Validation Report - amt@0.2.2.0
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 amt
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 156 |
| has_vignettes | 12 |
| export_help | 156 |
| has_website | TRUE |
| has_maintainer | Johannes Signer jsigner@gwdg.de |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| size_codebase | 4169 |
| has_source_control | https://github.com/jmsigner/amt |
| has_bug_reports_url | 0 |
| downloads_1yr | 15307 |
| reverse_dependencies | 1 |
| has_examples | 0.9906542 |
| dependencies | 24 |
| license | GPL-3 |
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 | checkmate | Imports |
| 2 | circular | Imports |
| 3 | ctmm | Imports |
| 4 | data.table | Imports |
| 5 | dplyr (>= 0.7.0) | Imports |
| 6 | fitdistrplus | Imports |
| 7 | FNN | Imports |
| 8 | graphics | Imports |
| 9 | grDevices | Imports |
| 10 | KernSmooth | Imports |
| 11 | lubridate | Imports |
| 12 | MASS | Imports |
| 13 | methods | Imports |
| 14 | purrr | Imports |
| 15 | Rdpack | Imports |
| 16 | rlang | Imports |
| 17 | sf | Imports |
| 18 | sfheaders | Imports |
| 19 | stats | Imports |
| 20 | survival | Imports |
| 21 | terra | Imports |
| 22 | tibble | Imports |
| 23 | tidyr (>= 1.0.0) | Imports |
| 24 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 1 reverse dependencies:
move
Namespace
Overall the package has 156 exported objects. 156 are documented:
add_nsd arrange
TRUE TRUE
as_degree as_ltraj
TRUE TRUE
as_moveHMM as_rad
TRUE TRUE
as_sf as_sf_lines
TRUE TRUE
as_sf_points as_sp
TRUE TRUE
as_telemetry as_track
TRUE TRUE
available_distr bbox
TRUE TRUE
calculate_sdr centroid
TRUE TRUE
clogit conf_envelope
TRUE TRUE
coords cum_dist
TRUE TRUE
days diff_x
TRUE TRUE
diff_y direction_abs
TRUE TRUE
direction_rel distinct
TRUE TRUE
extent_both extent_max
TRUE TRUE
extent_x extent_y
TRUE TRUE
extract_covariates extract_covariates_along
TRUE TRUE
extract_covariates_var_time filter
TRUE TRUE
filter_min_n_burst fit_clogit
TRUE TRUE
fit_ctmm fit_distr
TRUE TRUE
fit_issf fit_logit
TRUE TRUE
fit_rsf fit_ssf
TRUE TRUE
flag_defunct_clusters flag_duplicates
TRUE TRUE
flag_fast_steps flag_roundtrips
TRUE TRUE
from from_to
TRUE TRUE
get_amt_fisher_covars get_crs
TRUE TRUE
get_displacement get_max_dist
TRUE TRUE
get_sh_forest group_by
TRUE TRUE
has_crs hours
TRUE TRUE
hr_akde hr_area
TRUE TRUE
hr_cud hr_isopleths
TRUE TRUE
hr_kde hr_kde_lscv
TRUE TRUE
hr_kde_pi hr_kde_ref
TRUE TRUE
hr_kde_ref_scaled hr_locoh
TRUE TRUE
hr_mcp hr_od
TRUE TRUE
hr_overlap hr_overlap_feature
TRUE TRUE
hr_to_sf hr_ud
TRUE TRUE
inspect intensity_use
TRUE TRUE
log_rss make_distribution
TRUE TRUE
make_exp_distr make_gamma_distr
TRUE TRUE
make_hnorm_distr make_issf_model
TRUE TRUE
make_lnorm_distr make_start
TRUE TRUE
make_track make_trast
TRUE TRUE
make_unif_distr make_vonmises_distr
TRUE TRUE
map map_int
TRUE TRUE
minutes mk_track
TRUE TRUE
msd mutate
TRUE TRUE
NA_crs_ nest
TRUE TRUE
nsd od
TRUE TRUE
plot_sl prep_uhc
TRUE TRUE
pull random_numbers
TRUE TRUE
random_points random_steps
TRUE TRUE
random_steps_simple range_both
TRUE TRUE
range_x range_y
TRUE TRUE
redistribution_kernel remove_capture_effect
TRUE TRUE
remove_incomplete_strata rolling_od
TRUE TRUE
sampling_period sdr
TRUE TRUE
seconds select
TRUE TRUE
simulate_path sinuosity
TRUE TRUE
site_fidelity sl_distr
TRUE TRUE
sl_distr_name sl_distr_params
TRUE TRUE
speed ssf_formula
TRUE TRUE
step_lengths steps
TRUE TRUE
steps_by_burst straightness
TRUE TRUE
strata summarise
TRUE TRUE
summarize summarize_sampling_rate
TRUE TRUE
summarize_sampling_rate_many summarize_sl
TRUE TRUE
summarize_speed Surv
TRUE TRUE
ta_distr ta_distr_name
TRUE TRUE
ta_distr_params tac
TRUE TRUE
tibble time_of_day
TRUE TRUE
to tot_dist
TRUE TRUE
track track_resample
TRUE TRUE
tracked_from_to transform_coords
TRUE TRUE
ungroup unnest
TRUE TRUE
update_exp update_gamma
TRUE TRUE
update_hnorm update_lnorm
TRUE TRUE
update_sl_distr update_ta_distr
TRUE TRUE
update_vonmises weeks
TRUE TRUE Examples
There are 106 help pages with examples, from 107 (99.07 %).
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 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-14 06:53:15 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 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_4.4.2 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_1.8.9
[10] xfun_0.50 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
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ANDROID_NDK_LATEST_HOME
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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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CI true
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GITHUB_REF refs/heads/main
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GITHUB_RUN_NUMBER 86
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_f6c8d8cb-0607-4376-9ed1-89a505373e7d
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 d790b87bd807399b7640c7bca6ec67a96a6b839e
GITHUB_WORKSPACE /home/runner/work/pharmapkgs/pharmapkgs
GOROOT_1_21_X64 /opt/hostedtoolcache/go/1.21.13/x64
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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
3650
HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
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INVOCATION_ID 173b090202a445c984b291dd28076462
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
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LANG C.UTF-8
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LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
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NVM_DIR /home/runner/.nvm
PAGER /usr/bin/pager
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 500
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
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PIPX_HOME /opt/pipx
PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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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
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R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /opt/R/4.4.2/lib/R/doc
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R_PAPERSIZE letter
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,inconsolata,hyper
R_SESSION_TMPDIR /tmp/RtmpbJV7Qs
R_SHARE_DIR /opt/R/4.4.2/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
RUNNER_NAME GitHub Actions 13
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RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
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RUNNER_TRACKING_ID github_05609c14-ef8b-4640-9d49-0f5a08371745
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
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STATS_EXTP https://provjobdprod.z13.web.core.windows.net/settings/provjobdsettings-latest/provjobd.data
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STATS_VMFE true
SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 831
TAR /usr/bin/tar
TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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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
[1] "xdg-open"
$browserNLdisabled
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$callr.condition_handler_cli_message
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else {
cli_server_default(msg)
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<bytecode: 0x56115b803910>
<environment: namespace:cli>
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$demo.ask
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<bytecode: 0x56115c93bea0>
<environment: namespace:knitr>
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$locatorBell
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$matprod
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$pdfviewer
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$printcmd
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$repos
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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
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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: 0x56115acdb520>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$try.outFile
A connection with
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mode "w+b"
text "binary"
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can read "yes"
can write "yes"
$ts.eps
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$unzip
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$warning.length
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$width
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