Release 0.4.2

.circleci/config.yml

@@ -22,9 +22,13 @@ jobs:
       - restore_cache:
           keys:
             - cache-{{ .Environment.CIRCLE_JOB }}-{{ checksum "DESCRIPTION" }}
+      - run:
+          # see https://github.com/r-lib/remotes/issues/798
+          name: Update remotes pkg if on R 4.4
+          command: R --version | grep -qF 'version 4.4' && R -e 'devtools::install_git("https://github.com/r-lib/remotes.git")' || true
       - run:
           name: Install package dependencies
-          command: R -e "devtools::install_deps(dep = TRUE)"
+          command: R -e "devtools::install_deps(dep = TRUE); quit(status=sum(grepl('non-zero exit status', names(warnings()))))"
       - save_cache:
           key: cache-{{ .Environment.CIRCLE_JOB }}-{{ checksum "DESCRIPTION" }}
           paths:
@@ -33,6 +37,7 @@ jobs:
           name: Check versions
           command: |
             which R
+            R --version
             R --quiet -e 'installed.packages()[, "Version"]'
             which pandoc
             pandoc --version
@@ -53,7 +58,7 @@ jobs:
           command: Rscript exec/find_pandoc.R
       - run:
           name: "Run demo script"
-          command: bash exec/demo.sh $PWD/demo-files
+          command: bash exec/demo.sh $PWD/demo-files strict
       - store_artifacts:
           name: "Store Artifacts: demo: report"
           path: demo-files/str-results/report.html
@@ -62,7 +67,7 @@ jobs:
           path: demo-files/str-results/summary.csv
       - run:
           name: "Run demo script - empty case"
-          command: bash exec/demo_empty.sh $PWD/demo-empty-files
+          command: bash exec/demo_empty.sh $PWD/demo-empty-files strict
       - store_artifacts:
           name: "Store Artifacts: empty demo: report"
           path: demo-empty-files/str-results/report.html
@@ -80,4 +85,8 @@ workflows:
       - build:
           matrix:
             parameters:
-              rversion: ["3.6.3", "4.2.1", "4.2.2"]
+              rversion:
+                - "4.2.3"
+                - "4.3.3"
+                - "4.4.3"
+                - "4.5.2"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: chiimp
 Title: Computational, High-throughput Individual Identification through Microsatellite Profiling
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: person("Jesse", "Connell", email = "ancon@upenn.edu", role = c("aut", "cre"))
 Description: An R package to analyze microsatellites in high-throughput sequencing datasets.
 Depends: R (>= 3.6)
@@ -31,8 +31,8 @@ Imports:
   viridis (>= 0.5),
   yaml (>= 2.2)
 Remotes:
-  github::sherrillmix/dnar,
-  github::sherrillmix/dnaplotr
+  git::https://github.com/sherrillmix/dnar.git,
+  git::https://github.com/sherrillmix/dnaplotr.git
 RoxygenNote: 7.2.0
 Suggests:
   testthat,

NEWS.md

@@ -1,3 +1,8 @@
+# chiimp 0.4.2
+
+ * Updated software dependency handling to use generic git URLs
+ * Enforce strict error handling in test scripts
+
 # chiimp 0.4.1
 
  * Overhauled unit tests with more modular saved inputs and expected outputs

README.md

@@ -8,7 +8,7 @@ high-throughput sequencing datasets.
 
 For automated installation and program usage see [GUIDE.pdf] here or in a
 [released version](https://github.com/ShawHahnLab/chiimp/releases), and the [worked examples].
-The most recent released version is [0.4.1](https://github.com/ShawHahnLab/chiimp/releases/tag/0.4.1).
+The most recent released version is [0.4.2](https://github.com/ShawHahnLab/chiimp/releases/tag/0.4.2).
 For usage as an R package also see the built-in package documentation.  The
 package-level page (`?chiimp`) provides an overview with links to specific
 functions.

exec/demo.sh

@@ -3,6 +3,10 @@
 # Wrapper script to set up and execute a demo, using the "chiimp" executable
 # R script and the test data.
 
+if [[ "$2" == "strict" ]]; then
+	set -e
+fi
+
 cd "$(dirname $BASH_SOURCE)"
 dir=$(pwd -P)
 inst="../inst"

exec/demo_empty.sh

@@ -5,6 +5,10 @@
 #
 # Special case: all empty input files
 
+if [[ "$2" == "strict" ]]; then
+	set -e
+fi
+
 cd "$(dirname $BASH_SOURCE)"
 dir=$(pwd -P)
 inst="../inst"