* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘fsbrain’ ...
** this is package ‘fsbrain’ version ‘0.5.5’
** package ‘fsbrain’ 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 ‘fsbrain’
finding HTML links ... done
alphablend html
annot.outline html
annot.outline.border.vertices html
apply.label.to.morphdata html
apply.labeldata.to.morphdata html
apply.transform html
arrange.brainview.images html
arrange.brainview.images.grid html
boxcoords.from.bbox html
brain html
brainview.sd html
Rd warning: brainview.sd.Rd:23: missing link ‘bg3d’
Rd warning: brainview.sd.Rd:29: missing link ‘par3d’
brainview.si html
Rd warning: brainview.si.Rd:21: missing link ‘bg3d’
Rd warning: brainview.si.Rd:29: missing link ‘par3d’
brainview.sr html
Rd warning: brainview.sr.Rd:26: missing link ‘bg3d’
Rd warning: brainview.sr.Rd:34: missing link ‘spin3d’
Rd warning: brainview.sr.Rd:36: missing link ‘spin3d’
Rd warning: brainview.sr.Rd:38: missing link ‘spin3d’
Rd warning: brainview.sr.Rd:40: missing link ‘spin3d’
Rd warning: brainview.sr.Rd:42: missing link ‘spin3d’
Rd warning: brainview.sr.Rd:44: missing link ‘par3d’
brainview.t4 html
Rd warning: brainview.t4.Rd:21: missing link ‘bg3d’
Rd warning: brainview.t4.Rd:29: missing link ‘par3d’
brainview.t9 html
Rd warning: brainview.t9.Rd:21: missing link ‘bg3d’
Rd warning: brainview.t9.Rd:29: missing link ‘par3d’
brainviews html
Rd warning: brainviews.Rd:22: missing link ‘par3d’
can.plot.colorbar html
can.plot.colorbar.from.coloredmeshes html
check.subjects.files html
check.subjectslist html
clip.data html
clip_fun html
cm.cbry html
cm.div html
cm.heat html
cm.qual html
cm.seq html
collayer.bg html
collayer.bg.atlas html
collayer.bg.meancurv html
collayer.bg.sulc html
collayer.from.annot html
collayer.from.annotdata html
collayer.from.mask.data html
Rd warning: collayer.from.mask.data.Rd:18: missing link ‘makecmap’
collayer.from.morphlike.data html
Rd warning: collayer.from.morphlike.data.Rd:19: missing link ‘makecmap’
collayers.merge html
coloredmesh.from.annot html
Rd warning: coloredmesh.from.annot.Rd:30: missing link ‘tmesh3d’
coloredmesh.from.color html
Rd warning: coloredmesh.from.color.Rd:30: missing link ‘tmesh3d’
coloredmesh.from.label html
Rd warning: coloredmesh.from.label.Rd:28: missing link ‘makecmap’
Rd warning: coloredmesh.from.label.Rd:33: missing link ‘tmesh3d’
coloredmesh.from.mask html
Rd warning: coloredmesh.from.mask.Rd:30: missing link ‘makecmap’
Rd warning: coloredmesh.from.mask.Rd:33: missing link ‘tmesh3d’
coloredmesh.from.morph.native html
Rd warning: coloredmesh.from.morph.native.Rd:33: missing link ‘makecmap’
Rd warning: coloredmesh.from.morph.native.Rd:36: missing link ‘tmesh3d’
coloredmesh.from.morph.standard html
Rd warning: coloredmesh.from.morph.standard.Rd:42: missing link ‘makecmap’
Rd warning: coloredmesh.from.morph.standard.Rd:45: missing link ‘tmesh3d’
coloredmesh.from.morphdata html
Rd warning: coloredmesh.from.morphdata.Rd:27: missing link ‘makecmap’
Rd warning: coloredmesh.from.morphdata.Rd:30: missing link ‘tmesh3d’
coloredmesh.from.preloaded.data html
Rd warning: coloredmesh.from.preloaded.data.Rd:24: missing link ‘makecmap’
coloredmesh.plot.colorbar.separate html
coloredmeshes.combined.data.range html
coloredmeshes.from.color html
Rd warning: coloredmeshes.from.color.Rd:30: missing link ‘tmesh3d’
coloredmeshes.get.md html
colorlist.brain.clusters html
colors.are.grayscale html
colors.have.transparency html
combine.colorbar.with.brainview.animation
html
combine.colorbar.with.brainview.image html
combine.colorbar.with.brainview.image.vertical
html
common.makecmap.range html
