* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘neuroim2’ ...
** this is package ‘neuroim2’ version ‘0.8.1’
** package ‘neuroim2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmkCfME/R.INSTALL42d781849871/neuroim2/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c bilateral_filter_3d.cpp -o bilateral_filter_3d.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c bilateral_filter_4d.cpp -o bilateral_filter_4d.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from bilateral_filter_4d.cpp:3:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c conncomp.cpp -o conncomp.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c fast_laplacian_enhance.cpp -o fast_laplacian_enhance.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c indexFuns.cpp -o indexFuns.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c kernel_filter.cpp -o kernel_filter.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c radius_search_3d.cpp -o radius_search_3d.o
/bin/bash: line 2: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/bin/Rscript": No such file or directory
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o neuroim2.so RcppExports.o bilateral_filter_3d.o bilateral_filter_4d.o conncomp.o fast_laplacian_enhance.o indexFuns.o kernel_filter.o radius_search_3d.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
/bin/bash: line 3: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/bin/Rscript": No such file or directory
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmkCfME/R.INSTALL42d781849871/neuroim2/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmkCfME/R.INSTALL42d781849871/neuroim2/src'
/bin/bash: line 2: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/bin/Rscript": No such file or directory
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmkCfME/R.INSTALL42d781849871/neuroim2/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-neuroim2/00new/neuroim2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘scale’ in package ‘neuroim2’
Creating a new generic function for ‘ndim’ in package ‘neuroim2’
Creating a new generic function for ‘origin’ in package ‘neuroim2’
Creating a generic function from function ‘split_blocks’ in package ‘neuroim2’
** help
*** installing help indices
converting help for package ‘neuroim2’
finding HTML links ... done
AFNIMetaInfo html
AbstractSparseNeuroVec-class html
Arith-NeuroVec-NeuroVol-method html
Arith-NeuroVol-NeuroVec-method html
Arith-ROIVol-ROIVol-method html
Arith-methods html
ArrayLike3D-class html
ArrayLike4D-class html
ArrayLike5D-class html
AxisSet-class html
AxisSet1D-class html
AxisSet2D-class html
AxisSet3D-class html
AxisSet4D-class html
AxisSet5D-class html
BigNeuroVec-class html
BigNeuroVec-methods html
BinaryReader-class html
BinaryReader html
BinaryWriter-class html
BinaryWriter html
ClusteredNeuroVol-class html
ColumnReader-class html
ColumnReader html
Compare-methods html
DenseNeuroVec-class html
DenseNeuroVol-class html
FileBackedNeuroVec-class html
FileBackedNeuroVec html
FileFormat-class html
FileFormat-operations html
FileMetaInfo-class html
FileSource-class html
IndexLookupVol-class html
Kernel-class html
Kernel html
LogicalNeuroVol-class html
MappedNeuroVec-class html
MappedNeuroVecSource-class html
MetaInfo-class html
MetaInfo html
NIFTIMetaInfo html
NamedAxis-class html
NeuroBucket-class html
NeuroHyperVec-class html
NeuroHyperVec html
NeuroObj-class html
NeuroSlice-class html
NeuroSlice html
NeuroSpace-class html
NeuroSpace html
NeuroVec-class html
NeuroVecSeq-class html
NeuroVecSeq-methods html
NeuroVecSeq html
NeuroVecSource-class html
NeuroVecSource html
NeuroVol-class html
NeuroVol html
NeuroVolSource-class html
None html
NullAxis html
OrientationList2D html
OrientationList3D html
ROI-class html
ROICoords-class html
ROICoords html
ROIVec-class html
ROIVec html
ROIVecWindow-class html
ROIVol-class html
ROIVol html
ROIVolWindow-class html
SparseNeuroVec-class html
SparseNeuroVec-methods html
SparseNeuroVecSource-class html
SparseNeuroVol-array html
SparseNeuroVol-class html
SparseNeuroVol-numeric html
Summary-methods html
TIME html
TimeAxis html
add_dim-methods html
anatomical_axes html
as-ClusteredNeuroVol-DenseNeuroVol html
as-DenseNeuroVol-array html
as html
as.dense-methods html
as.dense html
as.list-methods html
as.logical-methods html
as.mask-methods html
as.mask html
as.matrix-methods html
as.matrix html
as.numeric-methods html
as.raster html
as.sparse-methods html
as.sparse html
as_nifti_header html
axes-methods html
bilateral_filter html
bootstrap_searchlight html
bounds-methods html
centroid-methods html
centroids-methods html
close-methods html
clustered_searchlight html
concat-methods html
conn_comp-methods html
conn_comp_3D html
coord_to_grid-methods html
coord_to_index-methods html
coords-methods html
coords html
createNIfTIHeader html
cuboid_roi html
data_file-methods html
data_file_matches-methods html
data_reader-methods html
data_reader html
dim-methods html
dim_of-methods html
drop-methods html
drop html
drop_dim-methods html
embed_kernel-methods html
extract-methods html
extractor3d html
extractor4d html
file_matches-methods html
findAnatomy3D html
gaussian_blur html
grid_to_coord-methods html
grid_to_grid-methods html
grid_to_index-methods html
guided_filter html
header_file-methods html
header_file_matches-methods html
image html
index_to_coord-methods html
index_to_grid-methods html
indices-methods html
indices html
inverse_trans-methods html
laplace_enhance html
length-methods html
linear_access-methods html
linear_access html
load_data-methods html
load_data html
lookup-methods html
lookup html
map-methods html
map_values-methods html
matricized_access-methods html
matrixToQuatern html
ndim-AxisSet-method html
ndim-methods html
neuro-ops html
neuro-resample html
neuroim2-package html
num_clusters-methods html
numericOrMatrix-class html
origin-methods html
partition-methods html
patch_set-methods html
patch_set html
perm_mat-AxisSet2D-method html
perm_mat-AxisSet3D-method html
perm_mat-methods html
plot-methods html
quaternToMatrix html
random_searchlight html
read_columns-methods html
read_elements-BinaryReader-numeric-method
html
read_elements-methods html
read_header html
read_meta_info-methods html
read_vec html
read_vol html
read_vol_list html
reorient-methods html
resample-methods html
scale html
scale_series-methods html
searchlight-methods html
searchlight html
searchlight_coords html
series-NeuroHyperVec-ANY-method html
series-methods html
series_roi html
show-methods html
slice-methods html
slices-methods html
space-methods html
spacing-methods html
spatial-filter html
spherical_roi html
spherical_roi_set html
split_blocks-methods html
split_clusters-methods html
split_fill-methods html
split_reduce-methods html
split_scale-methods html
square_roi html
strip_extension-methods html
sub-AbstractSparseNeuroVec-numeric-numeric-ANY-method
html
sub-sub-NeuroVec-numeric-method html
sub_vector-methods html
trans-methods html
values-methods html
vectors-methods html
vols-methods html
voxels-methods html
which_dim-methods html
write_elements-methods html
write_vec-methods html
write_vol-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (neuroim2)