Validation Report - ape@5.8.1
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 ape
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 340 |
| has_vignettes | 7 |
| export_help | 340 |
| has_website | TRUE |
| has_maintainer | Emmanuel Paradis Emmanuel.Paradis@ird.fr |
| bugs_status | 0.8 |
| has_source_control | https://github.com/emmanuelparadis/ape |
| has_bug_reports_url | 1 |
| downloads_1yr | 1107596 |
| reverse_dependencies | 414 |
| has_examples | 0.9946524 |
| dependencies | 10 |
| license | GPL-2 | GPL-3 |
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 | nlme | Imports |
| 2 | lattice | Imports |
| 3 | graphics | Imports |
| 4 | methods | Imports |
| 5 | stats | Imports |
| 6 | utils | Imports |
| 7 | parallel | Imports |
| 8 | Rcpp (>= 0.12.0) | Imports |
| 9 | digest | Imports |
| 10 | Rcpp | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 414 reverse dependencies:
abdiv, adaptiveGPCA, ade4, adegenet, adephylo, adespatial, adiv, admtools, alakazam, Anaconda, animalcules, AnnotationBustR, AntibodyForests, aPCoA, apex, aphid, aphylo, Apoderoides, aqp, arakno, asnipe, avotrex, babette, BAMMtools, BarcodingR, BAT, beastier, beautier, betapart, BIEN, bioregion, bioseq, bivariatemaps, bnpsd, BoSSA, brms, BSTZINB, CALANGO, canaper, Canopy, caper, castor, cati, cauphy, ccfindR, chemodiv, Claddis, cloneRate, clstutils, CluMSID, clusterExperiment, coalescentMCMC, colordistance, CommEcol, compcodeR, concatipede, CongreveLamsdell2016, convevol, copyseparator, corHMM, covid19.analytics, CRABS, CTNote, ctpm, DAISIE, DAISIEprep, DAMOCLES, dartR.base, data.tree, DCLEAR, DDD, ddtlcm, debar, deeptime, dendextend, DHARMa, DIAlignR, dispRity, distory, divent, diversitree, divraster, do3PCA, dowser, dynamicSDM, ecolottery, ecoregime, ecospat, ecotraj, ENMTools, entropart, enveomics.R, EnvNJ, EpiModel, epm, evobiR, evolqg, evolvability, evolved, EvoPhylo, fastreeR, FAVA, FD, fido, file2meco, FinePop, FishPhyloMaker, fishtree, FossilSim, FuncDiv, funspace, geiger, genBaRcode, geneHapR, geneplast, geomorph, ggimage, ggmsa, ggmuller, ggrasp, ggtree, ggtreeSpace, GIFT, glinvci, gllvm, glmmTMB, GLSME, GmicR, GOCompare, gquad, gromovlab, GUniFrac, HACSim, hagis, haplotypes, harmonicmeanp, harrietr, HGC, hierfstat, hilldiv, hillR, hisse, HMPTrees, Hmsc, holobiont, homals, HSAUR, HSAUR2, HSAUR3, HybridMicrobiomes, iCAMP, iCellR, idar, idpr, igraph, immunarch, indelmiss, iNEXT.3D, iNEXT.beta3D, infercnv, insect, insight, ipADMIXTURE, ips, itol.toolkit, jackalope, JNplots, jrich, jSDM, kmer, lingtypology, LinTInd, longreadvqs, LorMe, MACER, MAGNAMWAR, markophylo, mcbette, MCMCglmm, MCMCtreeR, mdendro, meconetcomp, mecoturn, MesKit, metacoder, metadat, metafor, metagear, mFD, MGnifyR, mia, miaSim, miaViz, MicrobiotaProcess, microeco, MiSPU, ML.MSBD, MLVSBM, mmodely, MonoPhy, motmot, MPSEM, msa, MSA2dist, msaR, MSCquartets, MSCsimtester, MVA, mvMORPH, mvSLOUCH, netdiffuseR, NicheBarcoding, nichevol, nLTT, nodeSub, nodiv, NormalyzerDE, nosoi, NST, numbat, occCite, OmaDB, ontophylo, openPrimeR, oposSOM, oppr, OptCirClust, orthGS, orthogene, ouch, outbreaker2, outbreaks, OUwie, packFinder, paco, palaeoverse, paleobuddy, paleoDiv, paleotree, PathoStat, PBD, pcmabc, PCMBase, PCPS, pctax, pegas, perspectev, pez, phangorn, philr, phyclust, phyext2, phylepic, phylobase, phylocanvas, phylocomr, PhylogeneticEM, phylogram, phylolm, phylopairs, phylopath, PhyloProfile, phyloraster, phyloregion, phylosem, phyloseq, phylosignal, phylosignalDB, phylospatial, phylotate, phylotools, phyloTop, phylter, phyr, PhySortR, phytools, picante, Plasmidprofiler, Platypus, plotbb, polysat, POMS, pooledpeaks, poolfstat, popkin, poppr, POSTm, POUMM, poweRbal, ppgm, primerTree, prioritizr, PVR, qlcData, QSutils, Quartet, quiddich, RAINBOWR, rapidphylo, ratematrix, rbiom, rdiversity, recluster, rehh, restez, RevGadgets, Revticulate, rhierbaps, rKOMICS, rncl, RNeXML, Rogue, rotl, RPANDA, Rphylopars, rphylopic, RPointCloud, rr2, rrnni, RRphylo, RRPP, rSWeeP, Rtapas, Rtropical, RVAideMemoire, rwty, sand, sangeranalyseR, scAnnotatR, scBubbletree, scFeatures, scistreer, scMultiSim, scrm, secsse, sensiPhy, SeqFeatR, Seurat, shazam, shinyTempSignal, shinyWGD, shipunov, sidier, SigTree, singleCellTK, SiPhyNetwork, sitePath, slendr, slouch, SoilTaxonomy, SpaceMarkers, spANOVA, SPARTAAS, spider, spiralize, STEPCAM, strap, STraTUS, stylo, supportR, supraHex, surface, symmoments, Sysrecon, systemPipeShiny, systemPipeTools, tanggle, tapnet, taxize, taxlist, tbea, TBRDist, TESS, TextMiningGUI, tidygraph, tidysq, tidytree, TiPS, TML, TotalCopheneticIndex, tracerer, TransPhylo, treats, TreeAndLeaf, treebalance, treebase, treeclimbR, treeDA, treedater, TreeDiagram, TreeDist, treeio, treekoR, treenomial, TreeSearch, TreeSim, TreeSimGM, treesliceR, treespace, treestartr, treestats, treestructure, TreeSummarizedExperiment, TreeTools, TSLA, universalmotif, vcfR, VDJgermlines, VERSO, vhica, warbleR, windex, Xplortext, yatah
Namespace
Overall the package has 340 exported objects. 340 are documented:
.compressTipLabel .PlotPhyloEnv .uncompressTipLabel
TRUE TRUE TRUE
[.DNAbin AAsubst abbreviateGenus
TRUE TRUE TRUE
ace add.scale.bar additive
TRUE TRUE TRUE
alex all.equal.DNAbin all.equal.phylo
TRUE TRUE TRUE
alview arecompatible as.AAbin
TRUE TRUE TRUE
as.AAbin.character as.alignment as.bitsplits
TRUE TRUE TRUE
as.bitsplits.prop.part as.character.AAbin as.character.DNAbin
TRUE TRUE TRUE
as.DNAbin as.DNAbin.alignment as.DNAbin.character
TRUE TRUE TRUE
as.DNAbin.list as.evonet as.evonet.phylo
TRUE TRUE TRUE
as.hclust.phylo as.igraph.evonet as.igraph.phylo
TRUE TRUE TRUE
as.list.AAbin as.list.DNAbin as.matching
TRUE TRUE TRUE
as.matching.phylo as.matrix.DNAbin as.network.evonet
TRUE TRUE TRUE
as.network.phylo as.networx.evonet as.phyDat.AAbin
TRUE TRUE TRUE
as.phylo as.phylo.evonet as.phylo.formula
TRUE TRUE TRUE
as.phylo.hclust as.phylo.matching as.phylo.phylog
TRUE TRUE TRUE
as.prop.part axisPhylo balance
TRUE TRUE TRUE
base.freq bd.ext bd.time
TRUE TRUE TRUE
binaryPGLMM binaryPGLMM.sim bind.tree
TRUE TRUE TRUE
bionj bionjs biplot.pcoa
TRUE TRUE TRUE
birthdeath bitsplits boot.phylo
TRUE TRUE TRUE
BOTHlabels branching.times bydir
TRUE TRUE TRUE
c.DNAbin CADM.global CADM.post
TRUE TRUE TRUE
cbind.DNAbin checkAlignment checkLabel
TRUE TRUE TRUE
checkValidPhylo cherry chronoMPL
TRUE TRUE TRUE
chronopl chronos chronos.control
TRUE TRUE TRUE
circular.plot cladewise cladogram.plot
TRUE TRUE TRUE
clustal clustalomega coalescent.intervals
TRUE TRUE TRUE
collapse.singles collapsed.intervals compar.cheverud
TRUE TRUE TRUE
compar.gee compar.lynch compar.ou
TRUE TRUE TRUE
comparePhylo complement compute.brlen
TRUE TRUE TRUE
compute.brtime consensus cophenetic.phylo
TRUE TRUE TRUE
cophyloplot corBlomberg corBrownian
TRUE TRUE TRUE
corGrafen corMartins corPagel
TRUE TRUE TRUE
corphylo correlogram.formula countBipartitions
TRUE TRUE TRUE
dbd dbdTime def
TRUE TRUE TRUE
degree del.colgapsonly del.gaps
