Validation Report - doBy@4.6.25
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 doBy
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 91 |
| has_vignettes | 6 |
| export_help | 91 |
| has_website | TRUE |
| has_maintainer | Søren Højsgaard sorenh@math.aau.dk |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_source_control | https://github.com/hojsgaard/doBy |
| has_bug_reports_url | 0 |
| downloads_1yr | 2063106 |
| reverse_dependencies | 24 |
| has_examples | 0.9852941 |
| dependencies | 14 |
| license | GPL (>= 2) |
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 | boot | Imports |
| 3 | broom | Imports |
| 4 | cowplot | Imports |
| 5 | Deriv | Imports |
| 6 | dplyr | Imports |
| 7 | ggplot2 | Imports |
| 8 | MASS | Imports |
| 9 | Matrix | Imports |
| 10 | modelr | Imports |
| 11 | microbenchmark | Imports |
| 12 | rlang | Imports |
| 13 | tibble | Imports |
| 14 | tidyr | Imports |
Package dependencies
Reverse dependencies
Overall the package has 24 reverse dependencies:
atable, BaalChIP, BayesNetBP, bfp, caracas, daltoolboxdp, datarobot, fdANOVA, ForestElementsR, frailtypack, gRim, miclust, NormData, pbkrtest, PracTools, R2MLwiN, rattle, Rphylopars, ScottKnott, SensMap, sicure, svydiags, TukeyC, wCorr
Namespace
Overall the package has 91 exported objects. 91 are documented:
aggregate_linest_list as_lhs_chr
TRUE TRUE
as_lhs_frm as_rhs_chr
TRUE TRUE
as_rhs_frm binomial_to_bernoulli_data
TRUE TRUE
bquote_fun_list cv_glm_fitlist
TRUE TRUE
descStat doby.xtabs
TRUE TRUE
esticon expr_to_fun
TRUE TRUE
firstobs formula_add
TRUE TRUE
formula_add_str formula_chr_to_form
TRUE TRUE
formula_nth formula_poly
TRUE TRUE
formula_to_interaction_matrix generate_data_list
TRUE TRUE
get_contrasts get_formulas
TRUE TRUE
get_fun get_linest_list
TRUE TRUE
get_section get_vartypes
TRUE TRUE
get_X get_xlevels
TRUE TRUE
getBy interaction_plot
TRUE TRUE
is_estimable is_grouped
TRUE TRUE
lapply_by lapplyBy
TRUE TRUE
lastobs LE_matrix
TRUE TRUE
linest lm_by
TRUE TRUE
lmBy LSmeans
TRUE TRUE
matrix2set_list mb_summary
TRUE TRUE
model_stability_glm order_by
TRUE TRUE
orderBy parseGroupFormula
TRUE TRUE
plot_lm popMeans
TRUE TRUE
recode_var recodeVar
TRUE TRUE
recover_pca_data renameCol
TRUE TRUE
response_plot rle2
TRUE TRUE
sample_by sampleBy
TRUE TRUE
sapply_by sapplyBy
TRUE TRUE
scale_by scale_df
TRUE TRUE
scale2 scaleBy
TRUE TRUE
section_fun section_fun_env
TRUE TRUE
section_fun_sub set_covariate_val
TRUE TRUE
set_default set_list2matrix
TRUE TRUE
set_xlevels simplify_rhs
TRUE TRUE
split_by split_bycol
TRUE TRUE
split_byrow splitBy
TRUE TRUE
sub_seq subSeq
TRUE TRUE
subset_by subsetBy
TRUE TRUE
summary_by summary_mb
TRUE TRUE
summaryBy taylor
TRUE TRUE
terms_labels timeSinceEvent
TRUE TRUE
to_str transform_by
TRUE TRUE
transformBy truncate0
TRUE TRUE
unique_formula which.maxn
TRUE TRUE
which.minn
TRUE Examples
There are 67 help pages with examples, from 68 (98.53 %).
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 | 2025-02-18 04:30:25 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
AZURE_EXTENSION_DIR /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
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BUNDLE_EXT linux-amd64.deb
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_b4db8720-2381-4f5c-84c9-546b4603e3d5
GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW Update package repositories
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GITHUB_WORKFLOW_SHA 157fff498035c254c88cbf9e2cfd3aeb384ab8f5
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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
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HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
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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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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 1000
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
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PIPX_BIN_DIR /opt/pipx_bin
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 /
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R_DOC_DIR /opt/R/4.4.2/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/4.4.2/lib/R/share
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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 17
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RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
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RUNNER_USER runner
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SED /usr/bin/sed
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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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SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 830
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)
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else {
cli_server_default(msg)
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}
<bytecode: 0x5636178f8910>
<environment: namespace:cli>
$catch.script.errors
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$contrasts
unordered ordered
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$defaultPackages
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$demo.ask
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$device
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{
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<bytecode: 0x563616f9d5d8>
<environment: namespace:knitr>
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$expressions
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[1] TRUE
$locatorBell
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$mailer
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$matprod
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$papersize
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$pdfviewer
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$pkgType
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$printcmd
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$prompt
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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
[1] TRUE
$show.error.messages
[1] TRUE
$show.signif.stars
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$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
function (x, ...)
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x563616dd0520>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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mode "w+b"
text "binary"
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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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$warn
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$warning.length
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$warnPartialMatchAttr
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$width
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