Validation Report - dad@4.1.5
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 dad
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 144 |
| has_vignettes | 4 |
| export_help | 144 |
| has_website | TRUE |
| has_maintainer | Pierre Santagostini pierre.santagostini@agrocampus-ouest.fr |
| bugs_status | scraping bug reports fromm BugReports host ‘inra’ not implemented |
| has_bug_reports_url | 1 |
| downloads_1yr | 70754 |
| reverse_dependencies | 0 |
| has_examples | 1 |
| dependencies | 8 |
| 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 | Imports |
| 2 | stats | Imports |
| 3 | graphics | Imports |
| 4 | grDevices | Imports |
| 5 | utils | Imports |
| 6 | ggplot2 | Imports |
| 7 | e1071 | Imports |
| 8 | DescTools | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 144 exported objects. 144 are documented:
appendtofolderh as.data.frame.folder as.data.frame.folderh
TRUE TRUE TRUE
as.data.frame.foldert as.folder as.folder.data.frame
TRUE TRUE TRUE
as.folder.folderh as.folderh as.folderh.foldermtg
TRUE TRUE TRUE
as.foldert as.foldert.array as.foldert.data.frame
TRUE TRUE TRUE
bandwidth.parameter cor.folder cramer.data.frame
TRUE TRUE TRUE
cramer.folder cut.data.frame cut.folder
TRUE TRUE TRUE
ddchisqsym ddchisqsympar ddhellinger
TRUE TRUE TRUE
ddhellingerpar ddjeffreys ddjeffreyspar
TRUE TRUE TRUE
ddjensen ddjensenpar ddlp
TRUE TRUE TRUE
ddlppar discdd.misclass discdd.predict
TRUE TRUE TRUE
distl2d distl2dnorm distl2dnormpar
TRUE TRUE TRUE
distl2dpar dstatis.inter fdiscd.misclass
TRUE TRUE TRUE
fdiscd.predict fhclustd fmdsd
TRUE TRUE TRUE
folder folderh foldert
TRUE TRUE TRUE
fpcad fpcat getcol.folder
TRUE TRUE TRUE
getcol.foldert getrow.folder getrow.foldert
TRUE TRUE TRUE
hclustdd hellinger hellingerpar
TRUE TRUE TRUE
interpret interpret.dstatis interpret.fmdsd
TRUE TRUE TRUE
interpret.fpcad interpret.fpcat interpret.mdsdd
TRUE TRUE TRUE
is.discdd.misclass is.discdd.predict is.dstatis
TRUE TRUE TRUE
is.fdiscd.misclass is.fdiscd.predict is.fhclustd
TRUE TRUE TRUE
is.fmdsd is.folder is.folderh
TRUE TRUE TRUE
is.foldermtg is.foldert is.fpcad
TRUE TRUE TRUE
is.mdsdd jeffreys jeffreyspar
TRUE TRUE TRUE
kurtosis.folder l2d l2dpar
TRUE TRUE TRUE
matddchisqsym matddchisqsympar matddhellinger
TRUE TRUE TRUE
matddhellingerpar matddjeffreys matddjeffreyspar
TRUE TRUE TRUE
matddjensen matddjensenpar matddlp
TRUE TRUE TRUE
matddlppar matdistl2d matdistl2dnorm
TRUE TRUE TRUE
matdistl2dnormpar matdistl2dpar mathellinger
TRUE TRUE TRUE
mathellingerpar matipl2d matipl2dpar
TRUE TRUE TRUE
matjeffreys matjeffreyspar matwasserstein
TRUE TRUE TRUE
matwassersteinpar mdsdd mean.folder
TRUE TRUE TRUE
mtgcomponents mtgorder mtgrank
TRUE TRUE TRUE
pearson.data.frame pearson.folder phi.data.frame
TRUE TRUE TRUE
phi.folder plot.dstatis plot.fhclustd
TRUE TRUE TRUE
plot.fmdsd plot.foldert plot.fpcad
TRUE TRUE TRUE
plot.fpcat plot.hclustdd plot.mdsdd
TRUE TRUE TRUE
plotframes print.discdd.misclass print.discdd.predict
TRUE TRUE TRUE
print.dstatis print.fdiscd.misclass print.fdiscd.predict
TRUE TRUE TRUE
print.fhclustd print.fmdsd print.foldermtg
TRUE TRUE TRUE
print.foldert print.fpcad print.fpcat
TRUE TRUE TRUE
print.hclustdd print.mdsdd read.mtg
TRUE TRUE TRUE
rmcol.folder rmcol.foldert rmrow.folder
TRUE TRUE TRUE
rmrow.foldert skewness.folder sqrtmatrix
TRUE TRUE TRUE
summary.folder summary.folderh summary.foldermtg
TRUE TRUE TRUE
summary.foldert tschuprow.data.frame tschuprow.folder
TRUE TRUE TRUE
var.folder wasserstein wassersteinpar
TRUE TRUE TRUE Examples
There are 153 help pages with examples, from 153 (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 | 2025-02-17 04:49:56 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
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GITHUB_TRIGGERING_ACTOR
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GRADLE_HOME /usr/share/gradle-8.12.1
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HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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LOGGER_LOG_LEVEL DEBUG
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_LIMIT 1000
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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
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
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RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
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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
[1] TRUE
$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
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else {
cli_server_default(msg)
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}
<bytecode: 0x5615c3c15910>
<environment: namespace:cli>
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$demo.ask
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<bytecode: 0x5615c33077a0>
<environment: namespace:knitr>
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$matprod
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$pdfviewer
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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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$show.coef.Pvalues
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$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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format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x5615c30ed520>
$str.dendrogram.last
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$tikzMetricsDictionary
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$try.outFile
A connection with
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mode "w+b"
text "binary"
opened "opened"
can read "yes"
can write "yes"
$ts.eps
[1] 1e-05
$ts.S.compat
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$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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$warnPartialMatchDollar
[1] FALSE
$width
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