Merge branch 'master' into develop

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

@@ -1,14 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# From: https://github.com/r-lib/actions/tree/v2-branch/examples#standard-ci-workflow
+
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,65 +18,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

R/read_fs_transform.R

@@ -262,10 +262,13 @@ parse.transform.matrix.lines <- function(file_lines, ignore_line_suffix=";") {
 
   line_idx = 1L;
   for(file_line in file_lines) {
+
+    file_line <- trimws(file_line)
+
     if(endsWith(file_line, ignore_line_suffix)) {
       file_line = substring(file_line, 1L, (nchar(file_line) - nchar(ignore_line_suffix)));
     }
-    matrix_row = as.double(strsplit(file_line, " ")[[1]]);
+    matrix_row = as.double(strsplit(trimws(file_line), " ")[[1]]);
     tm[line_idx, ] = matrix_row;
     line_idx = line_idx + 1L;
   }

README.md

@@ -1,3 +1,10 @@
+<!-- badges: start -->
+[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/dfsp-spirit/freesurferformats?branch=master&svg=true)](https://ci.appveyor.com/project/dfsp-spirit/freesurferformats)
+[![codecov](https://codecov.io/gh/dfsp-spirit/freesurferformats/branch/master/graph/badge.svg)](https://codecov.io/gh/dfsp-spirit/freesurferformats)
+[![](https://cranlogs.r-pkg.org/badges/freesurferformats)](https://CRAN.R-project.org/package=freesurferformats)
+<!-- badges: end -->
+
+
 # freesurferformats
 GNU R package to read and write structural neuroimaging file formats. Comes with support for file formats used by [FreeSurfer](https://freesurfer.net/), [CAT12](http://www.neuro.uni-jena.de/cat/)/[SPM](https://www.fil.ion.ucl.ac.uk/spm/software/), [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki), [BrainVoyager](http://www.brainvoyager.com/), [MRtrix3](https://www.mrtrix.org/), [Diffusion Toolkit/TrackVis](http://trackvis.org/dtk/) and other neuroimaging software packages.
 
@@ -267,4 +274,4 @@ If you found a bug, have any question, suggestion or comment on freesurferformat
 
 Please see [CONTRIBUTING.md](CONTRIBUTING.md) for instructions on how to contribute code.
 
-The freesurferformats package was written by [Tim Schäfer](http://rcmd.org/ts/). To contact me in person, please use the maintainer email address listed on the [CRAN webpage for freesurferformats](https://cran.r-project.org/package=freesurferformats).
+The freesurferformats package was written by [Tim Schäfer](https://ts.rcmd.org). To contact me in person, please use the maintainer email address listed on the [CRAN webpage for freesurferformats](https://cran.r-project.org/package=freesurferformats).