TRUE TRUE TRUE
del.rowgapsonly delta.plot deviance.ace
TRUE TRUE TRUE
di2multi di2multi.multiPhylo di2multi.phylo
TRUE TRUE TRUE
dist.aa dist.dna dist.gene
TRUE TRUE TRUE
dist.nodes dist.topo diversi.gof
TRUE TRUE TRUE
diversi.time diversity.contrast.test DNAbin2indel
TRUE TRUE TRUE
dnds drawSupportOnEdges drop.fossil
TRUE TRUE TRUE
drop.tip drop.tip.multiPhylo drop.tip.phylo
TRUE TRUE TRUE
dyule edgelabels edges
TRUE TRUE TRUE
editFileExtensions efastats estimate.dates
TRUE TRUE TRUE
estimate.mu evonet ewLasso
TRUE TRUE TRUE
extract.clade extract.popsize fancyarrows
TRUE TRUE TRUE
fastme.bal fastme.ols find.skyline.epsilon
TRUE TRUE TRUE
floating.pie.asp Ftab gammaStat
TRUE TRUE TRUE
GC.content getAnnotationsGenBank getMRCA
TRUE TRUE TRUE
has.singles howmanytrees image.AAbin
TRUE TRUE TRUE
image.DNAbin is.binary is.binary.multiPhylo
TRUE TRUE TRUE
is.binary.phylo is.binary.tree is.compatible
TRUE TRUE TRUE
is.compatible.bitsplits is.monophyletic is.rooted
TRUE TRUE TRUE
is.rooted.multiPhylo is.rooted.phylo is.ultrametric
TRUE TRUE TRUE
is.ultrametric.multiPhylo is.ultrametric.phylo keep.tip
TRUE TRUE TRUE
keep.tip.multiPhylo keep.tip.phylo kronoviz
TRUE TRUE TRUE
label2table labels.DNAbin ladderize
TRUE TRUE TRUE
LargeNumber latag2n letterconf
TRUE TRUE TRUE
lmorigin LTT ltt.coplot
TRUE TRUE TRUE
ltt.lines ltt.plot ltt.plot.coords
TRUE TRUE TRUE
makeChronosCalib makeLabel makeLabel.character
TRUE TRUE TRUE
makeNodeLabel mantel.test matexpo
TRUE TRUE TRUE
mcconwaysims.test mcmc.popsize mixedFontLabel
TRUE TRUE TRUE
mltt.plot Moran.I MPR
TRUE TRUE TRUE
mrca mst multi2di
TRUE TRUE TRUE
multi2di.multiPhylo multi2di.phylo muscle
TRUE TRUE TRUE
muscle5 mvr mvrs
TRUE TRUE TRUE
Nedge Nedge.evonet Nedge.multiPhylo
TRUE TRUE TRUE
Nedge.phylo new2old.phylo nexus2DNAbin
TRUE TRUE TRUE
nj njs Nnode
TRUE TRUE TRUE
Nnode.multiPhylo Nnode.phylo node_depth
TRUE TRUE TRUE
node_depth_edgelength node_height node_height_clado
TRUE TRUE TRUE
node.depth node.depth.edgelength node.height
TRUE TRUE TRUE
nodelabels nodepath Ntip
TRUE TRUE TRUE
Ntip.multiPhylo Ntip.phylo old2new.phylo
TRUE TRUE TRUE
ONEwise parafit pcoa
TRUE TRUE TRUE
perm.rowscols phydataplot phylogram.plot
TRUE TRUE TRUE
phymltest pic pic.ortho
TRUE TRUE TRUE
plot.evonet plot.multiPhylo plot.phylo
TRUE TRUE TRUE
plotBreakLongEdges plotPhyloCoor plotTreeTime
TRUE TRUE TRUE
polar2rect postorder postprocess.prop.part
TRUE TRUE TRUE
print.AAbin print.DNAbin print.phylo
TRUE TRUE TRUE
prop.clades prop.part rbdtree
TRUE TRUE TRUE
rbind.DNAbin rcoal rDNAbin
TRUE TRUE TRUE
read.caic read.dna read.evonet
TRUE TRUE TRUE
read.FASTA read.fastq read.GenBank
TRUE TRUE TRUE
read.gff read.nexus read.nexus.data
TRUE TRUE TRUE
read.tree reconstruct rect2polar
TRUE TRUE TRUE
reorder.evonet reorder.multiPhylo reorder.phylo
TRUE TRUE TRUE
reorderRcpp richness.yule.test ring
TRUE TRUE TRUE
rlineage rmtopology rmtree
TRUE TRUE TRUE
root root.multiPhylo root.phylo
TRUE TRUE TRUE
rotate rotateConstr rphylo
TRUE TRUE TRUE
rtopology rTraitCont rTraitDisc
TRUE TRUE TRUE
rTraitMult rtree rtt
TRUE TRUE TRUE
SDM seg.sites seq_root2tip
TRUE TRUE TRUE
SHORTwise skyline skylineplot
TRUE TRUE TRUE
skylineplot.deluxe slowinskiguyer.test solveAmbiguousBases
TRUE TRUE TRUE
speciesTree stree stripLabel
TRUE TRUE TRUE
subtreeplot subtrees summary.phylo
TRUE TRUE TRUE
tcoffee tiplabels trans
TRUE TRUE TRUE
treePop trex triangMtd
TRUE TRUE TRUE
triangMtds ultrametric unique.multiPhylo
TRUE TRUE TRUE
