Validation Report - fsbrain@0.5.5
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package fsbrain
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 220 |
| has_vignettes | 17 |
| export_help | 220 |
| has_website | TRUE |
| has_maintainer | Tim Schäfer ts+code@rcmd.org |
| bugs_status | subscript out of bounds |
| assess_size_codebase | 7656 |
| has_source_control | https://github.com/dfsp-spirit/fsbrain |
| has_bug_reports_url | 1 |
| downloads_1yr | 6525 |
| reverse_dependencies | 0 |
| has_examples | 1 |
| dependencies | 10 |
| license | MIT + file LICENSE |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | reshape | Imports |
| 2 | freesurferformats (>= 0.1.17) | Imports |
| 3 | pkgfilecache (>= 0.1.1) | Imports |
| 4 | rgl | Imports |
| 5 | squash | Imports |
| 6 | fields | Imports |
| 7 | viridis | Imports |
| 8 | data.table | Imports |
| 9 | magick | Imports |
| 10 | methods | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 220 exported objects. 220 are documented:
alphablend
TRUE
annot.outline
TRUE
annot.outline.border.vertices
TRUE
apply.label.to.morphdata
TRUE
apply.labeldata.to.morphdata
TRUE
apply.transform
TRUE
arrange.brainview.images
TRUE
arrange.brainview.images.grid
TRUE
brainviews
TRUE
clip_fun
TRUE
clip.data
TRUE
cm.cbry
TRUE
cm.div
TRUE
cm.heat
TRUE
cm.qual
TRUE
cm.seq
TRUE
collayer.bg
TRUE
collayer.bg.atlas
TRUE
collayer.bg.meancurv
TRUE
collayer.bg.sulc
TRUE
collayer.from.annot
TRUE
collayer.from.annotdata
TRUE
collayer.from.mask.data
TRUE
collayer.from.morphlike.data
TRUE
collayers.merge
TRUE
coloredmesh.from.annot
TRUE
coloredmesh.from.label
TRUE
coloredmesh.from.mask
TRUE
coloredmesh.from.morph.native
TRUE
coloredmesh.from.morph.standard
TRUE
coloredmesh.from.morphdata
TRUE
coloredmesh.from.preloaded.data
TRUE
coloredmesh.plot.colorbar.separate
TRUE
coloredmeshes.from.color
TRUE
colorlist.brain.clusters
TRUE
colors.are.grayscale
TRUE
colors.have.transparency
TRUE
combine.colorbar.with.brainview.animation
TRUE
combine.colorbar.with.brainview.image
TRUE
constant.pervertexdata
TRUE
cube3D.tris
TRUE
cubes3D.tris
TRUE
delete_all_optional_data
TRUE
demographics.to.fsgd.file
TRUE
demographics.to.qdec.table.dat
TRUE
desaturate
TRUE
download_fsaverage
TRUE
download_fsaverage3
TRUE
download_optional_data
TRUE
download_optional_paper_data
TRUE
export
TRUE
export.coloredmesh.ply
TRUE
face.edges
TRUE
find.freesurferhome
TRUE
find.subjectsdir.of
TRUE
fs.coloredmesh
TRUE
fs.home
TRUE
fs.surface.as.adjacencylist
TRUE
fs.surface.to.igraph
TRUE
fs.surface.to.tmesh3d
TRUE
fs.surface.vertex.neighbors
TRUE
fsaverage.path
TRUE
fsbrain.set.default.figsize
TRUE
fup
TRUE
gen.test.volume
TRUE
geod.patches.color.overlay
TRUE
geod.vert.neighborhood
TRUE
geodesic.dists.to.vertex
TRUE
geodesic.path
TRUE
get_optional_data_filepath
TRUE
get.atlas.region.names
TRUE
get.rglstyle
TRUE
get.view.angle.names
TRUE
getIn
TRUE
group.agg.atlas.native
TRUE
group.agg.atlas.standard
TRUE
group.annot
TRUE
group.concat.measures.native
TRUE
group.concat.measures.standard
TRUE
group.label
TRUE
group.label.from.annot
TRUE
group.morph.agg.native
TRUE
group.morph.agg.standard
TRUE
group.morph.agg.standard.vertex
TRUE
group.morph.native
TRUE
group.morph.standard
TRUE
group.morph.standard.sf
TRUE
group.multimorph.agg.native
TRUE
group.multimorph.agg.standard
TRUE
group.surface
TRUE
groupmorph.split.hemilist
TRUE
hasIn
TRUE
hemilist
TRUE
hemilist.derive.hemi
TRUE
hemilist.from.prefixed.list
TRUE
hemilist.get.combined.data
TRUE
hemilist.unwrap
TRUE
hemilist.wrap
TRUE
highlight.points.spheres
TRUE
highlight.vertices.on.subject
TRUE
highlight.vertices.on.subject.spheres
TRUE
highlight.vertices.spheres
TRUE
is.fs.coloredmesh
TRUE
is.fs.coloredvoxels
TRUE
