Validation Report - amadeus@1.2.3
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 amadeus
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | FALSE |
| exported_namespace | 120 |
| has_vignettes | 7 |
| export_help | 120 |
| has_website | TRUE |
| has_maintainer | Kyle Messier kyle.messier@nih.gov |
| bugs_status | subscript out of bounds |
| size_codebase | 6566 |
| has_bug_reports_url | 1 |
| downloads_1yr | 3141 |
| reverse_dependencies | 0 |
| has_examples | 1 |
| dependencies | 20 |
| 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 | dplyr | Imports |
| 2 | sf | Imports |
| 3 | sftime | Imports |
| 4 | stats | Imports |
| 5 | terra | Imports |
| 6 | methods | Imports |
| 7 | data.table | Imports |
| 8 | httr | Imports |
| 9 | rvest | Imports |
| 10 | exactextractr | Imports |
| 11 | utils | Imports |
| 12 | stringi | Imports |
| 13 | testthat (>= 3.0.0) | Imports |
| 14 | stars | Imports |
| 15 | tidyr | Imports |
| 16 | rlang | Imports |
| 17 | nhdplusTools | Imports |
| 18 | archive | Imports |
| 19 | collapse | Imports |
| 20 | Rdpack | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 120 exported objects. 120 are documented:
apply_extent as_mysftime
TRUE TRUE
calc_check_time calc_message
TRUE TRUE
calc_prepare_locs calc_return_locs
TRUE TRUE
calc_setcolumns calc_time
TRUE TRUE
calc_worker calculate_covariates
TRUE TRUE
calculate_ecoregion calculate_geos
TRUE TRUE
calculate_gmted calculate_gridmet
TRUE TRUE
calculate_groads calculate_hms
TRUE TRUE
calculate_koppen_geiger calculate_lagged
TRUE TRUE
calculate_merra2 calculate_modis
TRUE TRUE
calculate_modis_daily calculate_narr
TRUE TRUE
calculate_nei calculate_nlcd
TRUE TRUE
calculate_population calculate_temporal_dummies
TRUE TRUE
calculate_terraclimate calculate_tri
TRUE TRUE
check_destfile check_for_null_parameters
TRUE TRUE
check_geom check_mysf
TRUE TRUE
check_mysftime check_url_status
TRUE TRUE
check_urls download_aqs
TRUE TRUE
download_cropscape download_data
TRUE TRUE
download_ecoregion download_epa_certificate
TRUE TRUE
download_geos download_gmted
TRUE TRUE
download_gridmet download_groads
TRUE TRUE
download_hash download_hms
TRUE TRUE
download_huc download_koppen_geiger
TRUE TRUE
download_merra2 download_modis
TRUE TRUE
download_narr download_nei
TRUE TRUE
download_nlcd download_permit
TRUE TRUE
download_population download_prism
TRUE TRUE
download_remove_command download_remove_zips
TRUE TRUE
download_run download_sanitize_path
TRUE TRUE
download_setup_dir download_sink
TRUE TRUE
download_terraclimate download_tri
TRUE TRUE
download_unzip dt_as_mysftime
TRUE TRUE
extract_urls generate_date_sequence
TRUE TRUE
generate_time_sequence is_date_proper
TRUE TRUE
narr_variable process_aqs
TRUE TRUE
process_blackmarble process_blackmarble_corners
TRUE TRUE
process_collection process_conformity
TRUE TRUE
process_covariates process_cropscape
TRUE TRUE
process_ecoregion process_flatten_sds
TRUE TRUE
process_geos process_gmted
TRUE TRUE
process_gmted_codes process_gridmet
TRUE TRUE
process_gridmet_codes process_groads
TRUE TRUE
process_hms process_huc
TRUE TRUE
process_koppen_geiger process_locs_radius
TRUE TRUE
process_locs_vector process_merra2
TRUE TRUE
process_merra2_time process_modis_merge
TRUE TRUE
process_modis_sds process_modis_swath
TRUE TRUE
process_modis_warp process_narr
TRUE TRUE
process_nei process_nlcd
TRUE TRUE
process_population process_prism
TRUE TRUE
process_sedac_codes process_terraclimate
TRUE TRUE
process_terraclimate_codes process_tri
TRUE TRUE
process_variable_codes read_commands
TRUE TRUE
rename_time sf_as_mysftime
TRUE TRUE
sftime_as_mysftime sftime_as_sf
TRUE TRUE
sftime_as_spatraster sftime_as_spatrds
TRUE TRUE
sftime_as_spatvector spatraster_as_sftime
TRUE TRUE
spatrds_as_sftime spatvector_as_sftime
TRUE TRUE
sum_edc test_download_functions
TRUE TRUE Examples
There are 120 help pages with examples, from 120 (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 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-14 06:50:58 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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ANDROID_NDK_LATEST_HOME
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ANT_HOME /usr/share/ant
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BOOTSTRAP_HASKELL_NONINTERACTIVE
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GITHUB_REF refs/heads/main
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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
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GITHUB_WORKFLOW_SHA d790b87bd807399b7640c7bca6ec67a96a6b839e
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
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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JOURNAL_STREAM 8:7727
LANG C.UTF-8
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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=
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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 500
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/RtmpBUYGbc
POWERSHELL_DISTRIBUTION_CHANNEL
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PROCESSX_PS726d1a60da3c_1739515856
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_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/Rtmpttadem
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_TRACKING_ID github_05609c14-ef8b-4640-9d49-0f5a08371745
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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_V3PS true
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SWIFT_PATH /usr/share/swift/usr/bin
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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
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
{
custom_handler <- getOption("cli.default_handler")
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custom_handler(msg)
}
else {
cli_server_default(msg)
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}
<bytecode: 0x55ba732fd910>
<environment: namespace:cli>
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$citation.bibtex.max
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$demo.ask
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$device
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{
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<bytecode: 0x55ba74435ea0>
<environment: namespace:knitr>
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$locatorBell
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$mailer
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$matprod
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$pdfviewer
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$printcmd
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$prompt
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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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$showNCalls
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$str
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$str$digits.d
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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: 0x55ba727d5520>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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class "file"
mode "w+b"
text "binary"
opened "opened"
can read "yes"
can write "yes"
$ts.eps
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$ts.S.compat
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$unzip
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$useFancyQuotes
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$verbose
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$warn
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$warning.length
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$warnPartialMatchAttr
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$warnPartialMatchDollar
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$width
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