No v8

.travis.yml

@@ -12,7 +12,6 @@ dist: xenial
 os:
   - linux
   - osx
-  - windows
 
 # as xenial
 services:
@@ -59,7 +58,6 @@ before_install:
     then
       start_xvfb ;
     fi
-  - v8_install ;
   - export rver=`r_version`;
   - export gh_user=`get_gh_user` ; echo $gh_user ;
   - cat DESCRIPTION

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ANTsRCore
 Type: Package
 Title: Core Software Infrastructure for 'ANTsR'
-Version: 0.7.1
-Date: 2019-09-19
+Version: 0.7.1.9000
+Date: 2019-10-30
 Authors@R: c(
     person(given = "Brian B.", family = "Avants", role = "cre",
     email = "stnava@gmail.com"),

R/imagesToMatrix.R

@@ -40,5 +40,5 @@ imagesToMatrix <- function(imageList, mask) {
     print("Must pass a list of filenames")
     return(NA)
   }
-  return(.Call("imagesToMatrix", imageList, mask, n))
+  return(.Call("imagesToMatrix", imageList, mask, n, PACKAGE = "ANTsRCore"))
 }

R/mergeChannels.R

@@ -33,6 +33,6 @@ mergeChannels <- function(imageList) {
       }
   }
 
-  img = .Call("mergeChannels", imageList, package="ANTsR")
+  img = .Call("mergeChannels", imageList, package="ANTsRCore")
   return(img)
 }

R/n4BiasFieldCorrection.R

@@ -91,5 +91,6 @@ n4BiasFieldCorrection <- function( img,
   return(outimg)
 }
 .helpn4BiasFieldCorrection <- function(...) {
-  .Call("N4BiasFieldCorrection", .int_antsProcessArguments(c(...)))
+  .Call("N4BiasFieldCorrection", .int_antsProcessArguments(c(...)),
+        PACKAGE = "ANTsRCore")
 }

R/splitChannels.R

@@ -32,6 +32,6 @@ splitChannels <- function(image) {
     stop( "input must have more than 1 components")
   }
 
-  img = .Call("splitChannels", image, package="ANTsR")
+  img = .Call("splitChannels", image, package="ANTsRCore")
   return(img)
 }

configure.win

@@ -1,5 +1,15 @@
 #!/bin/bash
+git_exe=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=Sys.which('git'); cat(x)"`
+if [ -z "${git_exe}" ]; then
+    ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")'
+    str="repo = git2r::init();"
+    str="${str} if (length(git2r::commits(repo)) > 0) {"
+    str="${str} x=git2r::sha(git2r::last_commit(repo)) } else {x = ''};"
+    str="${str} cat(x)"
+    antsrtag=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}"`
+else 
     antsrtag=`git log --pretty=format:'%H' -n 1`
+fi    
 CXX_STD=CXX11
 CC=`${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD config CC`
 CXX=`${R_HOME}/bin${R_ARCH_BIN}/R.exe CMD config CXX`
@@ -29,6 +39,7 @@ PWD=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'cat(normalizePath(".", winslash=
 # platform-specific Makevars
 echo "PWD=${PWD}" > Makevars.win
 myantslib=${PWD}/antb/lib/
+antsexdir=${PWD}/antb/ANTS-build/Examples/
 echo "myantssource=\${PWD}/ants" >> Makevars.win
 echo "ITK=\"${ITKRCMAKE}\"" >> Makevars.win
 
@@ -44,7 +55,7 @@ echo "SHLIB_CXXLD=${CMAKE_EXE_LINKER_FLAGS}"
 
 # echo "myantslib=\"\${PWD}/antb/lib/\"" >> Makevars.win
 echo "myantslib=\${PWD}/antb/lib/">> Makevars.win
-
+echo "antsexdir=\${PWD}/antb/ANTS-build/Examples/">> Makevars.win
 # echo "libants=\`find \"\${myantslib}\" -name \"lib*.a\"\`" >> Makevars.win
 # echo "libitk=\`find \"${ITKRLIB}\" -name \"lib*.a\"\`" >> Makevars.win
 