unroot unroot.multiPhylo unroot.phylo
TRUE TRUE TRUE
unrooted.xy updateLabel varcomp
TRUE TRUE TRUE
varCompPhylip vcv vcv.corPhyl
TRUE TRUE TRUE
vcv.phylo vcv2phylo weight.taxo
TRUE TRUE TRUE
weight.taxo2 where which.edge
TRUE TRUE TRUE
write.dna write.evonet write.FASTA
TRUE TRUE TRUE
write.nexus write.nexus.data write.phyloXML
TRUE TRUE TRUE
write.tree Xplor Xplorefiles
TRUE TRUE TRUE
yule yule.cov yule.time
TRUE TRUE TRUE
zoom
TRUE Examples
There are 186 help pages with examples, from 187 (99.47 %).
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 13:09:29 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
/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
DOTNET_SKIP_FIRST_TIME_EXPERIENCE
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EDGEWEBDRIVER /usr/local/share/edge_driver
EDITOR vi
GECKOWEBDRIVER /usr/local/share/gecko_driver
GHCUP_INSTALL_BASE_PREFIX
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GITHUB_ACTION __run
GITHUB_ACTION_REF
GITHUB_ACTION_REPOSITORY
GITHUB_ACTIONS true
GITHUB_ACTOR Gotfrid
GITHUB_ACTOR_ID 8464262
GITHUB_API_URL https://api.github.com
GITHUB_BASE_REF
GITHUB_ENV /home/runner/work/_temp/_runner_file_commands/set_env_6c58152c-b416-4447-903d-6ecbe5b48c52
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GITHUB_HEAD_REF
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GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_6c58152c-b416-4447-903d-6ecbe5b48c52
GITHUB_REF refs/heads/main
GITHUB_REF_NAME main
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 13457382637
GITHUB_RUN_NUMBER 101
GITHUB_SERVER_URL https://github.com
GITHUB_SHA 9d087537577b11dd985321646640fd8d289e4b89
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_6c58152c-b416-4447-903d-6ecbe5b48c52
GITHUB_TRIGGERING_ACTOR
Gotfrid
GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA 9d087537577b11dd985321646640fd8d289e4b89
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
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HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
ImageVersion 20250209.1.0
INVOCATION_ID 679c817089664dfd9a72db0ab1acdb0b
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 8:5789
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 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/RtmpfZnwFR
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1d0a462364a2_1740143366
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/RtmpvG3CPZ
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 6
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_9041cca5-17dd-4550-aa4d-6d44b1df7fc9
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 836
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: 0x56058b9c1910>
<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
[1] "default"
$deparse.cutoff
[1] 60
$device
function (width = 7, height = 7, ...)
{
grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x56058b084a48>
<environment: namespace:knitr>
$device.ask.default
[1] FALSE
$digits
[1] 7
$dvipscmd
[1] "dvips"
$echo
[1] FALSE
$editor
[1] "vi"
$encoding
[1] "native.enc"
$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
[1] "R/4.4.2 R (4.4.2 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions"
$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
[1] "na.omit"
$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: 0x56058ae99520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_ape_v5.8.1-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