is.fsbrain
TRUE
is.hemilist
TRUE
label.border
TRUE
label.colFn
TRUE
label.colFn.inv
TRUE
label.from.annotdata
TRUE
label.to.annot
TRUE
labeldata.from.mask
TRUE
limit_fun
TRUE
limit_fun_na
TRUE
limit_fun_na_inside
TRUE
list_optional_data
TRUE
mask.from.labeldata.for.hemi
TRUE
mesh.vertex.neighbors
TRUE
mkco.cluster
TRUE
mkco.div
TRUE
mkco.heat
TRUE
mkco.seq
TRUE
numverts.lh
TRUE
numverts.rh
TRUE
principal.curvatures
TRUE
qc.for.group
TRUE
qc.from.regionwise.df
TRUE
qc.from.segstats.tables
TRUE
qc.vis.failcount.by.region
TRUE
qdec.table.skeleton
TRUE
ras2vox_tkr
TRUE
read.colorcsv
TRUE
read.md.demographics
TRUE
read.md.subjects
TRUE
read.md.subjects.from.fsgd
TRUE
regions.to.ignore
TRUE
report.on.demographics
TRUE
rglactions
TRUE
rglo
TRUE
rglot
TRUE
rglvoxels
TRUE
scale01
TRUE
shape.descriptor.names
TRUE
shape.descriptors
TRUE
shift.hemis.apart
TRUE
sjd.demo
TRUE
sjld
TRUE
spread.values.over.annot
TRUE
spread.values.over.hemi
TRUE
spread.values.over.subject
TRUE
subject.annot
TRUE
subject.atlas.agg
TRUE
subject.filepath.morph.native
TRUE
subject.filepath.morph.standard
TRUE
subject.label
TRUE
subject.label.from.annot
TRUE
subject.lobes
TRUE
subject.mask
TRUE
subject.morph.native
TRUE
subject.morph.standard
TRUE
subject.num.verts
TRUE
subject.surface
TRUE
subject.volume
TRUE
surface.curvatures
TRUE
tmesh3d.to.fs.surface
TRUE
vdata.split.by.hemi
TRUE
vertex.coords
TRUE
vertex.hemis
TRUE
vis.color.on.subject
TRUE
vis.coloredmeshes
TRUE
vis.coloredmeshes.rotating
TRUE
vis.colortable.legend
TRUE
vis.data.on.fsaverage
TRUE
vis.data.on.group.native
TRUE
vis.data.on.group.standard
TRUE
vis.data.on.subject
TRUE
vis.dti.trk
TRUE
vis.export.from.coloredmeshes
TRUE
vis.fs.surface
TRUE
vis.group.annot
TRUE
vis.group.coloredmeshes
TRUE
vis.group.morph.native
TRUE
vis.group.morph.standard
TRUE
vis.labeldata.on.subject
TRUE
vis.mask.on.subject
TRUE
vis.path.along.verts
TRUE
vis.paths
TRUE
vis.paths.along.verts
TRUE
vis.region.values.on.subject
TRUE
vis.seg.legend
TRUE
vis.subject.annot
TRUE
vis.subject.label
TRUE
vis.subject.morph.native
TRUE
vis.subject.morph.standard
TRUE
vis.subject.pre
TRUE
vis.symmetric.data.on.subject
TRUE
vislayout.from.coloredmeshes
TRUE
vol.boundary.box
TRUE
vol.boundary.box.apply
TRUE
vol.hull
TRUE
vol.imagestack
TRUE
vol.intensity.to.color
TRUE
vol.mask.from.segmentation
TRUE
vol.merge
TRUE
vol.overlay.colors.from.activation
TRUE
vol.overlay.colors.from.colortable
TRUE
vol.planes
TRUE
vol.slice
TRUE
vol.vox.from.crs
TRUE
volvis.contour
TRUE
volvis.lb
TRUE
volvis.lightbox
TRUE
volvis.voxels
TRUE
vox2ras_tkr
TRUE
write.group.morph.standard
TRUE
write.group.morph.standard.mf
TRUE
write.group.morph.standard.sf
TRUE
write.region.aggregated
TRUE
write.region.values
TRUE
write.region.values.fsaverage
TRUE Examples
There are 336 help pages with examples, from 336 (100.00 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.2 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-03-17 03:30:34 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.3 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.50 jsonlite_1.9.1
[10] xfun_0.51 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
_R_CHECK_SYSTEM_CLOCK_
FALSE
ACCEPT_EULA Y
ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE
/opt/actionarchivecache
AGENT_TOOLSDIRECTORY /opt/hostedtoolcache
ANDROID_HOME /usr/local/lib/android/sdk
ANDROID_NDK /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_HOME /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_LATEST_HOME
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ANDROID_NDK_ROOT /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_SDK_ROOT /usr/local/lib/android/sdk
ANT_HOME /usr/share/ant
AZURE_EXTENSION_DIR /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
