Validation Report - ade4@1.7.23
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 ade4
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 227 |
| has_vignettes | 2 |
| export_help | 227 |
| has_website | TRUE |
| has_maintainer | Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr |
| bugs_status | 0.7 |
| has_bug_reports_url | 1 |
| downloads_1yr | 445829 |
| reverse_dependencies | 86 |
| has_examples | 0.9896194 |
| dependencies | 11 |
| 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 | graphics | Imports |
| 2 | grDevices | Imports |
| 3 | methods | Imports |
| 4 | stats | Imports |
| 5 | utils | Imports |
| 6 | MASS | Imports |
| 7 | pixmap | Imports |
| 8 | sp | Imports |
| 9 | Rcpp | Imports |
| 10 | Rcpp | LinkingTo |
| 11 | RcppArmadillo | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 86 reverse dependencies:
adductomicsR, ade4TkGUI, adegenet, adegraphics, adehabitatHR, adehabitatHS, adehabitatLT, adephylo, adespatial, adiv, ads, Autoplotprotein, BalanceCheck, berryFunctions, bikm1, bioregion, brainGraph, CAESAR.Suite, cati, clusterSim, corral, covRNA, dispRity, divent, DrBats, ecospat, ecostats, entropart, epimdr, epimdr2, explor, FactoClass, factoextra, FD, funrar, funspace, GDAtools, genoPlotR, glmmTMB, gSeg, gTests, gTestsMulti, Guerry, GUniFrac, hierfstat, hillR, iBBiG, kissDE, Laterality, LearnPCA, made4, memgene, metaprotr, mFD, mia, MiSPU, MorphoTools2, motifStack, multiblock, OGI, omicade4, packMBPLSDA, PBD, pctax, pez, phylobase, phyloseq, plotprotein, polysat, PopGenReport, poppr, ProcMod, revtools, rgTest, RVAideMemoire, SCGLR, Select, seqhandbook, seqinr, SPARTAAS, STEPCAM, symbolicDA, Thresher, treespace, virtualspecies, wallace
Namespace
Overall the package has 227 exported objects. 227 are documented:
acm.burt acm.disjonctif
TRUE TRUE
add.scatter add.scatter.eig
TRUE TRUE
adegraphicsLoaded amova
TRUE TRUE
apqe area.plot
TRUE TRUE
area2link area2poly
TRUE TRUE
as.dudi as.krandboot
TRUE TRUE
as.krandtest as.krandxval
TRUE TRUE
as.randboot as.randtest
TRUE TRUE
as.randxval as.taxo
TRUE TRUE
bca betweenvarCpp
TRUE TRUE
bicenter.wt bwca.dpcoa
TRUE TRUE
cailliez coinertia
TRUE TRUE
col.names col.names<-
TRUE TRUE
combine.4thcorner combine.randtest.rlq
TRUE TRUE
costatis costatis.randtest
TRUE TRUE
covfacwt covwt
TRUE TRUE
dagnelie.test disc
TRUE TRUE
discrimin discrimin.coa
TRUE TRUE
dist.binary dist.dudi
TRUE TRUE
dist.ktab dist.neig
TRUE TRUE
dist.prop dist.quant
TRUE TRUE
dist.taxo divc
TRUE TRUE
divcmax dotchart.phylog
TRUE TRUE
dotcircle dpcoa
TRUE TRUE
dudi.acm dudi.coa
TRUE TRUE
dudi.dec dudi.fca
TRUE TRUE
dudi.fpca dudi.hillsmith
TRUE TRUE
dudi.mix dudi.nsc
TRUE TRUE
dudi.pca dudi.pco
TRUE TRUE
dudi.type enum.phylog
TRUE TRUE
foucart fourthcorner
TRUE TRUE
fourthcorner.rlq fourthcorner2
TRUE TRUE
gearymoran gridrowcol
TRUE TRUE
haar2level hclust2phylog
TRUE TRUE
inerbetweenCpp inertia
TRUE TRUE
inertia.dudi is.dudi
TRUE TRUE
is.euclid is.ktab
TRUE TRUE
is.orthobasis kdist
TRUE TRUE
kdist.cor kdist2ktab
TRUE TRUE
kdisteuclid kplot
TRUE TRUE
kplotsepan.coa kplotX.mdpcoa
TRUE TRUE
ktab.data.frame ktab.list.df
TRUE TRUE
ktab.list.dudi ktab.match2ktabs
TRUE TRUE
ktab.within ldist.ktab
TRUE TRUE
lingoes loocv
TRUE TRUE
mantel.randtest mantel.rtest
TRUE TRUE
mantelkdist mbpcaiv
TRUE TRUE
mbpls mcoa
TRUE TRUE
mdpcoa meanfacwt
TRUE TRUE
mfa mld
TRUE TRUE
mstree nb2neig
TRUE TRUE
neig neig2mat
TRUE TRUE
neig2nb newick2phylog
TRUE TRUE
niche niche.param
TRUE TRUE
nipals originality
TRUE TRUE
orthobasis.circ orthobasis.haar
TRUE TRUE
orthobasis.line orthobasis.mat
TRUE TRUE
orthobasis.neig p.adjust.4thcorner
TRUE TRUE
pcaiv pcaivortho
TRUE TRUE
pcoscaled phylog.extract
TRUE TRUE
phylog.permut PI2newick
TRUE TRUE
poly2area prep.binary
TRUE TRUE
prep.circular prep.fuzzy
TRUE TRUE
prep.fuzzy.var prep.mdpcoa
TRUE TRUE
procuste procuste.randtest
TRUE TRUE
procuste.rtest procusterandtestCpp
TRUE TRUE
pta quasieuclid
TRUE TRUE
radial.phylog randboot
TRUE TRUE
randtest reciprocal.coa
TRUE TRUE
reconst redo.dudi
TRUE TRUE
rlq rtest
TRUE TRUE
RV.randtest RV.rtest
TRUE TRUE
RVdist.randtest RVintra.randtest
TRUE TRUE
RVintrarandtestCpp RVkdist
TRUE TRUE
RVrandtestCpp s.arrow
TRUE TRUE
s.chull s.class
TRUE TRUE
s.corcircle s.distri
TRUE TRUE
s.hist s.image
TRUE TRUE
s.kde2d s.label
TRUE TRUE
s.logo s.match
TRUE TRUE
s.match.class s.multinom
TRUE TRUE
s.traject s.value
TRUE TRUE
scalefacwt scalewt
TRUE TRUE
scatter scatterutil.base
TRUE TRUE
scatterutil.chull scatterutil.convrot90
TRUE TRUE
scatterutil.eigen scatterutil.ellipse
TRUE TRUE
scatterutil.eti scatterutil.eti.circ
TRUE TRUE
scatterutil.grid scatterutil.legend.bw.square
TRUE TRUE
scatterutil.legend.square.grey scatterutil.legendgris
