Validation Report - EDIutils@1.0.3
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 EDIutils
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 72 |
| has_vignettes | 12 |
| export_help | 72 |
| has_website | TRUE |
| has_maintainer | Colin Smith colin.smith@wisc.edu |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/ropensci/EDIutils |
| has_bug_reports_url | 1 |
| downloads_1yr | 3381 |
| reverse_dependencies | 0 |
| has_examples | 1 |
| dependencies | 4 |
| 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 | curl | Imports |
| 2 | httr | Imports |
| 3 | jsonlite | Imports |
| 4 | xml2 | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 72 exported objects. 72 are documented:
check_status_create
TRUE
check_status_evaluate
TRUE
check_status_update
TRUE
create_data_package
TRUE
create_data_package_archive
TRUE
create_dn
TRUE
create_event_subscription
TRUE
create_journal_citation
TRUE
create_reservation
TRUE
delete_event_subscription
TRUE
delete_journal_citation
TRUE
delete_reservation
TRUE
evaluate_data_package
TRUE
execute_event_subscription
TRUE
get_audit_count
TRUE
get_audit_record
TRUE
get_audit_report
TRUE
get_docid_reads
TRUE
get_event_subscription
TRUE
get_event_subscription_schema
TRUE
get_journal_citation
TRUE
get_packageid_reads
TRUE
get_provenance_metadata
TRUE
get_recent_uploads
TRUE
is_authorized
TRUE
list_active_reservations
TRUE
list_data_descendants
TRUE
list_data_entities
TRUE
list_data_package_citations
TRUE
list_data_package_identifiers
TRUE
list_data_package_revisions
TRUE
list_data_package_scopes
TRUE
list_data_sources
TRUE
list_deleted_data_packages
TRUE
list_principal_owner_citations
TRUE
list_recent_changes
TRUE
list_recent_uploads
TRUE
list_reservation_identifiers
TRUE
list_service_methods
TRUE
list_user_data_packages
TRUE
list_working_on
TRUE
login
TRUE
logout
TRUE
query_event_subscriptions
TRUE
read_data_entity
TRUE
read_data_entity_checksum
TRUE
read_data_entity_name
TRUE
read_data_entity_names
TRUE
read_data_entity_resource_metadata
TRUE
read_data_entity_size
TRUE
read_data_entity_sizes
TRUE
read_data_package
TRUE
read_data_package_archive
TRUE
read_data_package_citation
TRUE
read_data_package_doi
TRUE
read_data_package_error
TRUE
read_data_package_from_doi
TRUE
read_data_package_report
TRUE
read_data_package_report_checksum
TRUE
read_data_package_report_resource_metadata
TRUE
read_data_package_report_summary
TRUE
read_data_package_resource_metadata
TRUE
read_evaluate_report
TRUE
read_evaluate_report_summary
TRUE
read_metadata
TRUE
read_metadata_checksum
TRUE
read_metadata_dublin_core
TRUE
read_metadata_entity
TRUE
read_metadata_format
TRUE
read_metadata_resource_metadata
TRUE
search_data_packages
TRUE
update_data_package
TRUE Examples
There are 72 help pages with examples, from 72 (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 | 2025-02-19 03:42:20 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
/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
/usr/local/lib/android/sdk/ndk/27.2.12479018
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
1
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
DENO_DOM_PLUGIN /opt/quarto/bin/tools/x86_64/deno_dom/libplugin.so
DENO_NO_UPDATE_CHECK 1
DENO_TLS_CA_STORE system,mozilla
DEPLOYMENT_BASEPATH /opt/runner
DOTNET_MULTILEVEL_LOOKUP
0
DOTNET_NOLOGO 1
DOTNET_SKIP_FIRST_TIME_EXPERIENCE
1
EDGEWEBDRIVER /usr/local/share/edge_driver
EDITOR vi
GECKOWEBDRIVER /usr/local/share/gecko_driver
GHCUP_INSTALL_BASE_PREFIX
/usr/local
GITHUB_ACTION __run
GITHUB_ACTION_REF
GITHUB_ACTION_REPOSITORY
GITHUB_ACTIONS true
GITHUB_ACTOR llrs-roche
GITHUB_ACTOR_ID 185338939
GITHUB_API_URL https://api.github.com
GITHUB_BASE_REF
GITHUB_ENV /home/runner/work/_temp/_runner_file_commands/set_env_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_EVENT_NAME schedule
GITHUB_EVENT_PATH /home/runner/work/_temp/_github_workflow/event.json
GITHUB_GRAPHQL_URL https://api.github.com/graphql
GITHUB_HEAD_REF
GITHUB_JOB main
GITHUB_OUTPUT /home/runner/work/_temp/_runner_file_commands/set_output_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_REF refs/heads/main
