Merge pull request #172 from isoverse/dev

switch workflow from deprecated ubuntu 16.04 to latest

.Rbuildignore

@@ -31,3 +31,4 @@
 ^LICENSE$
 ^paper.bib$
 ^paper.md$
+^[^/]*\.feather$

.github/workflows/R-CMD-check-devel.yaml

@@ -33,7 +33,7 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
       - name: Remove .Rprofile
         run: rm .Rprofile

.github/workflows/R-CMD-check.yaml

@@ -22,7 +22,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -35,6 +35,8 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
 
+      - uses: r-lib/actions/setup-pandoc@v1
+
       - name: Remove .Rprofile
         run: rm .Rprofile
 
@@ -68,6 +70,15 @@ jobs:
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Install stringi from source (for Linux)
+        if: runner.os == 'Linux'
+        run: |
+          remove.packages("stringr")
+          remove.packages("stringi")
+          install.packages("stringi", type="source")
+          install.packages("stringr", type="source")
+        shell: Rscript {0}
+
       - name: Install package
         run: |
           # install isoreader before check so parallel processing examples work

.gitignore

@@ -49,3 +49,5 @@ inst/doc
 doc
 docs
 Meta
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: isoreader
 Title: Read Stable Isotope Data Files
 Description: Interface to the raw data file formats commonly encountered in scientific disciplines that make use of stable isotopes.
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: 
     c(person(
         given = "Sebastian", family = "Kopf", 
@@ -57,6 +57,5 @@ Suggests:
 biocViews: 
 License: GPL (>= 2)
 Encoding: UTF-8
-LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2

Makefile

@@ -17,3 +17,10 @@ auto_test:
 # test with all example files (= as if not on CRAN)
 auto_test_all:
 	R -q -e "rm(list = ls()); testthat::auto_test_package()"
+
+# check code complexity
+count:
+	scc R tests --include-ext r --sort lines
+
+count_all:
+	scc . --sort lines

R/isoread.R

@@ -516,6 +516,7 @@ create_read_process <- function(process, data_structure, files) {
           process = process, data_structure = data_structure, files = files,
           log_file = log_file, progress_file = progress_file, all_opts = all_opts)),
         packages = packages,
+        seed = NULL,
         expr = {
           # require namespace if running in a separate session during parallel processing
           base::requireNamespace("isoreader", quietly = TRUE)