TRUE TRUE
scatterutil.logo scatterutil.scaling
TRUE TRUE
scatterutil.sco scatterutil.star
TRUE TRUE
scatterutil.sub sco.boxplot
TRUE TRUE
sco.class sco.distri
TRUE TRUE
sco.gauss sco.label
TRUE TRUE
sco.match sco.quant
TRUE TRUE
score scores.neig
TRUE TRUE
sepan statico
TRUE TRUE
statico.krandtest statis
TRUE TRUE
supcol supdist
TRUE TRUE
suprow symbols.phylog
TRUE TRUE
tab.names tab.names<-
TRUE TRUE
table.cont table.dist
TRUE TRUE
table.paint table.phylog
TRUE TRUE
table.value taxo2phylog
TRUE TRUE
testdim testdiscriminCpp
TRUE TRUE
testertraceCpp testertracenubisCpp
TRUE TRUE
testertracenuCpp testinterCpp
TRUE TRUE
testmantelCpp triangle.biplot
TRUE TRUE
triangle.class triangle.plot
TRUE TRUE
uniquewt.df varfacwt
TRUE TRUE
variance.phylog varipart
TRUE TRUE
varwt wca
TRUE TRUE
withinpca witwit.coa
TRUE TRUE
witwitsepan
TRUE Examples
There are 286 help pages with examples, from 289 (98.96 %).
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 | 2025-02-21 13:07:48 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_1.9.0
[10] xfun_0.51 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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ANT_HOME /usr/share/ant
AZURE_EXTENSION_DIR /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
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BUNDLE_EXT linux-amd64.deb
CHROME_BIN /usr/bin/google-chrome
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GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA 9d087537577b11dd985321646640fd8d289e4b89
GITHUB_WORKSPACE /home/runner/work/pharmapkgs/pharmapkgs
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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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LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 100
PHARMAPKGS_PLATFORM ubuntu-22.04
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
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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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QUARTO_PROJECT_ROOT /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_ROOT /
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
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RUNNER_ENVIRONMENT github-hosted
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SGX_AESM_ADDR 1
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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
/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
$callr.condition_handler_cli_message
function (msg)
{
custom_handler <- getOption("cli.default_handler")
if (is.function(custom_handler)) {
custom_handler(msg)
}
else {
cli_server_default(msg)
}
}
<bytecode: 0x55faff62d910>
<environment: namespace:cli>
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$CBoundsCheck
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$citation.bibtex.max
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$continue
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$contrasts
unordered ordered
"contr.treatment" "contr.poly"
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[1] TRUE
$defaultPackages
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$demo.ask
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$deparse.cutoff
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$device
function (width = 7, height = 7, ...)
{
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<bytecode: 0x55fafecf0a48>
<environment: namespace:knitr>
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$example.ask
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$expressions
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$help.search.types
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$internet.info
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$knitr.in.progress
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$locatorBell
[1] TRUE
$mailer
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$matprod
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$max.contour.segments
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$max.print
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$na.action
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$OutDec
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$papersize
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$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
[1] TRUE
$show.signif.stars
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$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: 0x55fafeb05520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_ade4_v1.7.23-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