* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘neuroim’ ... ** package ‘neuroim’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (Debian 13.3.0-1) 13.3.0’ make[1]: Entering directory '/tmp/RtmplB7Z3n/R.INSTALL20a58a7ee88fc3/neuroim/src' g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c indexFuns.cpp -o indexFuns.o g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o neuroim.so RcppExports.o indexFuns.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmplB7Z3n/R.INSTALL20a58a7ee88fc3/neuroim/src' make[1]: Entering directory '/tmp/RtmplB7Z3n/R.INSTALL20a58a7ee88fc3/neuroim/src' make[1]: Leaving directory '/tmp/RtmplB7Z3n/R.INSTALL20a58a7ee88fc3/neuroim/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-neuroim/00new/neuroim/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘as.mask’ in package ‘neuroim’ ** help *** installing help indices converting help for package ‘neuroim’ finding HTML links ... done AFNIFileDescriptor-class html AFNIMetaInfo-class html AxisSet-class html AxisSet1D-class html AxisSet2D-class html AxisSet3D-class html AxisSet4D-class html AxisSet5D-class html Base-class html BaseMetaInfo-class html BaseSource-class html BinaryReader-class html BinaryReader html BinaryWriter-class html BootstrapSearchlight html BrainBucket-class html BrainBucketSource-class html BrainData-class html BrainFileDescriptor-class html BrainFileSource-class html BrainMetaInfo-class html BrainSlice-class html BrainSlice html BrainSource-class html BrainSpace-class html BrainSpace html BrainSurface-class html BrainSurfaceSource-class html BrainSurfaceVector-class html BrainSurfaceVectorSource-class html BrainVector-class html BrainVectorSource-class html BrainVectorSource html BrainVolume-class html BrainVolume html BrainVolumeSource-class html ClusteredBrainVolume-class html ColumnReader-class html ColumnReader html DenseBrainVector-class html DenseBrainVolume-class html FileMetaInfo-class html REDIRECT:topic Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-neuroim/00new/neuroim/help/AFNIMetaInfo-class.html FreeSurferSurfaceGeometryMetaInfo-class html FreesurferAsciiSurfaceFileDescriptor-class html IndexLookupVolume-class html Kernel-class html Kernel html Layer-class html Layer html LogicalBrainVolume-class html MNI_SPACE_1MM html NIMLSurfaceDataMetaInfo-class html NIMLSurfaceDataMetaInfo html NIMLSurfaceFileDescriptor-class html NIfTIFileDescriptor-class html NIfTIMetaInfo-class html NamedAxis-class html NullMetaInfo-class html ROIVolume-class html ROIVolume html RandomSearchlight html RegionCube html RegionSphere html RegionSquare html Searchlight html SparseBrainVector-class html SparseBrainVectorSource-class html SparseBrainVolume-class html SurfaceDataMetaInfo-class html SurfaceDataMetaInfo html SurfaceGeometryMetaInfo-class html SurfaceGeometryMetaInfo html addDim-methods html as-methods html as.array-BrainData-method html as.list-methods html as.logical-methods html as.mask-methods html as.matrix-BrainData-method html as.matrix-methods html as.numeric-methods html as.raster-methods html as.sparse-methods html as.vector-BrainData-method html axes-methods html axisToIndex-methods html bounds-methods html close-methods html clusterCenters-methods html concat-methods html connComp-methods html connComp3D html coordToGrid-methods html coordToIndex-methods html coords-methods html dataFile-methods html dataFileMatches-methods html dataReader-methods html dim-BrainData-method html dim-BrainSpace-method html dim-FileMetaInfo-method html dropDim-methods html eachSeries-methods html eachSlice-methods html eachVolume-methods html fileMatches-methods html fill-methods html gridToCoord-methods html gridToIndex-methods html headerFile-methods html headerFileMatches-methods html image-methods html imageGrid html indexToCoord-methods html indexToGrid-methods html indices-methods html internal-methods html inverseTrans-methods html length-methods html loadBucket html loadData-methods html loadFSSurface html loadSurface html loadVector html loadVolume html loadVolumeList html lookup-methods html makeVector html makeVolume html map-methods html mapToColors html matchAnatomy2D html matchAnatomy3D html matrixToVolumeList html mergePartitions-methods html names-methods html ndim-methods html neuroim html numClusters-methods html origin-methods html overlay-methods html partition-methods html permMat-methods html pick-methods html print-AxisSet2D-method html print-AxisSet3D-method html print-NamedAxis-method html print-methods html readAFNIHeader html readColumns-methods html readElements-methods html readHeader html readMetaInfo-methods html render-methods html renderSlice-methods html scaleSeries-methods html series-methods html seriesIter html show-AxisSet1D-method html show-AxisSet2D-method html show-AxisSet3D-method html show-AxisSet4D-method html show-BaseMetaInfo-method html show-BrainSpace-method html show-BrainVector-method html show-BrainVectorSource-method html show-BrainVolume-method html show-FileMetaInfo-method html show-NamedAxis-method html show-NullMetaInfo-method html show-ROIVolume-method html show-SparseBrainVector-method html show-SurfaceDataMetaInfo-method html show-SurfaceGeometryMetaInfo-method html slice-methods html sliceData html space-methods html spacing-methods html splitFill-methods html splitReduce-methods html splitScale-methods html stripExtension-methods html sub-BrainBucket-index-missing-ANY-method html sub-ROIVolume-numeric-missing-ANY-method html sub-SparseBrainVector-missing-missing-ANY-method html sub-SparseBrainVector-missing-numeric-ANY-method html sub-SparseBrainVector-numeric-missing-ANY-method html sub-SparseBrainVector-numeric-numeric-ANY-method html sub-SparseBrainVolume-matrix-missing-ANY-method html sub-SparseBrainVolume-missing-missing-ANY-method html sub-SparseBrainVolume-missing-numeric-ANY-method html sub-SparseBrainVolume-numeric-missing-missing-method html sub-SparseBrainVolume-numeric-numeric-ANY-method html sub-sub-BrainBucket-index-missing-method html subVector-methods html takeSeries-methods html takeVolume-methods html tesselate-methods html trans-methods html values-methods html voxels-methods html writeElements-methods html writeVector-methods html writeVolume-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 (neuroim)