Rd warning: common.makecmap.range.Rd:15: missing link ‘makecmap’
constant.pervertexdata html
cube3D.tris html
Rd warning: cube3D.tris.Rd:39: missing link ‘triangles3d’
cubes3D.tris html
deepcopylist.long html
deg2rad html
delete_all_optional_data html
demo html
demographics.to.fsgd.file html
demographics.to.qdec.table.dat html
desaturate html
download_fsaverage html
download_fsaverage3 html
download_optional_data html
download_optional_paper_data html
draw.colorbar html
Rd warning: draw.colorbar.Rd:17: missing link ‘bgplot3d’
eeg_coords html
ensure.fs.surface html
ensure.tmesh3d html
export html
export.coloredmesh.ply html
extend_neighbors html
extract.volume.3D html
face.edges html
find.freesurferhome html
find.subjectsdir.of html
flc html
force.to.range html
fs.coloredmesh html
Rd warning: fs.coloredmesh.Rd:17: missing link ‘tmesh3d’
fs.home html
fs.surface.as.adjacencylist html
fs.surface.to.igraph html
fs.surface.to.tmesh3d html
fs.surface.vertex.neighbors html
fs.value.list.from.agg.res html
fsaverage.path html
fsbrain.renderable html
fsbrain.set.default.figsize html
fslong.subjects.detect html
fslong.subjects.finished html
fup html
gen.test.volume html
geod.patches.color.overlay html
geod.patches.color.overlay.singlehemi html
geod.patches.pervertexdata html
geod.patches.pervertexdata.singlehemi html
geod.vert.neighborhood html
geodesic.average.distance html
geodesic.ballstats html
geodesic.circles html
geodesic.dists.to.vertex html
geodesic.path html
get.atlas.region.names html
get.rglstyle html
Rd warning: get.rglstyle.Rd:16: missing link ‘material3d’
Rd warning: get.rglstyle.Rd:13: missing link ‘material3d’
Rd warning: get.rglstyle.Rd:19: missing link ‘shade3d’
get.rglstyle.default html
Rd warning: get.rglstyle.default.Rd:13: missing link ‘material3d’
Rd warning: get.rglstyle.default.Rd:10: missing link ‘shade3d’
get.rglstyle.edges html
Rd warning: get.rglstyle.edges.Rd:10: missing link ‘shade3d’
get.rglstyle.glass html
Rd warning: get.rglstyle.glass.Rd:13: missing link ‘material3d’
Rd warning: get.rglstyle.glass.Rd:10: missing link ‘shade3d’
get.rglstyle.glass2 html
Rd warning: get.rglstyle.glass2.Rd:13: missing link ‘material3d’
Rd warning: get.rglstyle.glass2.Rd:10: missing link ‘shade3d’
get.rglstyle.parameters html
Rd warning: get.rglstyle.parameters.Rd:15: missing link ‘material3d’
get.rglstyle.semitransparent html
Rd warning: get.rglstyle.semitransparent.Rd:13: missing link ‘material3d’
Rd warning: get.rglstyle.semitransparent.Rd:10: missing link ‘shade3d’
get.rglstyle.shiny html
Rd warning: get.rglstyle.shiny.Rd:13: missing link ‘material3d’
Rd warning: get.rglstyle.shiny.Rd:10: missing link ‘shade3d’
get.slice.indices html
get.subject.class html
get.view.angle.names html
getIn html
get_optional_data_filepath html
group.agg.atlas.native html
group.agg.atlas.standard html
group.annot html
group.concat.measures.native html
group.concat.measures.standard html
group.data.to.array html
group.label html
group.label.from.annot html
group.morph.agg.native html
group.morph.agg.standard html
group.morph.agg.standard.vertex html
group.morph.native html
group.morph.standard html
group.morph.standard.sf html
group.multimorph.agg.native html
group.multimorph.agg.standard html
group.surface html
groupmorph.split.hemilist html
handle.rglactions.highlight.points html
hasIn html
hemi.lobe.labels html
hemilist html
hemilist.derive.hemi html
hemilist.from.prefixed.list html
hemilist.get.combined.data html
hemilist.unwrap html
hemilist.wrap html
hemlist.ensure.contains html
highlight.points.spheres html
highlight.vertices.on.subject html
Rd warning: highlight.vertices.on.subject.Rd:35: missing link ‘par3d’
