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Changed test data location (GitHub), tests for stringsAsFactors loading, and added Actions workflow #312

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14e3f68
Added workflow .yml and test .txt file
bilalhsyed Sep 8, 2022
6f85df1
Updated getRMINCTestData() to download from GitHub. Updated tests to …
bilalhsyed Sep 12, 2022
5e8cd0f
Updated workflow .yml to setup R and run RMINC tests
bilalhsyed Sep 8, 2022
c33169a
Changed mincTFCE lm randomization test to not run on CI
bilalhsyed Sep 29, 2022
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46 changes: 46 additions & 0 deletions .github/workflows/r-package.yml
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@@ -0,0 +1,46 @@
# This workflow will install R dependencies and run tests with a variety of R versions.

name: R package

on:
push:
branches: [master, develop]
pull_request:
branches: [master, develop]

jobs:
build:
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
r-version: ["4.1.1"]

steps:
- uses: actions/checkout@v3
- name: Setup R
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.r-version }}
- name: Setup R dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check
- name: Installing dependencies
run: |
sudo apt-get -y install libminc-dev
wget --quiet http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.18-20220625-Ubuntu_20.04-x86_64.deb
sudo dpkg -i minc-toolkit-1.9.18-20220625-Ubuntu_20.04-x86_64.deb
source /opt/minc/1.9.18/minc-toolkit-config.sh
git clone --recursive https://github.com/Mouse-Imaging-Centre/minc-stuffs.git
cd minc-stuffs
./autogen.sh
./configure --with-build-path=/opt/minc/1.9.18/
sudo make
sudo make install
sudo python setup.py install
- name: Running R CMD Check
run: |
source /opt/minc/1.9.18/minc-toolkit-config.sh
Rscript -e 'rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), build_args = "--no-manual", error_on = "warning", check_dir = "check")'
4 changes: 2 additions & 2 deletions R/minc_interface.R
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Expand Up @@ -1346,12 +1346,12 @@ runRMINCTestbed <- function(..., dataPath = getOption("RMINC_DATA_DIR", tempdir(
getRMINCTestData <- function(dataPath = getOption("RMINC_DATA_DIR", tempdir()), method = "libcurl") {

downloadPath <- file.path(dataPath, "rminctestdata.tar.gz")
extractedPath <- file.path(dataPath, "rminctestdata/")
extractedPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

if(!file.exists(extractedPath)){
if(!file.exists(downloadPath)){
dir.create(dataPath, showWarnings = FALSE, recursive = TRUE)
download.file("https://wiki.mouseimaging.ca/download/attachments/1654/rminctestdata2.tar.gz",
download.file("https://github.com/Mouse-Imaging-Centre/RMINC-test-data/archive/master.tar.gz",
destfile = downloadPath,
method = method) # changed from "wget" to stop freakouts on mac
}
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5 changes: 5 additions & 0 deletions src/RcppExports.cpp
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Expand Up @@ -5,6 +5,11 @@

using namespace Rcpp;

#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// anat_summary
List anat_summary(CharacterVector filenames, IntegerVector atlas, std::string method);
RcppExport SEXP _RMINC_anat_summary(SEXP filenamesSEXP, SEXP atlasSEXP, SEXP methodSEXP) {
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4 changes: 2 additions & 2 deletions tests/testthat/test_anatAnova.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"))
gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"), stringsAsFactors = TRUE)
gf <- civet.getAllFilenames(gf,"ID","TEST",file.path(dataPath, "CIVET"),"TRUE","1.1.12")
gf <- civet.readAllCivetFiles(file.path(dataPath, "AAL.csv"),gf)

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4 changes: 2 additions & 2 deletions tests/testthat/test_anatApply.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"))
gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"), stringsAsFactors = TRUE)
gf <- civet.getAllFilenames(gf,"ID","TEST",file.path(dataPath, "CIVET"),"TRUE","1.1.12")
gf <- civet.readAllCivetFiles(file.path(dataPath, "AAL.csv"),gf)

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4 changes: 2 additions & 2 deletions tests/testthat/test_anatFDR.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"))
gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"), stringsAsFactors = TRUE)
gf <- civet.getAllFilenames(gf,"ID","TEST",file.path(dataPath, "CIVET"),"TRUE","1.1.12")
gf <- civet.readAllCivetFiles(file.path(dataPath, "AAL.csv"),gf)

