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dfsp-spirit committed Mar 27, 2023
2 parents a6fc0ec + ec631b5 commit b44e351
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77 changes: 20 additions & 57 deletions .github/workflows/R-CMD-check.yaml
Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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
5 changes: 4 additions & 1 deletion R/read_fs_transform.R
Original file line number Diff line number Diff line change
Expand Up @@ -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;
}
Expand Down
9 changes: 8 additions & 1 deletion README.md
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@@ -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.

Expand Down Expand Up @@ -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).

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