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BUNDLE_EXT linux-amd64.deb
CHROME_BIN /usr/bin/google-chrome
CHROMEWEBDRIVER /usr/local/share/chromedriver-linux64
CI true
CONDA /usr/share/miniconda
DEBIAN_FRONTEND noninteractive
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DENO_TLS_CA_STORE system,mozilla
DEPLOYMENT_BASEPATH /opt/runner
DOTNET_MULTILEVEL_LOOKUP
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EDITOR vi
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GHCUP_INSTALL_BASE_PREFIX
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GITHUB_ACTION __run_2
GITHUB_ACTION_REF
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GITHUB_ACTOR_ID 185338939
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GITHUB_EVENT_NAME schedule
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GITHUB_HEAD_REF
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GITHUB_REF refs/heads/main
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GITHUB_REPOSITORY_OWNER_ID
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GITHUB_RETENTION_DAYS 90
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GITHUB_RUN_NUMBER 137
GITHUB_SERVER_URL https://github.com
GITHUB_SHA 4202376d670fac0a022e165ebfa1ebb3b5c6ee5f
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_35de53e0-bba8-48db-994a-b6d141992fd4
GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA 4202376d670fac0a022e165ebfa1ebb3b5c6ee5f
GITHUB_WORKSPACE /home/runner/work/pharmapkgs/pharmapkgs
GOROOT_1_21_X64 /opt/hostedtoolcache/go/1.21.13/x64
GOROOT_1_22_X64 /opt/hostedtoolcache/go/1.22.12/x64
GOROOT_1_23_X64 /opt/hostedtoolcache/go/1.23.7/x64
GRADLE_HOME /usr/share/gradle-8.13
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
3650
HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
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INVOCATION_ID 8c2fa24f222040819c358512a4892c23
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_11_X64 /usr/lib/jvm/temurin-11-jdk-amd64
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JOURNAL_STREAM 8:6807
LANG C.UTF-8
LD_LIBRARY_PATH /opt/R/4.4.3/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.3/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server
LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
MEMORY_PRESSURE_WATCH /sys/fs/cgroup/system.slice/runner-provisioner.service/memory.pressure
MEMORY_PRESSURE_WRITE c29tZSAyMDAwMDAgMjAwMDAwMAA=
NOT_CRAN true
NVM_DIR /home/runner/.nvm
PAGER /usr/bin/pager
PATH /snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 100
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
https://cloud.r-project.org/
PIPX_BIN_DIR /opt/pipx_bin
PIPX_HOME /opt/pipx
PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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PROCESSX_PS1dd9669d82c8_1742182230
YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_BIN_PATH /opt/quarto/bin
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
QUARTO_PROJECT_DIR /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_PROJECT_ROOT /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_ROOT /
QUARTO_SHARE_PATH /opt/quarto/share
R_ARCH
R_BROWSER xdg-open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /opt/R/4.4.3/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /opt/R/4.4.3/lib/R
R_INCLUDE_DIR /opt/R/4.4.3/lib/R/include
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R_PAPERSIZE letter
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R_PDFVIEWER /usr/bin/xdg-open
R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,inconsolata,hyper
R_SESSION_TMPDIR /tmp/RtmpbaHkPe
R_SHARE_DIR /opt/R/4.4.3/lib/R/share
R_STRIP_SHARED_LIB strip --strip-unneeded
