* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘freesurferformats’ ...
** this is package ‘freesurferformats’ version ‘1.1.0’
** package ‘freesurferformats’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘freesurferformats’
finding HTML links ... done
CIFTI_EXTENSION_CODE html
adjust.face.indices.to html
analyze.dtype.info html
analyze.header.check html
analyze.header.to.vox2ras html
analyze.mat.sidecar.to.vox2ras html
analyze.pair.files html
analyze.read.char.field html
analyze.read.header.internal html
analyze.read.magic html
analyze.write.data.internal html
analyzeheader.for.data html
analyzeheader.template html
annot.max.region.idx html
annot.unique html
apply.affine.to.coords html
as.fs.tracts html
as.list.fs.tracts html
as.tsf.scalars html
assert.surface html
atlas.from.lut.and.csv html
axcodes2ornt html
build.mrtrix.header html
build.mrtrix.header.stable html
bvsmp html
cdata html
check.dtype.for.data html
check_all_finite html
check_data_and_settings_consistency html
check_file_size html
cifti.annot.list html
cifti.annot.parcels html
cifti.array.with.new.first.dim html
cifti.assign.rows html
cifti.axes.to.maps html
cifti.axis.brain.models html
cifti.axis.for.maps html
cifti.axis.from.template html
cifti.axis.labels html
cifti.axis.named.maps html
cifti.axis.parcels html
cifti.axis.parcels.from.annot html
cifti.axis.scalars html
cifti.axis.series html
cifti.axis.size html
cifti.axis.surface.sizes html
cifti.axis.surfaces html
cifti.brain.model.surface html
cifti.brain.model.volume html
cifti.brainordinate.dim html
cifti.brainordinate.dims html
cifti.check.axes html
cifti.check.data.for.axes html
cifti.check.index.list html
cifti.check.index.selection html
cifti.check.label.table html
cifti.check.object html
cifti.compute.index.ranges html
cifti.connectome.axes html
cifti.data.for.all.vertices html
cifti.data.for.connectome html
cifti.data.for.grayordinates html
cifti.data.object html
cifti.data.per.structure html
cifti.data.structures html
cifti.data.surface.size html
cifti.dense.structure.matrix html
cifti.dim.labels html
cifti.dim.to.front html
cifti.file.looks.like.cifti1 html
cifti.file.looks.like.cifti2 html
cifti.file.type.for.axes html
cifti.file.type.for.extension html
cifti.file.types html
cifti.grayordinates html
cifti.grayordinates.for.axes html
cifti.grayordinates.for.model html
cifti.header.from.axes html
cifti.header.of html
cifti.index.type.short html
cifti.index.types html
cifti.is.connectome.axis html
cifti.label.table html
cifti.label.table.for.writing html
cifti.map.for.dim html
cifti.map.name html
cifti.map.type.description html
cifti.matrix.dim.sizes html
cifti.merge.axes html
cifti.model.types html
cifti.nifti.header.for.axes html
cifti.other.dim html
cifti.parcel html
cifti.parcels html
cifti.parcels.axis.of html
cifti.parse.attr html
cifti.parse.brain.models html
cifti.parse.child.int.vector html
cifti.parse.child.voxel.indices html
cifti.parse.indices.map html
cifti.parse.int.vector html
cifti.parse.label.table html
cifti.parse.metadata html
cifti.parse.named.maps html
cifti.parse.numeric.vector html
cifti.parse.parcels html
cifti.parse.series html
cifti.parse.surfaces html
cifti.parse.volumes html
cifti.parse.xml html
cifti.prepare.surface.data html
cifti.read.matrix html
cifti.read.rows html
cifti.read.values html
cifti.region.name.without.hemisphere html
cifti.series.info html
cifti.stop.if.cifti html
cifti.stop.if.cifti.name html
cifti.structure.canonical html
cifti.structure.data html
cifti.structure.data.dim html
cifti.structure.data.one html
