Validation Report - geiger@2.0.11
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 geiger
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 101 |
| has_vignettes | 0 |
| export_help | 101 |
| has_website | FALSE |
| has_maintainer | Luke Harmon lukeh@uidaho.edu |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| assess_size_codebase | 10574 |
| has_bug_reports_url | 0 |
| downloads_1yr | 42332 |
| reverse_dependencies | 27 |
| has_examples | 0.925 |
| dependencies | 13 |
| 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 | ape (>= 3.0-6) | Depends |
| 2 | phytools (>= 1.5-1) | Depends |
| 3 | MASS | Imports |
| 4 | mvtnorm | Imports |
| 5 | subplex | Imports |
| 6 | deSolve (>= 1.7) | Imports |
| 7 | digest | Imports |
| 8 | Rcpp (>= 0.11.0) | Imports |
| 9 | coda | Imports |
| 10 | ncbit | Imports |
| 11 | colorspace | Imports |
| 12 | methods | Imports |
| 13 | Rcpp | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 27 reverse dependencies:
cauphy, convevol, diversitree, evobiR, FishPhyloMaker, fishtree, hilldiv, hillR, hisse, markophylo, nichevol, nodeSub, OUwie, pcmabc, phytools, pmc, ppgm, ratematrix, RNeXML, RPANDA, secsse, sensiPhy, surface, treats, TreeSim, treestats, windex
Namespace
Overall the package has 101 exported objects. 101 are documented:
aicm aicw aov.phylo
TRUE TRUE TRUE
argn argn<- as.Qmatrix.gfit
TRUE TRUE TRUE
bd.km bd.ms BDsim
TRUE TRUE TRUE
bf birthdeath.tree bm.lik
TRUE TRUE TRUE
calibrate.mecca calibrate.rjmcmc cherries
TRUE TRUE TRUE
congruify.phylo crown.limits crown.p
TRUE TRUE TRUE
dcount deltaTree disparity
TRUE TRUE TRUE
dlunif drop.extinct drop.random
TRUE TRUE TRUE
dtpois dtt edgelabels.auteur
TRUE TRUE TRUE
edges.phylo ess ex.jumpsimulator
TRUE TRUE TRUE
ex.ratesimulator ex.traitgram exemplar.phylo
TRUE TRUE TRUE
exponentialchangeTree fitContinuous fitContinuousMCMC
TRUE TRUE TRUE
fitDiscrete gbcontain gbresolve
TRUE TRUE TRUE
getAncStates glomogram.phylo hash.node
TRUE TRUE TRUE
hashes.phylo hashes.rjmcmc hdr
TRUE TRUE TRUE
heights hme ic.sigma
TRUE TRUE TRUE
is.constrained is.extinct is.phylo
TRUE TRUE TRUE
is.root kappaTree lambdaTree
TRUE TRUE TRUE
linearchangeTree Linnaean load.rjmcmc
TRUE TRUE TRUE
lookup.phylo make.bm.relaxed make.gbm
TRUE TRUE TRUE
mecca medusa mkn.lik
TRUE TRUE TRUE
name.check nh.test node.leaves
TRUE TRUE TRUE
nodelabel.phylo ouTree PATHd8.phylo
TRUE TRUE TRUE
phylo.clades phylo.lookup pp.mcmc
TRUE TRUE TRUE
prune.extinct.taxa prune.random.taxa r8s.phylo
TRUE TRUE TRUE
rate.estimate ratematrix rc
TRUE TRUE TRUE
rescaleTree rjmcmc.bm sem
TRUE TRUE TRUE
sim.bd sim.bdtree sim.char
TRUE TRUE TRUE
sim.mecca span.phylo speciationalTree
TRUE TRUE TRUE
startingpt.mecca stem.limits stem.p
TRUE TRUE TRUE
tip.disparity tips to.auteur
TRUE TRUE TRUE
to.coda treedata tworateTree
TRUE TRUE TRUE
uniqueMultiPhylo white.mkn write.pathd8
TRUE TRUE TRUE
write.r8s write.treePL
TRUE TRUE Examples
There are 37 help pages with examples, from 40 (92.50 %).
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 24.04.2 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-03-21 03:30:18 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 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_4.4.3 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.50 jsonlite_1.9.1
[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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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
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BUNDLE_EXT linux-amd64.deb
CHROME_BIN /usr/bin/google-chrome
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CI true
CONDA /usr/share/miniconda
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DENO_TLS_CA_STORE system,mozilla
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DOTNET_MULTILEVEL_LOOKUP
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GITHUB_REF refs/heads/main
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GITHUB_REF_TYPE branch
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_b9f8e0a8-d447-48c8-940f-7bbff5230431
GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW Update package repositories
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GITHUB_WORKFLOW_SHA a0954536fd2e494515f55f1a61993d3124a0309d
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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/1.23.7/x64
GRADLE_HOME /usr/share/gradle-8.13
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
3650
HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
ImageVersion 20250316.1.0
INVOCATION_ID 64daa6dd65fb41ddac3b6f7bd9293add
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
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JOURNAL_STREAM 8:5601
LANG C.UTF-8
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LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
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MEMORY_PRESSURE_WRITE c29tZSAyMDAwMDAgMjAwMDAwMAA=
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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 100
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/Rtmpn5nYwz
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1c0213c67468_1742527814
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/4.4.3/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /opt/R/4.4.3/lib/R
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R_PAPERSIZE letter
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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/Rtmp52sMO4
R_SHARE_DIR /opt/R/4.4.3/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-1000000633
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_88c85fac-f0c6-4b1c-8d70-a8143ca35010
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
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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 833
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)
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}
<bytecode: 0x563105429330>
<environment: namespace:cli>
$catch.script.errors
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$CBoundsCheck
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$citation.bibtex.max
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$continue
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$contrasts
unordered ordered
"contr.treatment" "contr.poly"
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$defaultPackages
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$demo.ask
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$device
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<bytecode: 0x563104996200>
<environment: namespace:knitr>
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$digits
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$example.ask
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$expressions
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$locatorBell
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$mailer
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$matprod
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$max.print
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$na.action
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$Ncpus
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$OutDec
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$papersize
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$PCRE_limit_recursion
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$PCRE_study
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$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
<environment: R_GlobalEnv>
$scipen
[1] 0
$show.coef.Pvalues
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$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
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<environment: 0x563104904688>
$str.dendrogram.last
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$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"
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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$warning.length
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$warnPartialMatchAttr
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$warnPartialMatchDollar
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$width
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