Validation Report - aqp@2.1.0
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 aqp
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 165 |
| has_vignettes | 14 |
| export_help | 242 |
| has_website | TRUE |
| has_maintainer | Dylan Beaudette dylan.beaudette@usda.gov |
| bugs_status | subscript out of bounds |
| size_codebase | 11536 |
| has_source_control | https://github.com/ncss-tech/aqp |
| has_bug_reports_url | 1 |
| downloads_1yr | 26337 |
| reverse_dependencies | 2 |
| has_examples | 1 |
| dependencies | 11 |
| license | 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 | grDevices | Imports |
| 2 | graphics | Imports |
| 3 | stats | Imports |
| 4 | utils | Imports |
| 5 | methods | Imports |
| 6 | grid | Imports |
| 7 | lattice | Imports |
| 8 | cluster | Imports |
| 9 | stringr | Imports |
| 10 | data.table | Imports |
| 11 | farver | Imports |
Package dependencies
Reverse dependencies
Overall the package has 2 reverse dependencies:
soilassessment, soilDB
Namespace
Overall the package has 165 exported objects. 237 are documented:
accumulateDepths addBracket
TRUE TRUE
addDiagnosticBracket addVolumeFraction
TRUE TRUE
aggregateColor aggregateSoilDepth
TRUE TRUE
alignTransect allocate
TRUE TRUE
aqp.env argillic.clay.increase.depth
TRUE TRUE
barron.torrent.redness.LAB bootstrapSoilTexture
TRUE TRUE
brierScore buntley.westin.index
TRUE TRUE
checkHzDepthLogic checkSPC
TRUE TRUE
col2Munsell collapseHz
TRUE TRUE
colorChart colorContrast
TRUE TRUE
colorContrastPlot colorQuantiles
TRUE TRUE
compareSites compositeSPC
TRUE TRUE
confusionIndex contrastChart
TRUE TRUE
contrastClass correctAWC
TRUE TRUE
crit.clay.argillic denormalize
TRUE TRUE
depthOf depthWeights
TRUE TRUE
dissolve_hz duplicate
TRUE TRUE
electroStatics_1D equivalentMunsellChips
TRUE TRUE
estimateAWC estimatePSCS
TRUE TRUE
estimateSoilColor estimateSoilDepth
TRUE TRUE
evalGenHZ evalMissingData
TRUE TRUE
explainPlotSPC fillHzGaps
TRUE TRUE
findOverlap fixOverlap
TRUE TRUE
flagOverlappingHz fragmentClasses
TRUE TRUE
fragmentSieve fragvol_to_texmod
TRUE TRUE
generalize.hz genhzTableToAdjMat
TRUE TRUE
genSlabLabels get.increase.depths
TRUE TRUE
get.increase.matrix get.ml.hz
TRUE TRUE
get.slice getArgillicBounds
TRUE TRUE
getCambicBounds getClosestMunsellChip
TRUE TRUE
getLastHorizonID getMineralSoilSurfaceDepth
TRUE TRUE
getPlowLayerDepth getSoilDepthClass
TRUE TRUE
getSurfaceHorizonDepth glom
TRUE TRUE
glomApply grepSPC
TRUE TRUE
groupedProfilePlot groupSPC
TRUE TRUE
guessGenHzLevels guessHzAttrName
TRUE TRUE
guessHzDesgnName guessHzTexClName
TRUE TRUE
harden.melanization harden.rubification
TRUE TRUE
hasDarkColors horizonColorIndices
TRUE TRUE
huePosition huePositionCircle
TRUE TRUE
hurst.redness hz_dissolve
TRUE TRUE
hz_intersect hz_lag
TRUE TRUE
hz_segment hz_to_taxpartsize
TRUE TRUE
hzAbove hzBelow
TRUE TRUE
HzDepthLogicSubset hzDepthTests
TRUE TRUE
hzDistinctnessCodeToOffset hzOffset
TRUE TRUE
hzTopographyCodeToLineType hzTopographyCodeToOffset
TRUE TRUE
hzTransitionProbabilities invertLabelColor
TRUE TRUE
L1_profiles lookup_taxpartsize
TRUE TRUE
lunique maxDepthOf
TRUE TRUE
minDepthOf missingDataGrid
TRUE TRUE
mixMunsell mollic.thickness.requirement
TRUE TRUE
mostLikelyHzSequence munsell2rgb
TRUE TRUE
mutate_profile mutate_profile_raw
TRUE TRUE
NCSP overlapMetrics
TRUE TRUE
panel.depth_function parseMunsell
TRUE TRUE
pbindlist pc
TRUE TRUE
pc.SPC perturb
TRUE TRUE
ph_to_rxnclass plot_distance_graph
TRUE TRUE
plotColorMixture plotColorQuantiles
TRUE TRUE
plotMultipleSPC plotSPC
TRUE TRUE
prepanel.depth_function previewColors
TRUE TRUE
profileGroupLabels profileInformationIndex
TRUE TRUE
quickSPC random_profile
TRUE TRUE
ReactionClassLevels rebuildSPC
TRUE TRUE
reduceSPC repairMissingHzDepths
TRUE TRUE
rgb2munsell rxnclass_to_ph
TRUE TRUE
SANN_1D segment
TRUE TRUE
shannonEntropy sim
TRUE TRUE
simulateColor slab_function
TRUE TRUE
slice.fast slicedHSD
TRUE TRUE
soilColorSignature soilPalette
TRUE TRUE
SoilProfileCollection soilTextureColorPal
TRUE TRUE
SoilTextureLevels spc_in_sync
TRUE TRUE
spec2Munsell splitLogicErrors
TRUE TRUE
ssc_to_texcl subApply
TRUE TRUE
summarizeSPC summaryTauW
TRUE TRUE
tauW texcl_to_ssc
TRUE TRUE
texmod_to_fragvoltot texture_to_taxpartsize
TRUE TRUE
texture_to_texmod textureTriangleSummary
TRUE TRUE
thicknessOf thompson.bell.darkness
TRUE TRUE
unroll warpHorizons
TRUE TRUE
xtableTauW
TRUE Examples
There are 214 help pages with examples, from 214 (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 | 2025-02-14 07:19:59 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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GITHUB_TRIGGERING_ACTOR
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HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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PHARMAPKGS_LIMIT 500
PHARMAPKGS_PLATFORM ubuntu-22.04
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PHARMAPKGS_REMOTE_REPO
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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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R_UNZIPCMD /usr/bin/unzip
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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:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
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$browserNLdisabled
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$callr.condition_handler_cli_message
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<bytecode: 0x55af342de910>
<environment: namespace:cli>
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$rlang_trace_top_env
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