highlight.vertices.on.subject.spheres html
highlight.vertices.spheres html
hull.retain.along.axis html
image.remap.color html
images.annotate html
images.dimmax html
images.rescale.to.max.canvas html
images.same.height html
images.same.width html
is.Triangles3D html
is.fs.coloredmesh html
is.fs.coloredvoxels html
is.fsbrain html
is.hemilist html
label.border html
label.border.fast html
label.colFn html
label.colFn.inv html
label.from.annotdata html
label.to.annot html
labeldata.from.mask html
limit_fun html
limit_fun_na html
limit_fun_na_inside html
list_optional_data html
magick.grid html
mask.from.labeldata.for.hemi html
mergehemi.annots html
mesh.vertex.included.faces html
mesh.vertex.neighbors html
mkco.cluster html
mkco.div html
mkco.heat html
mkco.seq html
normalize html
numverts.lh html
numverts.rh html
path.colors.from.orientation html
path.slopes html
per.hemi.vertex.indices html
perform.na.mapping html
perform.rglactions html
pervertexdata.smoothgaussian html
pervertexdata.smoothnn html
pervertexdata.smoothnn.compute.fwhm html
pervertexdata.smoothnn.compute.numiter
html
plot.fsbrain.colorbar html
pp.named.list html
principal.curvatures html
print.fs.coloredmesh html
print.fs.coloredvoxels html
print.fsbrain html
qc.for.group html
qc.from.regionwise.df html
qc.from.segstats.table html
qc.from.segstats.tables html
qc.fslong.checkidenticaldata html
qc.report.html html
qc.vis.failcount.by.region html
qdec.table.filter html
qdec.table.skeleton html
rad2deg html
ras2vox_tkr html
read.colorcsv html
read.md.demographics html
read.md.subjects html
read.md.subjects.from.fsgd html
recycle html
regions.to.ignore html
report.on.demographics html
rgl.coord.lines html
rglactions html
Rd warning: rglactions.Rd:16: missing link ‘text3d’
rglactions.has.key html
rglactions.transform html
rglo html
rglot html
rglvoxels html
Rd warning: rglvoxels.Rd:24: missing link ‘spheres3d’
Rd warning: rglvoxels.Rd:24: missing link ‘triangles3d’
Rd warning: rglvoxels.Rd:18: missing link ‘triangles3d’
rotation.matrix.for.axis.rot html
scale.to.range.zero.one html
scale01 html
shape.descriptor.names html
shape.descriptors html
shift.hemis.apart html
shift.hemis.rglactions html
sjd.demo html
sjld html
sortcoloredmeshes.by.hemi html
sph2fs html
spread.values.over.annot html
spread.values.over.hemi html
spread.values.over.subject html
subject.annot html
subject.annot.border html
subject.atlas.agg html
subject.descriptor.geodesic.average.distance
html
subject.filepath.any html
subject.filepath.morph.native html
subject.filepath.morph.standard html
subject.label html
subject.label.from.annot html
subject.lobes html
subject.mask html
subject.morph.native html
subject.morph.standard html
subject.num.verts html
subject.report.html html
subject.surface html
subject.volume html
submesh.vertex html
surf.avg.vertexradius html
surf.center.fsaverage html
surf.metric.properties html
surf.radius.fsaverage html
surf.sphere.dist html
surf.sphere.gaussianweights html
surf.sphere.spatialfilter html
surface.curvatures html
surfs.props html
symmrange html
test.numerical.meandiff html
test.numerical.meandiff.paired html
test.numerical.meandiff.unpaired html
tmesh3d.to.fs.surface html
track.length html
vdata.split.by.hemi html
vertex.coords html
vertex.hemis html
vis.color.on.subject html
Rd warning: vis.color.on.subject.Rd:33: missing link ‘par3d’
vis.coloredmesh html
vis.coloredmeshes html
Rd warning: vis.coloredmeshes.Rd:26: missing link ‘par3d’
vis.coloredmeshes.rotating html
Rd warning: vis.coloredmeshes.rotating.Rd:30: missing link ‘spin3d’
Rd warning: vis.coloredmeshes.rotating.Rd:32: missing link ‘spin3d’
