Validation Report - fmesher@0.2.0
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 fmesher
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 159 |
| has_vignettes | 9 |
| export_help | 159 |
| has_website | TRUE |
| has_maintainer | Finn Lindgren finn.lindgren@gmail.com |
| bugs_status | subscript out of bounds |
| assess_size_codebase | 10045 |
| has_source_control | https://github.com/inlabru-org/fmesher |
| has_bug_reports_url | 1 |
| downloads_1yr | 54286 |
| reverse_dependencies | 14 |
| has_examples | 1 |
| dependencies | 14 |
| license | MPL-2.0 |
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 | methods | Depends |
| 2 | dplyr | Imports |
| 3 | graphics | Imports |
| 4 | grDevices | Imports |
| 5 | lifecycle | Imports |
| 6 | Matrix | Imports |
| 7 | rlang | Imports |
| 8 | sf | Imports |
| 9 | stats | Imports |
| 10 | tibble | Imports |
| 11 | utils | Imports |
| 12 | withr | Imports |
| 13 | Rcpp | Imports |
| 14 | Rcpp | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 14 reverse dependencies:
clustTMB, disaggregation, excursions, FRK, GeoAdjust, inlabru, INLAspacetime, intSDM, MetricGraph, PointedSDMs, rSPDE, sdmTMB, stelfi, SUMMER
Namespace
Overall the package has 159 exported objects. 159 are documented:
fm_as_bbox fm_as_dgCMatrix
TRUE TRUE
fm_as_dgTMatrix fm_as_fm
TRUE TRUE
fm_as_fmesher_sparse fm_as_inla_mesh
TRUE TRUE
fm_as_inla_mesh_segment fm_as_lattice_2d
TRUE TRUE
fm_as_lattice_2d_list fm_as_list
TRUE TRUE
fm_as_mesh_1d fm_as_mesh_1d_list
TRUE TRUE
fm_as_mesh_2d fm_as_mesh_2d_list
TRUE TRUE
fm_as_segm fm_as_segm_list
TRUE TRUE
fm_as_sfc fm_as_sp_crs
TRUE TRUE
fm_as_tensor fm_as_tensor_list
TRUE TRUE
fm_as_unpackedMatrix fm_bary
TRUE TRUE
fm_basis fm_basis_mesh_1d
TRUE TRUE
fm_basis_mesh_2d fm_bbox
TRUE TRUE
fm_block fm_block_eval
TRUE TRUE
fm_block_log_shift fm_block_log_weights
TRUE TRUE
fm_block_logsumexp_eval fm_block_prep
TRUE TRUE
fm_block_weights fm_call_stack
TRUE TRUE
fm_caller_name fm_centroids
TRUE TRUE
fm_contains fm_covariance
TRUE TRUE
fm_cprod fm_crs
TRUE TRUE
fm_CRS fm_CRS_as_list
TRUE TRUE
fm_crs_bounds fm_crs_detect_manifold
TRUE TRUE
fm_crs_get_ellipsoid_radius fm_crs_get_lengthunit
TRUE TRUE
fm_crs_get_wkt fm_crs_graticule
TRUE TRUE
fm_crs_is_geocent fm_crs_is_identical
TRUE TRUE
fm_crs_is_null fm_crs_oblique
TRUE TRUE
fm_crs_oblique<- fm_crs_plot
TRUE TRUE
fm_crs_projection_type fm_crs_set_ellipsoid_radius
TRUE TRUE
fm_crs_set_lengthunit fm_crs_tissot
TRUE TRUE
fm_crs<- fm_CRSargs
TRUE TRUE
fm_CRSargs_as_list fm_delaunay_2d
TRUE TRUE
fm_detect_manifold fm_diameter
TRUE TRUE
fm_dof fm_ellipsoid_radius
TRUE TRUE
fm_ellipsoid_radius<- fm_evaluate
TRUE TRUE
fm_evaluator fm_evaluator_lattice
TRUE TRUE
fm_evaluator_mesh_1d fm_evaluator_mesh_2d
TRUE TRUE
fm_extensions fm_fem
TRUE TRUE
fm_generate_colors fm_has_PROJ6
TRUE TRUE
fm_identical_CRS fm_int
TRUE TRUE
fm_int_mesh_2d fm_int_mesh_2d_core
TRUE TRUE
fm_int_multi_sampler fm_is_bnd
TRUE TRUE
fm_is_bnd<- fm_is_within
TRUE TRUE
fm_lattice_2d fm_length_unit
TRUE TRUE
fm_length_unit<- fm_list
TRUE TRUE
fm_list_as_CRS fm_manifold
TRUE TRUE
fm_manifold_dim fm_manifold_get
TRUE TRUE
fm_manifold_type fm_matern_precision
TRUE TRUE
fm_matern_sample fm_mesh_1d
TRUE TRUE
fm_mesh_2d fm_mesh_2d_inla
TRUE TRUE
fm_mesh_2d_map fm_mesh_2d_map_lim
TRUE TRUE
fm_mesh_intersection fm_nonconvex_hull
TRUE TRUE
fm_nonconvex_hull_inla fm_nonconvex_hull_inla_basic
TRUE TRUE
fm_pixels fm_proj4string
TRUE TRUE
fm_raw_basis fm_rcdt_2d
TRUE TRUE
fm_rcdt_2d_inla fm_refine
TRUE TRUE
fm_row_kron fm_safe_sp
TRUE TRUE
fm_sample fm_segm
TRUE TRUE
fm_segm_contour_helper fm_segm_join
TRUE TRUE
fm_segm_split fm_simplify
TRUE TRUE
fm_simplify_helper fm_sp_get_crs
TRUE TRUE
fm_sp2segment fm_split_lines
TRUE TRUE
fm_spTransform fm_store_points
TRUE TRUE
fm_subdivide fm_tensor
TRUE TRUE
fm_transform fm_try_callstack
TRUE TRUE
fm_unify_coords fm_vertex_projection
TRUE TRUE
fm_vertices fm_wkt
TRUE TRUE
fm_wkt_as_wkt_tree fm_wkt_get_ellipsoid_radius
TRUE TRUE
fm_wkt_get_lengthunit fm_wkt_is_geocent
TRUE TRUE
fm_wkt_predef fm_wkt_projection_type
TRUE TRUE
fm_wkt_set_ellipsoid_radius fm_wkt_set_lengthunit
TRUE TRUE
fm_wkt_tree_as_wkt fm_wkt_tree_get_item
TRUE TRUE
fm_wkt_tree_projection_type fm_wkt_tree_set_item
TRUE TRUE
fm_wkt_unit_params fmesher_bary
TRUE TRUE
fmesher_fem fmesher_globe_points
TRUE TRUE
fmesher_rcdt fmesher_spherical_bsplines
TRUE TRUE
fmesher_spherical_bsplines1 fmesher_split_lines
TRUE TRUE
fmexample_sp geom_fm
TRUE TRUE
lines_rgl local_fm_testthat_assign
TRUE TRUE
local_fm_testthat_setup local_fm_testthat_tolerances
TRUE TRUE
plot_rgl
TRUE Examples
There are 87 help pages with examples, from 87 (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 | 2025-03-04 08:54:30 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_1.49 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
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AGENT_TOOLSDIRECTORY /opt/hostedtoolcache