@@ -67,27 +78,28 @@ echo "Running ${libitk}"
 # echo "Running libants"
 # libants="-L${myantslib} ${libants}"
 # echo "Running ${libants}"
-libants="-L${myantslib} -lantsUtilities -ll_antsAffineInitializer -ll_antsApplyTransforms "
+libants="-L${myantslib} -L${antsexdir} -lantsUtilities -ll_antsAffineInitializer -ll_antsApplyTransforms "
 libants="${libants} -ll_antsApplyTransformsToPoints -ll_antsJointFusion -ll_antsMotionCorr "
 libants="${libants} -ll_antsMotionCorrStats -ll_antsRegistration -ll_Atropos -ll_DenoiseImage "
 libants="${libants} -ll_KellyKapowski -ll_LabelClustersUniquely -ll_LabelGeometryMeasures "
 libants="${libants} -ll_N3BiasFieldCorrection -ll_N4BiasFieldCorrection -ll_ResampleImage "
 libants="${libants} -ll_sccan -ll_SurfaceBasedSmoothing -ll_ThresholdImage "
 
-echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \
-               ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \
-               ${libants}" >> Makevars.win
-# echo "PKG_LIBS=${PKG_LIBS} -L${ITKRLIB} \${libants} \${libitk} \${libants} \${libitk} \
-#                \${libants} \${libitk} \${libants} \${libitk} \${libants} \${libitk} \
-#                \${libitk} \${libants}" >> Makevars.win
+# echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \
+#                ${libants} ${libitk} ${libants} ${libitk} ${libants} ${libitk} \
+#                ${libants}" >> Makevars.win
+echo "PKG_LIBS=${PKG_LIBS} ${libitk} ${libants} ${libitk} ${libants} " >> Makevars.win
 
 echo ".PHONY: all libs" >> Makevars.win
 
 echo "all: \$(SHLIB)" >> Makevars.win
 
 echo "\$(SHLIB): libs" >> Makevars.win
 # MAKER=c:/Rtools/mingw_64/bin${R_ARCH_BIN}/mingw32-make.exe
-MAKER=mingw32-make
+# MAKER=`${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "x=normalizePath(Sys.which('make'), winslash = '/'); cat(x)"`
+MAKER=mingw32-make.exe
+echo "MAKE IS"
+echo "${MAKER}"
 echo "libs: ; mkdir -p libs; cd antb && ls && ${MAKER} -j 4 && cd ANTS-build && ls && ${MAKER} all install && rm -rf ${R_PACKAGE_DIR}/libs/bin && cd ../../" >> Makevars.win
 
 echo "cleaner: ; cd ../libs/bin && rm -f antsRegistration antsApplyTransforms antsMotionCorr \
@@ -101,8 +113,16 @@ ThresholdImage LabelClustersUniquely SurfaceBasedSmoothing" >> Makevars
 # antsgit=https://github.com/ANTsX/ANTs.git
 # antstag=c60752a7a6eca0371b0f5ff5ffa13385a5f5ea4f # n4 bug
 antsgit=https://github.com/muschellij2/ANTs.git
-antstag=c39585e656f7162cf74fd2d9b0438963671e03d2
+antstag=7ca882f532ae7fdf9b9a5ccb94810a39a98c9ef2
+if [ -z "${git_exe}" ]; then
+    ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")'
+    str="repo = git2r::clone(\""
+    str="${str}${antsgit}"
+    str="${str}\", local_path = \"./ants\")"
+    ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}"  
+else
     git clone $antsgit ants
+fi
 mkdir -p ../data
 