Rd warning: vis.coloredmeshes.rotating.Rd:34: missing link ‘spin3d’
Rd warning: vis.coloredmeshes.rotating.Rd:36: missing link ‘spin3d’
Rd warning: vis.coloredmeshes.rotating.Rd:38: missing link ‘spin3d’
Rd warning: vis.coloredmeshes.rotating.Rd:40: missing link ‘par3d’
vis.colortable.legend html
vis.data.on.fsaverage html
Rd warning: vis.data.on.fsaverage.Rd:36: missing link ‘par3d’
Rd warning: vis.data.on.fsaverage.Rd:42: missing link ‘makecmap’
vis.data.on.group.native html
vis.data.on.group.standard html
vis.data.on.subject html
Rd warning: vis.data.on.subject.Rd:36: missing link ‘par3d’
Rd warning: vis.data.on.subject.Rd:42: missing link ‘makecmap’
vis.dti.trk html
vis.export.from.coloredmeshes html
vis.fs.surface html
Rd warning: vis.fs.surface.Rd:25: missing link ‘makecmap’
vis.group.annot html
vis.group.coloredmeshes html
vis.group.morph.native html
vis.group.morph.standard html
vis.labeldata.on.subject html
Rd warning: vis.labeldata.on.subject.Rd:35: missing link ‘par3d’
Rd warning: vis.labeldata.on.subject.Rd:41: missing link ‘makecmap’
vis.mask.on.subject html
Rd warning: vis.mask.on.subject.Rd:34: missing link ‘par3d’
Rd warning: vis.mask.on.subject.Rd:40: missing link ‘makecmap’
vis.path.along.verts html
vis.paths html
vis.paths.along.verts html
vis.region.values.on.subject html
Rd warning: vis.region.values.on.subject.Rd:41: missing link ‘par3d’
Rd warning: vis.region.values.on.subject.Rd:49: missing link ‘makecmap’
vis.renderable html
vis.rotated.coloredmeshes html
Rd warning: vis.rotated.coloredmeshes.Rd:18: missing link ‘rotate3d’
Rd warning: vis.rotated.coloredmeshes.Rd:20: missing link ‘rotate3d’
Rd warning: vis.rotated.coloredmeshes.Rd:22: missing link ‘rotate3d’
Rd warning: vis.rotated.coloredmeshes.Rd:24: missing link ‘rotate3d’
vis.seg.legend html
vis.subject.annot html
Rd warning: vis.subject.annot.Rd:33: missing link ‘par3d’
vis.subject.label html
Rd warning: vis.subject.label.Rd:36: missing link ‘par3d’
Rd warning: vis.subject.label.Rd:42: missing link ‘makecmap’
vis.subject.morph.native html
Rd warning: vis.subject.morph.native.Rd:36: missing link ‘par3d’
Rd warning: vis.subject.morph.native.Rd:46: missing link ‘makecmap’
vis.subject.morph.standard html
Rd warning: vis.subject.morph.standard.Rd:45: missing link ‘par3d’
Rd warning: vis.subject.morph.standard.Rd:53: missing link ‘makecmap’
vis.subject.pre html
Rd warning: vis.subject.pre.Rd:29: missing link ‘par3d’
Rd warning: vis.subject.pre.Rd:37: missing link ‘makecmap’
vis.symmetric.data.on.subject html
Rd warning: vis.symmetric.data.on.subject.Rd:37: missing link ‘par3d’
Rd warning: vis.symmetric.data.on.subject.Rd:43: missing link ‘makecmap’
vislayout.from.coloredmeshes html
Rd warning: vislayout.from.coloredmeshes.Rd:25: missing link ‘par3d’
Rd warning: vislayout.from.coloredmeshes.Rd:29: missing link ‘material3d’
vol.boundary.box html
vol.boundary.box.apply html
vol.boundary.mask html
vol.hull html
vol.imagestack html
vol.intensity.to.color html
vol.mask.from.segmentation html
vol.merge html
vol.overlay.colors.from.activation html
vol.overlay.colors.from.colortable html
vol.plane.axes html
vol.planes html
vol.slice html
vol.vox.from.crs html
volvis.contour html
volvis.lb html
volvis.lightbox html
volvis.voxels html
Rd warning: volvis.voxels.Rd:16: missing link ‘triangles3d’
vox2ras_tkr html
wrapped.image.append html
write.group.morph.standard html
write.group.morph.standard.mf html
write.group.morph.standard.sf html
write.group.morph.standard.singlehemi html
write.region.aggregated html
write.region.values html
write.region.values.fsaverage 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 (fsbrain)