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6 changes: 3 additions & 3 deletions tests/testthat/test_anatGet.R
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Expand Up @@ -10,13 +10,13 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"))
gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"), stringsAsFactors = TRUE)
first_file <- gf$jacobians_0.2[1]
segmentation <- file.path(dataPath, "test_segmentation.mnc")
labels <- file.path(dataPath, "test_defs.csv")
label_frame <- read.csv(labels)
label_frame <- read.csv(labels, stringsAsFactors = TRUE)
known_labels <- with(label_frame, union(left.label, right.label))

unanat <- function(anat){
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4 changes: 2 additions & 2 deletions tests/testthat/test_anatLm.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"))
gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"), stringsAsFactors = TRUE)
gf <- civet.getAllFilenames(gf,"ID","TEST",file.path(dataPath, "CIVET"),"TRUE","1.1.12")
gf <- civet.readAllCivetFiles(file.path(dataPath, "AAL.csv"),gf)

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6 changes: 3 additions & 3 deletions tests/testthat/test_anatLmer.R
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Expand Up @@ -16,13 +16,13 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"))
gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"), stringsAsFactors = TRUE)
first_file <- gf$jacobians_0.2[1]
segmentation <- file.path(dataPath, "test_segmentation.mnc")
labels <- file.path(dataPath, "test_defs.csv")
label_frame <- read.csv(labels)
label_frame <- read.csv(labels, stringsAsFactors = TRUE)
known_labels <- with(label_frame, union(left.label, right.label))

anat_env <- new.env()
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4 changes: 2 additions & 2 deletions tests/testthat/test_anatomy.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"))
gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"), stringsAsFactors = TRUE)
gf <- civet.getAllFilenames(gf,"ID","TEST",file.path(dataPath, "CIVET"),"TRUE","1.1.12")
gf <- civet.readAllCivetFiles(file.path(dataPath, "AAL.csv"),gf)

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10 changes: 5 additions & 5 deletions tests/testthat/test_civet.R
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Expand Up @@ -5,16 +5,16 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"))
gf <- read.csv(file.path(dataPath, "CIVET_TEST.csv"), stringsAsFactors = TRUE)
gf <- civet.getAllFilenames(gf,"ID","TEST",file.path(dataPath, "CIVET"),"TRUE","1.1.12")
gf <- civet.readAllCivetFiles(file.path(dataPath, "AAL.csv"),gf)

dataFile <- gf$lobeThickness
AALAtlas <- read.csv(file.path(dataPath, "AAL.csv"))
verticesL <- read.csv(file.path(dataPath, "AAL_atlas_left.txt"),header = FALSE)
verticesR <- read.csv(file.path(dataPath, "AAL_atlas_right.txt"),header = FALSE)
AALAtlas <- read.csv(file.path(dataPath, "AAL.csv"), stringsAsFactors = TRUE)
verticesL <- read.csv(file.path(dataPath, "AAL_atlas_left.txt"),header = FALSE, stringsAsFactors = TRUE)
verticesR <- read.csv(file.path(dataPath, "AAL_atlas_right.txt"),header = FALSE, stringsAsFactors = TRUE)
reducedVertices <- c(verticesL[0:40961,1],verticesR[0:40961,1])

atlasIndex <- pmatch(names(dataFile[1,1]),AALAtlas[,3])
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincAnova.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)

voxel_left <- mincGetVoxel(gf$jacobians_fixed_2[1:10], 0,0,0)
voxel_right <- mincGetVoxel(gf$jacobians_fixed_2[11:20], 0,0,0)
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincApply.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)

mm <- verboseRun("mincMean(gf$jacobians_fixed_2)",getOption("verbose"))
ma <- verboseRun("mincApply(gf$jacobians_fixed_2,quote(mean(x)))",getOption("verbose"))
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincFDR.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)

voxel_left <- mincGetVoxel(gf$jacobians_fixed_2[1:10], 0,0,0)
voxel_right <- mincGetVoxel(gf$jacobians_fixed_2[11:20], 0,0,0)
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincLm.R
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Expand Up @@ -6,9 +6,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)

voxel_left <- mincGetVoxel(gf$jacobians_fixed_2[1:10], 0,0,0)
voxel_right <- mincGetVoxel(gf$jacobians_fixed_2[11:20], 0,0,0)
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincLmer.R
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Expand Up @@ -13,9 +13,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)
maskfile <- file.path(dataPath, "testminc-mask.mnc")

# pick a voxel inside the mask
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincSummary.R
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Expand Up @@ -7,9 +7,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"))
gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"), stringsAsFactors = TRUE)
gf$vox <- mincGetVoxel(gf$jacobians_0.2, 0, 0, 0)