R_STRIP_STATIC_LIB strip --strip-debug
R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
RUNNER_NAME GitHub-Actions-1000000515
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_7dcadf91-7a7c-4938-bcc4-8aedfcb81488
RUNNER_USER runner
RUNNER_WORKSPACE /home/runner/work/pharmapkgs
SED /usr/bin/sed
SELENIUM_JAR_PATH /usr/share/java/selenium-server.jar
SGX_AESM_ADDR 1
SHLVL 1
STATS_D true
STATS_D_D true
STATS_D_TC true
STATS_EXT true
STATS_EXTP https://provjobdprod.z13.web.core.windows.net/settings/provjobdsettings-latest/provjobd.data
STATS_PIP false
STATS_RDCL true
STATS_TRP true
STATS_UE true
STATS_V3PS true
STATS_VMD true
STATS_VMFE true
SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 832
TAR /usr/bin/tar
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
/usr/local/share/vcpkg
XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
[1] TRUE
$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
{
custom_handler <- getOption("cli.default_handler")
if (is.function(custom_handler)) {
custom_handler(msg)
}
else {
cli_server_default(msg)
}
}
<bytecode: 0x55e2739e0330>
<environment: namespace:cli>
$catch.script.errors
[1] FALSE
$CBoundsCheck
[1] FALSE
$check.bounds
[1] FALSE
$citation.bibtex.max
[1] 1
$continue
[1] "+ "
$contrasts
unordered ordered
"contr.treatment" "contr.poly"
$covr.record_tests
[1] TRUE
$defaultPackages
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
$demo.ask
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$deparse.cutoff
[1] 60
$device
function (width = 7, height = 7, ...)
{
grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x55e27307f988>
<environment: namespace:knitr>
$device.ask.default
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$digits
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$dvipscmd
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$echo
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$editor
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$encoding
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$example.ask
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$expressions
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$help.search.types
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$help.try.all.packages
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$htmltools.preserve.raw
[1] TRUE
$HTTPUserAgent
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[1] 2
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[1] TRUE
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[1] FALSE
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[1] FALSE
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[1] FALSE
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[1] TRUE
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[1] TRUE
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[1] "mailto"
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[1] "default"
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[1] 25000
$max.print
[1] 99999
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[1] TRUE
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[1] 1
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[1] 50
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CRAN
"https://cran.rstudio.com"
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<environment: R_GlobalEnv>
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function (x, ...)
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<environment: 0x55e272ebb688>
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mode "w+b"
text "binary"
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can write "yes"
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