 echo "Dependency;GitTag" > ../data/antsVersions.csv
@@ -111,6 +131,23 @@ echo "ANTsRCore;${antsrtag}" >> ../data/antsVersions.csv
 echo "ANTsURL;${antsgit}" >> ../data/antsVersions.csv
 echo "ITK;${ITKTAG}" >> ../data/antsVersions.csv
 cd ants
+
+if [ -z "${git_exe}" ]; then
+    ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e 'if (!requireNamespace("git2r")) install.packages("git2r")'
+    str="repo = git2r::init()"   
+    if [ -n "${antstag}" ]; then
+        str="${str}; git2r::checkout(repo, branch = \""
+        str="${str}${antstag}"
+        str="${str}\");"
+    fi    
+    ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}"
+else
+    git checkout master;
+    git pull;
+    git checkout $antstag ;
+fi
+
+# windows workaround for warning
 if [[ -a "./CMake/ITKSetStandardCompilerFlags.cmake" ]]; 
 then
     echo "working on ITKSetStandardCompilerFlags.cmake"
@@ -120,9 +157,7 @@ then
     str=${str}'writeLines(x, fname)}'
     ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe -e "${str}"
 fi
-git checkout master;
-git pull;
-git checkout $antstag
+
 cd ../
 mkdir -p antb
 cp ../inst/include/antscore.h ./ants/Examples/include/ants.h
@@ -170,6 +205,7 @@ ${cmaker} \
     -DCMAKE_NEED_RESPONSE=1 \
     -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON \
     -DCOPY_SCRIPT_FILES_TO_BIN_DIR=OFF \
+    -DCMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE="../ants/lib/" \
     -DCMAKE_INSTALL_PREFIX:PATH="${R_PACKAGE_DIR}/libs/" \
     -DCMAKE_BUILD_TYPE:STRING="${CMAKE_BUILD_TYPE}" \
     -DVNL_CONFIG_ENABLE_SSE2_ROUNDING:BOOL=ON \

data/antsVersions.csv

@@ -1,3 +1,5 @@
 Dependency;GitTag
-ANTs;554b696927351c0de998fa6cde346c16630212fb
-ANTsRCore;44880fce95158ba5cc77e2b6b0df0cfc9b1d6d33
+ANTs;1c421a5853f343a020aaae861a751545112e0807
+ANTsRCore;0d3c153eb80e56a04332cd2d28ed9e3389d388f1
+ANTsURL;https://github.com/ANTsX/ANTs.git
+ITK;

tests/testthat/test-antsImage.R

@@ -271,15 +271,15 @@ test_that("antsImage %% antsImage, preserves header", {
 
 test_that("antsImage %% antsImage", {
   expect_true(is.antsImage(img1 %% img2))
-  expect_true(sum(img1 %% img2) == sum(valuesm %% values2))
+  expect_equal(sum(img1 %% img2), sum(valuesm %% values2))
 })
 test_that("antsImage %% antsImage, preserves header", {
   expect_true(antsImagePhysicalSpaceConsistency(data.type = TRUE, img, img %% img))
 })
 
 test_that("antsImage %/% scalar", {
   expect_true(is.antsImage(img1 %/% 2))
-  expect_true(sum(img1 %/% 2) == sum(valuesm %/% 2))
+  expect_equal(sum(img1 %/% 2), sum(valuesm %/% 2))
 })
 test_that("antsImage %/% scalar, preserves header", {
   expect_true(antsImagePhysicalSpaceConsistency(data.type = TRUE, img, img %/% 2))
@@ -295,7 +295,7 @@ test_that("antsImage %% antsImage, preserves header", {
 
 test_that("antsImage %/% antsImage", {
   expect_true(is.antsImage(img1 %% img2))
-  expect_true(sum(img1 %/% img2) == sum(valuesm %/% values2))
+  expect_equal(sum(img1 %/% img2), sum(valuesm %/% values2))
 })
 test_that("antsImage %/% antsImage, preserves header", {
   expect_true(antsImagePhysicalSpaceConsistency(data.type = TRUE, img1, img1 %/% img2))