ANDROID_HOME /usr/local/lib/android/sdk
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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
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DOTNET_MULTILEVEL_LOOKUP
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GITHUB_REF refs/heads/main
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GITHUB_REPOSITORY pharmaR/pharmapkgs
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pharmaR
GITHUB_REPOSITORY_OWNER_ID
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GITHUB_RETENTION_DAYS 90
GITHUB_RUN_ATTEMPT 1
GITHUB_RUN_ID 13649644829
GITHUB_RUN_NUMBER 118
GITHUB_SERVER_URL https://github.com
GITHUB_SHA d3359ac25a60bcac49a77a07b16d4e687b366326
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_a1954713-960c-4e60-8a2b-a1e14aaae52f
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_a1954713-960c-4e60-8a2b-a1e14aaae52f
GITHUB_TRIGGERING_ACTOR
Gotfrid
GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA d3359ac25a60bcac49a77a07b16d4e687b366326
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/1.23.6/x64
GRADLE_HOME /usr/share/gradle-8.12.1
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
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JOURNAL_STREAM 8:5788
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
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MEMORY_PRESSURE_WRITE c29tZSAyMDAwMDAgMjAwMDAwMAA=
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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
/tmp/RtmpnntivO
POWERSHELL_DISTRIBUTION_CHANNEL
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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
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R_DOC_DIR /opt/R/4.4.3/lib/R/doc
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,inconsolata,hyper
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R_SHARE_DIR /opt/R/4.4.3/lib/R/share
R_STRIP_SHARED_LIB strip --strip-unneeded
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R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
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RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_78b26d6b-ef3a-47c2-8e5a-cdedc96cd338
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RUNNER_WORKSPACE /home/runner/work/pharmapkgs
SED /usr/bin/sed
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SGX_AESM_ADDR 1
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STATS_EXTP https://provjobdprod.z13.web.core.windows.net/settings/provjobdsettings-latest/provjobd.data
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SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 838
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:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
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$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
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else {
cli_server_default(msg)
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<bytecode: 0x562f920f0330>
<environment: namespace:cli>
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$continue
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unordered ordered
"contr.treatment" "contr.poly"
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$demo.ask
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<bytecode: 0x562f916beff0>
<environment: namespace:knitr>
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$matprod
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$na.action
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$repos
CRAN
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$rl_word_breaks
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$rlang_trace_top_env
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$scipen
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$show.coef.Pvalues
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$show.error.messages
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$show.signif.stars
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$showErrorCalls
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$str$vec.len
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$str$list.len
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$str$deparse.lines
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$str$drop.deparse.attr
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$str$formatNum
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<environment: 0x562f915cb688>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
description ""
class "file"
mode "w+b"
text "binary"
opened "opened"
can read "yes"
can write "yes"
$ts.eps
[1] 1e-05
$ts.S.compat
[1] FALSE
$unzip
[1] "/usr/bin/unzip"
$useFancyQuotes
[1] FALSE
$verbose
[1] FALSE
$warn
[1] 0
$warning.length
[1] 1000
$warnPartialMatchArgs
[1] FALSE
$warnPartialMatchAttr
[1] FALSE
$warnPartialMatchDollar
[1] FALSE
$width
[1] 80