cifti.structure.from.specifier html
cifti.structure.short html
cifti.structures html
cifti.subset.dim html
cifti.surface.vertex.count html
cifti.surface.vertex.counts html
cifti.validate.axes html
cifti.validate.brain.models html
cifti.validate.dims.coverage html
cifti.validate.file.extension html
cifti.validate.index.range html
cifti.validate.indices.map html
cifti.validate.parcels html
cifti.validate.read.size html
cifti.volume html
cifti.xml.add.indices.map html
cifti.xml.add.metadata html
cifti.xml.int.vector html
cifti.xml.num html
cifti.xml.num.vector html
cifti.xml.version html
closest.vert.to.point html
colortable.from.annot html
coord.bbox html
coord.to.key html
delete_all_opt_data html
detect.dti.tract.format html
doapply.transform.mtx html
dot-canonicalize.gradient.table html
dot-cifti.label.table.for.users html
dot-dti.bzero.threshold html
dot-find.bval.file html
dot-format.gradient.values html
dot-format.header.size html
dot-name.gradient.table.columns html
dot-read.dti.tcktsf html
dot-read.numeric.table html
dot-write.numeric.table html
download_opt_data html
dti.track.bbox html
dti.track.count html
dti.track.iterator html
euclidian.dist html
faces.quad.to.tris html
faces.tris.to.quad html
fileopen.gz.or.not html
fileopen.write.gz.or.not html
filepath.ends.with html
finite.rows html
fixed.vec.format.int html
flip2D html
flip3D html
format_bytes_human html
fread3 html
fs.get.morph.file.ext.for.format html
fs.get.morph.file.format.from.filename
html
fs.patch html
fs.surface.to.tmesh3d html
fs.tracts html
fs.tracts.coords html
fs.tracts.count html
fs.tracts.lengths html
fs.tracts.point.count html
fs.transform html
fsl.scaled.voxel.matrix html
fwrite3 html
get.dti.trk.endianness html
get.slice.orientation html
get_max_alloc_bytes html
get_opt_data_filepath html
gifti_writer html
gifti_xml html
gifti_xml_add_global_metadata html
gifti_xml_write html
giftixml_add_labeltable_from_annot html
giftixml_add_labeltable_posneg html
group.start.rows html
groups.in.bbox html
guess.filename.is.gzipped html
guess.transform.format html
guess.writable.transform.format html
has_pandoc html
infinite.rows html
int.to.col.brainvoyager html
inv.ornt.aff html
invert.fs.transform html
io.orientation html
is.analyze.file html
is.bvsmp html
is.fs.annot html
is.fs.label html
is.fs.surface html
is.fs.tracts html
is.fs.transform html
is.fs.volume html
is.gzip.file html
is.identity.matrix html
is.mghheader html
is.mrtrix.end.line html
itk.key.value html
itk.numeric.value html
length.fs.tracts html
linesplit.fixed html
list_opt_data html
lta.volume.info.lines html
m44_to_quaternion html
merge.bbox html
mesh.face.normals html
mgh.is.conformed html
mghheader html
mghheader.centervoxelRAS.from.firstvoxelRAS
html
mghheader.crs.orientation html
mghheader.is.conformed html
mghheader.is.ras.valid html
mghheader.primary.slice.direction html
mghheader.ras2vox html
mghheader.ras2vox.tkreg html
mghheader.scanner2tkreg html
mghheader.tkreg2scanner html
mghheader.update.from.vox2ras html
mghheader.vox2ras html
mghheader.vox2ras.tkreg html
mghheader.vox2vox html
mni152reg html
mri_dtype_numbytes html
mrtrix.track.iterator html
next.buffer.capacity html
ni1header.for.data html
ni1header.template html
ni2header.for.data html
ni2header.template html
nifti.datadim.from.dimfield html
nifti.datadim.to.dimfield html
nifti.dtype.info html
nifti.dtypebitpix.info.from.mgh.dtype html
nifti.field.check.length html
nifti.field.check.nchar.max html
nifti.file.uses.fshack html
nifti.file.version html
nifti.header.check html
nifti.header.to.vox2ras html
nifti.info.from.file html
