Validation Report - extras@0.8.0
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 extras
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 130 |
| has_vignettes | 4 |
| export_help | 130 |
| has_website | TRUE |
| has_maintainer | Nicole Hill nicole@poissonconsulting.ca |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/poissonconsulting/extras |
| has_bug_reports_url | 1 |
| downloads_1yr | 6869 |
| reverse_dependencies | 4 |
| has_examples | 0.9916667 |
| dependencies | 3 |
| 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 | chk | Imports |
| 2 | lifecycle | Imports |
| 3 | stats | Imports |
Package dependencies
Reverse dependencies
Overall the package has 4 reverse dependencies:
mcmcderive, mcmcr, nlist, term
Namespace
Overall the package has 130 exported objects. 130 are documented:
as_list as_list_unnamed chk_index
TRUE TRUE TRUE
chk_indices chk_pars dbern
TRUE TRUE TRUE
dev_bern dev_beta_binom dev_binom
TRUE TRUE TRUE
dev_gamma dev_gamma_pois dev_gamma_pois_zi
TRUE TRUE TRUE
dev_lnorm dev_neg_binom dev_norm
TRUE TRUE TRUE
dev_pois dev_pois_zi dev_skewnorm
TRUE TRUE TRUE
dev_student dskewnorm exp10
TRUE TRUE TRUE
exp2 fabs fill_all
TRUE TRUE TRUE
fill_na ilog ilog10
TRUE TRUE TRUE
ilog2 ilogit inv_logit
TRUE TRUE TRUE
inv_odds invlogit kurtosis
TRUE TRUE TRUE
log_lik_bern log_lik_beta_binom log_lik_binom
TRUE TRUE TRUE
log_lik_gamma log_lik_gamma_pois log_lik_gamma_pois_zi
TRUE TRUE TRUE
log_lik_lnorm log_lik_neg_binom log_lik_norm
TRUE TRUE TRUE
log_lik_pois log_lik_pois_zi log_lik_skewnorm
TRUE TRUE TRUE
log_lik_student log_odds log_odds_ratio
TRUE TRUE TRUE
log_odds_ratio2 log_odds<- log<-
TRUE TRUE TRUE
log10<- log2<- logit
TRUE TRUE TRUE
logit<- lower numericise
TRUE TRUE TRUE
numericize odds odds_ratio
TRUE TRUE TRUE
odds_ratio2 odds<- par_pattern
TRUE TRUE TRUE
params pbern pextreme
TRUE TRUE TRUE
phi pow proportional_change
TRUE TRUE TRUE
proportional_change2 proportional_difference proportional_difference2
TRUE TRUE TRUE
pskewnorm pvalue pzeros
TRUE TRUE TRUE
qbern qskewnorm ran_bern
TRUE TRUE TRUE
ran_beta_binom ran_binom ran_gamma
TRUE TRUE TRUE
ran_gamma_pois ran_gamma_pois_zi ran_lnorm
TRUE TRUE TRUE
ran_neg_binom ran_norm ran_pois
TRUE TRUE TRUE
ran_pois_zi ran_skewnorm ran_student
TRUE TRUE TRUE
rbern res_bern res_beta_binom
TRUE TRUE TRUE
res_binom res_gamma res_gamma_pois
TRUE TRUE TRUE
res_gamma_pois_zi res_lnorm res_neg_binom
TRUE TRUE TRUE
res_norm res_pois res_pois_zi
TRUE TRUE TRUE
res_skewnorm res_student rskewnorm
TRUE TRUE TRUE
sens_beta sens_exp sens_gamma
TRUE TRUE TRUE
sens_gamma_pois sens_gamma_pois_zi sens_lnorm
TRUE TRUE TRUE
sens_neg_binom sens_norm sens_pois
TRUE TRUE TRUE
sens_skewnorm sens_student sextreme
TRUE TRUE TRUE
skewness step svalue
TRUE TRUE TRUE
upper variance vld_index
TRUE TRUE TRUE
vld_indices vld_pars xtr_mean
TRUE TRUE TRUE
xtr_median xtr_sd zeros
TRUE TRUE TRUE
zscore
TRUE Examples
There are 119 help pages with examples, from 120 (99.17 %).
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 04:56:42 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
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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
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
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DOTNET_NOLOGO 1
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EDITOR vi
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GHCUP_INSTALL_BASE_PREFIX
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GITHUB_ACTION __run
GITHUB_ACTION_REF
GITHUB_ACTION_REPOSITORY
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GITHUB_ACTOR llrs-roche
GITHUB_ACTOR_ID 185338939
GITHUB_API_URL https://api.github.com
GITHUB_BASE_REF
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GITHUB_EVENT_NAME schedule
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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
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GITHUB_REF_PROTECTED false
GITHUB_REF_TYPE branch
GITHUB_REPOSITORY pharmaR/pharmapkgs
GITHUB_REPOSITORY_ID 798326913
GITHUB_REPOSITORY_OWNER
pharmaR
GITHUB_REPOSITORY_OWNER_ID
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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_PS1d456877abf2_1739940996
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/Rtmpi5xBh8
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: 0x558034cdf910>
<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: 0x5580341162d0>
<environment: namespace:knitr>
$device.ask.default
[1] FALSE
$digits
[1] 7
$dvipscmd
[1] "dvips"
$echo
[1] FALSE
$editor
[1] "vi"
$encoding
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$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
$HTTPUserAgent
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$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
$na.action
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$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: 0x5580341b7520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_extras_v0.8.0-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