#Calculate mean, sd, variance, and sum
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6 changes: 3 additions & 3 deletions tests/testthat/test_mincTFCE.R
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Expand Up @@ -4,9 +4,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"))
gf <- read.csv(file.path(dataPath, "minc_summary_test_data.csv"), stringsAsFactors = TRUE)
first_file <- gf$jacobians_0.2[1]

first_vol <- mincGetVolume(first_file)
Expand Down Expand Up @@ -69,7 +69,7 @@ context("MincLm Randomization TFCE")
test_that("lm randomization works", {
evalq({
skip_on_cran()
skip_on_travis()
skip_on_ci()

verboseRun(lmod <- mincLm(jacobians_0.2 ~ Genotype, gf))
verboseRun(randomization_results <- mincTFCE(lmod, R = 10))
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4 changes: 2 additions & 2 deletions tests/testthat/test_mincTable.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)
maskfile <- file.path(dataPath, "testminc-mask.mnc")

ref <- sapply(gf$jacobians_fixed, function(f) mincGetVolume(f))
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4 changes: 2 additions & 2 deletions tests/testthat/test_minc_apply_rcpp.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)

mm <- verboseRun("mincMean(gf$jacobians_fixed_2)",getOption("verbose"))
ma <- verboseRun(
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2 changes: 1 addition & 1 deletion tests/testthat/test_misc.R
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Expand Up @@ -6,7 +6,7 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

matrix_3x4 <- mincGetTagFile(file.path(dataPath, "3rows_4cols.tag"))
matrix_4x3 <- mincGetTagFile(file.path(dataPath, "4rows_3cols_2comments.tag"))
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4 changes: 2 additions & 2 deletions tests/testthat/test_objects.R
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Expand Up @@ -7,9 +7,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)


a <- structure(1, class = "mincSingleDim")
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8 changes: 4 additions & 4 deletions tests/testthat/test_qminc.R
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Expand Up @@ -21,7 +21,7 @@ test_parallel <-
dataPath <- "."
}

if(!file.exists(file.path(dataPath, "rminctestdata"))){
if(!file.exists(file.path(dataPath, "RMINC-test-data-main/rminctestdata"))){

if(getOption("verbose")){
getRMINCTestData(dataPath)
Expand All @@ -30,15 +30,15 @@ test_parallel <-
}

on.exit({
unlink(file.path(dataPath, "rminctestdata"), recursive = TRUE)
unlink(file.path(dataPath, "RMINC-test-data-main/rminctestdata"), recursive = TRUE)
unlink(file.path("rminctestdata.tar.gz"))
}, add = TRUE)

}

dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gf <- read.csv(file.path(dataPath, "test_data_set.csv"))
gf <- read.csv(file.path(dataPath, "test_data_set.csv"), stringsAsFactors = TRUE)
mask_file <- file.path(dataPath, "testminc-mask.mnc")
}

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4 changes: 2 additions & 2 deletions tests/testthat/test_vertexAnova.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gftest <- read.csv(file.path(dataPath, "subject.csv"))
gftest <- read.csv(file.path(dataPath, "subject.csv"), stringsAsFactors = TRUE)

subjectFile = matrix(data=NA,nrow=10,1)
subjectFile[1,1] = file.path(dataPath, "vertex2.txt")
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4 changes: 2 additions & 2 deletions tests/testthat/test_vertexApply.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gftest <- read.csv(file.path(dataPath, "subject.csv"))
gftest <- read.csv(file.path(dataPath, "subject.csv"), stringsAsFactors = TRUE)

subjectFile = matrix(data=NA,nrow=10,1)
subjectFile[1,1] = file.path(dataPath, "vertex2.txt")
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4 changes: 2 additions & 2 deletions tests/testthat/test_vertexFDR.R
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Expand Up @@ -5,9 +5,9 @@ if(!exists("dataPath"))
dataPath <- tempdir()

getRMINCTestData(dataPath)
dataPath <- file.path(dataPath, "rminctestdata/")
dataPath <- file.path(dataPath, "RMINC-test-data-main/rminctestdata/")

gftest <- read.csv(file.path(dataPath, "subject.csv"))
gftest <- read.csv(file.path(dataPath, "subject.csv"), stringsAsFactors = TRUE)

subjectFile = matrix(data=NA,nrow=10,1)
subjectFile[1,1] = file.path(dataPath, "vertex2.txt")
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