nifti.info.from.oro.instance html
nifti.resolve.filepath html
nifti.space.info html
nifti.time.info html
nifti.transform.type.name html
nifti2.extension html
nifti2.extension.content html
nifti2.extension.size html
nifti2.extension.text html
nifti2.get.extension html
nifti2.read.extensions html
nifti2.strip.nul html
nifti2.trailing.nul.removed html
nifti2.write.extensions html
nii1header.for.mgh html
nrrd.dwi.info html
nrrd.field html
nrrd.field.key html
nrrd.parse.field.value html
nrrd.parse.header html
nrrd.parse.matrix html
nrrd.parse.quoted.list html
nrrd.parse.vector html
nrrd.parse.vector.list html
nrrd.raw.to.numeric html
nrrd.read.data html
nrrd.read.header.lines html
nrrd.read.remainder html
nrrd.read.values html
nrrd.resolve.data.files html
nrrd.skip.lines html
nrrd.type.info html
nrrd.vox2ras html
open.maybe.gzip html
open.mrtrix.payload html
ornt.transform html
ornt2axcodes html
parse.mrtrix.count html
parse.mrtrix.datatype html
parse.mrtrix.file.entry html
parse.mrtrix.header html
parse.mrtrix.write.datatype html
parse.stl.ascii.face html
parse.transform.matrix.lines html
ply.header.lines html
polygon.soup.to.indexed.mesh html
print.dti.track.iterator html
print.fs.annot html
print.fs.cifti html
print.fs.cifti.data html
print.fs.connectome html
print.fs.label html
print.fs.patch html
print.fs.surface html
print.fs.tracts html
print.fs.transform html
print.fs.volume html
ras.to.surfaceras html
ras.to.talairachras html
read.analyze.data html
read.analyze.header html
read.cifti html
read.cifti.header html
read.cifti.rows html
read.dti.bval html
read.dti.bvec html
read.dti.grad html
read.dti.gradients html
read.dti.tck html
read.dti.tck.header html
read.dti.trk html
read.dti.trk.header html
read.dti.tsf html
read.dti.tsf.header html
read.element.counts.ply.header html
read.fixed.char.binary html
read.fs.annot html
read.fs.annot.gii html
read.fs.colortable html
read.fs.connectome.cifti html
read.fs.curv html
read.fs.gca html
read.fs.label html
read.fs.label.gii html
read.fs.label.native html
read.fs.mgh html
read.fs.morph html
read.fs.morph.asc html
read.fs.morph.bvsmp html
read.fs.morph.cifti html
read.fs.morph.gii html
read.fs.morph.ni1 html
read.fs.morph.ni2 html
read.fs.morph.nii html
read.fs.morph.txt html
read.fs.parcellation.cifti html
read.fs.patch html
read.fs.patch.asc html
read.fs.series.cifti html
read.fs.surface html
read.fs.surface.asc html
read.fs.surface.bvsrf html
read.fs.surface.byu html
read.fs.surface.geo html
read.fs.surface.gii html
read.fs.surface.ico html
read.fs.surface.mz3 html
read.fs.surface.obj html
read.fs.surface.off html
read.fs.surface.ply html
read.fs.surface.stl html
read.fs.surface.stl.ascii html
read.fs.surface.stl.bin html
read.fs.surface.vtk html
read.fs.tracts.vtk html
read.fs.transform html
read.fs.transform.dat html
read.fs.transform.fslmat html
read.fs.transform.itk html
read.fs.transform.lta html
read.fs.transform.xfm html
read.fs.volume html
read.fs.volume.analyze html
read.fs.volume.nii html
read.fs.volume.nrrd html
read.fs.weight html
read.fs.weight.asc html
read.matlab.v4.matrix html
read.mesh.brainvoyager html
read.mrtrix.header html
read.mrtrix.stream html
read.nifti.values html
read.nifti1.data html
read.nifti1.header html
read.nifti1.header.internal html
read.nifti2.data html
read.nifti2.header html
read.nifti2.header.internal html
read.nrrd.header html
read.smp.brainvoyager html
read.smp.brainvoyager.v1or2 html
read.smp.brainvoyager.v3 html
read.smp.brainvoyager.v4or5 html
read.trk.records html
read.vtk.legacy.polydata html
read_nisurface html