GITHUB_REF_NAME main
GITHUB_REF_PROTECTED false
GITHUB_REF_TYPE branch
GITHUB_REPOSITORY pharmaR/pharmapkgs
GITHUB_REPOSITORY_ID 798326913
GITHUB_REPOSITORY_OWNER
pharmaR
GITHUB_REPOSITORY_OWNER_ID
42115094
GITHUB_RETENTION_DAYS 90
GITHUB_RUN_ATTEMPT 1
GITHUB_RUN_ID 13404668958
GITHUB_RUN_NUMBER 96
GITHUB_SERVER_URL https://github.com
GITHUB_SHA a8b95a62e6dc098bb3af41043304208245a9ed4a
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_c412a26f-cd8a-499e-b689-b0767882aa5e
GITHUB_TRIGGERING_ACTOR
llrs-roche
GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA a8b95a62e6dc098bb3af41043304208245a9ed4a
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
1
ImageOS ubuntu24
ImageVersion 20250209.1.0
INVOCATION_ID 8bd4b7db4d15432e8df0477a564753c1
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_11_X64 /usr/lib/jvm/temurin-11-jdk-amd64
JAVA_HOME_17_X64 /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_21_X64 /usr/lib/jvm/temurin-21-jdk-amd64
JAVA_HOME_8_X64 /usr/lib/jvm/temurin-8-jdk-amd64
JOURNAL_STREAM 8:7410
LANG C.UTF-8
LD_LIBRARY_PATH /opt/R/4.4.2/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.2/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 1000
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/RtmpZYt03y
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1d452c93cfc9_1739936534
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/4.4.2/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /opt/R/4.4.2/lib/R
R_INCLUDE_DIR /opt/R/4.4.2/lib/R/include
R_LIB_FOR_PAK /opt/R/4.4.2/lib/R/site-library
R_LIBS_SITE /opt/R/4.4.2/lib/R/site-library
R_LIBS_USER /home/runner/work/_temp/Library
R_PAPERSIZE letter
R_PAPERSIZE_USER letter
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/Rtmp4Towr0
R_SHARE_DIR /opt/R/4.4.2/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 2
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_40220c0a-4f03-4847-8b7e-3a374b87939a
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 837
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: 0x563c2de70910>
<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
[1] "default"
$deparse.cutoff
[1] 60
$device
function (width = 7, height = 7, ...)
{
grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x563c2d3e7a68>
<environment: namespace:knitr>
$device.ask.default
[1] FALSE
$digits
[1] 7
$dvipscmd
[1] "dvips"
$echo
[1] FALSE
$editor
[1] "vi"
$encoding
[1] "native.enc"
$example.ask
[1] "default"
$expressions
[1] 5000
$help.search.types
[1] "vignette" "demo" "help"
$help.try.all.packages
[1] FALSE
$htmltools.preserve.raw
[1] TRUE
$HTTPUserAgent
[1] "R/4.4.2 R (4.4.2 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions"
$internet.info
[1] 2
$keep.parse.data
[1] TRUE
$keep.parse.data.pkgs
[1] FALSE
$keep.source
[1] FALSE
$keep.source.pkgs
[1] FALSE
$knitr.in.progress
[1] TRUE
$locatorBell
[1] TRUE
$mailer
[1] "mailto"
$matprod
[1] "default"
$max.contour.segments
[1] 25000
$max.print
[1] 99999
$menu.graphics
[1] TRUE
$na.action
[1] "na.omit"
$Ncpus
[1] 1
$nwarnings
[1] 50
$OutDec
[1] "."
$pager
[1] "/opt/R/4.4.2/lib/R/bin/pager"
$papersize
[1] "letter"
$PCRE_limit_recursion
[1] NA
$PCRE_study
[1] FALSE
$PCRE_use_JIT
[1] TRUE
$pdfviewer
[1] "/usr/bin/xdg-open"
$pkgType
[1] "source"
$printcmd
[1] "/usr/bin/lpr"
$prompt
[1] "> "
$repos
CRAN
"https://cran.rstudio.com"
$rl_word_breaks
[1] " \t\n\"\\'`><=%;,|&{()}"
$rlang_trace_top_env
<environment: R_GlobalEnv>
$scipen
[1] 0
$show.coef.Pvalues
[1] TRUE
$show.error.messages
[1] TRUE
$show.signif.stars
[1] TRUE
$showErrorCalls
[1] TRUE
$showNCalls
[1] 50
$showWarnCalls
[1] FALSE
$str
$str$strict.width
[1] "no"
$str$digits.d
[1] 3
$str$vec.len
[1] 4
$str$list.len
[1] 99
$str$deparse.lines
NULL
$str$drop.deparse.attr
[1] TRUE
$str$formatNum
function (x, ...)
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x563c2d348520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_EDIutils_v1.0.3-tikzDictionary"
$timeout
[1] 60
$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