments.md
@@ -2,5 +2,11 @@
 
 0 errors | 0 warnings | 1 note
 
-Package was archived because the function `gdata::read.xls()` was removed, this 
-is now replaced in this version by using `readxl::read_excel()` function.
+Resubmission to fix failing CRAN checks:
+
+- One test is skipped if pandoc is not available on the test system
+- Vignettes only evaluate code if pandoc is available
+- Some changes made to try and address the warning "format string is not a 
+  string literal (potentially insecure) [-Wformat-security]", although note 
+  that Rcpp also currently throws this warning on 
+  r-devel-linux-x86_64-fedora-clang and r-devel-linux-x86_64-debian-clang
diff --git a/src/ac_titers.cpp b/src/ac_titers.cpp
@@ -22,7 +22,7 @@ void check_valid_titer(
       ) {
 
       std::string msg = "Invalid titer '"+titer+"'";
-      Rf_error(msg.c_str());
+      Rf_error("%s", msg.c_str());
 
     }
 

diff --git a/src/utils_error.cpp b/src/utils_error.cpp
@@ -5,14 +5,14 @@ void ac_error(
     const char* msg
 ){
 
-  Rf_error(msg);
+  Rf_error("%s", msg);
 
 }
 
 void ac_error(
     const std::string msg
 ){
 
-  Rf_error(msg.c_str());
+  Rf_error("%s", msg.c_str());
 
 }
diff --git a/src/utils_progress.h b/src/utils_progress.h
@@ -64,7 +64,7 @@ class AcProgressBar: public ProgressBar{
         REprintf("\n");
       }
 
-      REprintf(msg);
+      REprintf("%s", msg);
       REprintf("\n");
 
     }

diff --git a/tests/testthat/test-view_map.R b/tests/testthat/test-view_map.R
@@ -143,8 +143,9 @@ test_that("Viewing a 3D map with sphere outlines", {
 # Exporting the viewer
 test_that("Exporting a map viewer", {
 
+  if (!rmarkdown::pandoc_available()) skip()
   tmp <- tempfile(fileext = ".html")
-  export_viewer(map, tmp)
+  export_viewer(map, tmp, selfcontained = FALSE)
   expect_true(file.exists(tmp))
   unlink(tmp)
 

diff --git a/vignettes/adding-sequences.Rmd b/vignettes/adding-sequences.Rmd
@@ -10,7 +10,8 @@ vignette: >
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#>",
+  eval = rmarkdown::pandoc_available()
 )
 ```
 

diff --git a/vignettes/comparing-maps.Rmd b/vignettes/comparing-maps.Rmd
@@ -10,7 +10,8 @@ vignette: >
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#>",
+  eval = rmarkdown::pandoc_available()
 )
 ```
 

diff --git a/vignettes/making-a-map-from-scratch.Rmd b/vignettes/making-a-map-from-scratch.Rmd
@@ -11,7 +11,8 @@ vignette: >
 set.seed(100)
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#>",
+  eval = rmarkdown::pandoc_available()
 )
 ```
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,7 +22,7 @@ void check_valid_titer( @@
           ) {
           std::string msg = "Invalid titer '"+titer+"'";
-          Rf_error(msg.c_str());
+          Rf_error("%s", msg.c_str());
         }
@@ Expand Down @@