read_nisurfacefile html
read_nisurfacefile.fsascii html
read_nisurfacefile.fsnative html
read_nisurfacefile.gifti html
read_safe_bin html
readable.files html
readcolortable html
readcolortable_oldformat html
rotate2D html
rotate3D html
rotate90 html
scan.dti.tract.file html
scan.mrtrix.file html
scan.trk.file html
scann html
skip.connection.bytes html
sm0to1 html
sm1to0 html
split.mrtrix.chunk html
stl.format.file.is.ascii html
sub-.fs.tracts html
sub-sub-.fs.tracts html
subset.groups html
summary.fs.transform html
surfaceras.to.ras html
surfaceras.to.talairach html
talairachras.to.ras html
text.line.is.numeric html
trackvis.affine.to.rasmm html
transform.bbox html
transform.descriptor.path html
transform.file.sniff.text html
transform.flip.handedness html
transform.geometry.for.side html
transform.matrix.row.lines html
transform.value.text html
transform.values.text html
transform.world.frame html
transform2lps html
transform2ras html
transform2voxel html
transform2world html
translate.mri.dtype html
trk.track.iterator html
validate.bbox html
validate.dti.gradients html
validate.fs.transform html
validate_allocation_size html
vertex.euclid.dist html
vertexdists.to.point html
volume.descriptor html
volume.geometry html
vtk.as.indices html
vtk.cell.section.layout html
vtk.check.triangles html
vtk.data.type.info html
vtk.next.line html
vtk.next.section html
vtk.parse.cell.section html
vtk.parse.count html
vtk.peek.line html
vtk.read.header html
vtk.reader.bytes html
vtk.reader.close html
vtk.reader.fill html
vtk.reader.new html
vtk.reader.numbers html
vtk.reader.peek html
vtk.section.values html
vtk.section.values.ascii html
vtk.split.line html
vtk.write.surface.ascii html
vtk.write.surface.binary html
write.analyze html
write.analyze.char.field html
write.analyze.header.internal html
write.atlas.to.lut.and.csv html
write.cifti html
write.dti.bval html
write.dti.bvec html
write.dti.grad html
write.dti.tck html
write.dti.trk html
write.dti.tsf html
write.fs.annot html
write.fs.annot.gii html
write.fs.colortable html
write.fs.connectome.cifti html
write.fs.curv html
write.fs.label html
write.fs.label.gii html
write.fs.mgh html
write.fs.morph html
write.fs.morph.asc html
write.fs.morph.cifti html
write.fs.morph.gii html
write.fs.morph.ni1 html
write.fs.morph.ni2 html
write.fs.morph.smp html
write.fs.morph.txt html
write.fs.parcellated.cifti html
write.fs.parcellation.cifti html
write.fs.patch html
write.fs.series.cifti html
write.fs.surface html
write.fs.surface.asc html
write.fs.surface.bvsrf html
write.fs.surface.byu html
write.fs.surface.gii html
write.fs.surface.mz3 html
write.fs.surface.obj html
write.fs.surface.off html
write.fs.surface.off.ply2 html
write.fs.surface.ply html
write.fs.surface.ply2 html
write.fs.surface.stl html
write.fs.surface.vtk html
write.fs.transform html
write.fs.transform.dat html
write.fs.transform.fslmat html
write.fs.transform.itk html
write.fs.transform.lta html
write.fs.transform.xfm html
write.fs.volume html
write.fs.weight html
write.fs.weight.asc html
write.mrtrix.streamlines html
write.nifti1 html
write.nifti1.data.internal html
write.nifti1.header.internal html
write.nifti2 html
write.smp.brainvoyager html
write.smp.brainvoyager.v2 html
write.smp.brainvoyager.v3or4or5 html
write.stl.ascii html
write.stl.binary html
write.trk.header html
xml_node_gifti_MD html
xml_node_gifti_coordtransform html
xml_node_gifti_label html
xml_node_gifti_label_table html
xml_node_gifti_label_table_from_annot html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (freesurferformats)