Validation Report - AFM@2.0
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 AFM
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 96 |
| has_vignettes | 0 |
| export_help | 110 |
| has_website | FALSE |
| has_maintainer | Mathieu Beauvais beauvais.escp@gmail.com |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| size_codebase | 5576 |
| has_bug_reports_url | 0 |
| downloads_1yr | 4985 |
| reverse_dependencies | 0 |
| has_examples | 0.95 |
| dependencies | 21 |
| license | AGPL-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 | data.table(>= 1.9.6) | Imports |
| 2 | stringr(>= 1.0.0) | Imports |
| 3 | gstat(>= 1.0-26) | Imports |
| 4 | fractaldim(>= 0.8-4) | Imports |
| 5 | rgl(>= 0.96) | Imports |
| 6 | pracma(>= 1.8.6) | Imports |
| 7 | grid(>= 3.1.3) | Imports |
| 8 | gridExtra(>= 2.0.0) | Imports |
| 9 | moments(>= 0.14) | Imports |
| 10 | ggplot2(>= 1.0.1) | Imports |
| 11 | sp(>= 1.2-0) | Imports |
| 12 | png(>= 0.1-7) | Imports |
| 13 | plyr(>= 1.8.3) | Imports |
| 14 | igraph(>= 1.0.1) | Imports |
| 15 | methods(>= 3.1.3) | Imports |
| 16 | shiny(>= 0.12.2) | Imports |
| 17 | shinyjs(>= 0.4.0) | Imports |
| 18 | scales(>= 0.4.0) | Imports |
| 19 | dbscan(>= 0.9-8) | Imports |
| 20 | mixtools(>= 1.0.4) | Imports |
| 21 | fftwtools(>= 0.9-8) | Imports |
Package dependencies
Reverse dependencies
Overall the package has 0 reverse dependencies:
Namespace
Overall the package has 96 exported objects. 109 are documented:
AFMImage
TRUE
AFMImageAnalyser
TRUE
AFMImageFractalDimensionMethod
TRUE
AFMImageFractalDimensionsAnalysis
TRUE
AFMImageGaussianMixAnalysis
TRUE
AFMImageNetworksAnalysis
TRUE
AFMImagePSDAnalysis
TRUE
AFMImagePSDSlopesAnalysis
TRUE
AFMImageVariogramAnalysis
TRUE
AFMImageVariogramModel
TRUE
analyse
TRUE
AreNodesConnected
TRUE
calculateDirectionalVariograms
TRUE
calculateGaussianMixture
TRUE
calculateHolesCharacteristics
TRUE
calculateIgraph
TRUE
calculateNetworkParameters
TRUE
calculateNetworkSkeleton
TRUE
calculateOmnidirectionalVariogram
TRUE
calculatePhysicalDistanceFromPath
TRUE
calculateShortestPaths
TRUE
canBeRemoved
TRUE
checkIsotropy
TRUE
checkNormality
TRUE
createGraph
TRUE
displayColoredNetworkWithVerticesSize
TRUE
displaygridIgraphPlot
TRUE
displaygridIgraphPlotFromEdges
TRUE
displayHolesIn3D
TRUE
displayIn3D
TRUE
dnormalmix
TRUE
existsEdge
TRUE
existsSegment
TRUE
exportToSTL
TRUE
extractAFMImage
TRUE
filterAFMImage
TRUE
fusionCloseNodes
TRUE
generateAFMImageReport
TRUE
generateCheckReport
TRUE
generatePolygonEnvelope
TRUE
generateReport
TRUE
generateReportFromNanoscopeImageDirectory
TRUE
get3DImageFullfilename
TRUE
getAllPointsToRemove
TRUE
getAngle
TRUE
getAutoIntersectionForOmnidirectionalVariogram
TRUE
getAutoIntersectionForRoughnessAgainstLengthscale
TRUE
getAutomaticWidthForVariogramCalculation
TRUE
getBresenham2DSegment
TRUE
getCircleSpatialPoints
TRUE
getCoordinatesFromVertexId
TRUE
getFractalDimensions
TRUE
getHolesStatistics
TRUE
getIntersectionForRoughnessAgainstLengthscale
TRUE
getIntersectionPointWithBorder
TRUE
getListOfDiameters
TRUE
getLogLogOmnidirectionalSlopeGraph
TRUE
getMaxCircleMatrix
TRUE
getNetworkGridLayout
TRUE
getPaddedAFMImage
TRUE
getSpplotFromAFMImage
TRUE
getSurroundingVertexesList
TRUE
getTopologyAFMImage
TRUE
getTriangle
TRUE
getVertexId
TRUE
gridIgraphPlot
TRUE
identifyEdgesFromCircles
TRUE
identifyIsolatedNodes
TRUE
identifyNodesAndEdges
TRUE
identifyNodesWithCircles
TRUE
importFromNanoscope
TRUE
invertBinaryAFMImage
TRUE
isAdjacentToBetterVertex
TRUE
isAngleBetweenEdgesAlwaysSuperiorToMinAngle
TRUE
isBinary
TRUE
loglike.normalmix
TRUE
makeBinaryAFMImage
TRUE
multiplyHeightsAFMImage
TRUE
omniVariogramSlopeAnalysis
TRUE
performAllPSDCalculation
TRUE
performGaussianMixCalculation
TRUE
pnormmix
TRUE
printVariogramModelEvaluations
TRUE
putImagesFromAnalysisOnDisk
TRUE
runAFMApp
TRUE
sampleAFMImage
TRUE
saveOnDisk
TRUE
saveOnDiskIntersectionForRoughnessAgainstLengthscale
TRUE
saveSpplotFromAFMImage
TRUE
shiftedPSDuv
TRUE
shiftFFT2D
TRUE
simplifyAFMImage
TRUE
simplifyNetwork
TRUE
thinImage
TRUE
totalRMSRoughness
TRUE
updateProgress
TRUE Examples
There are 114 help pages with examples, from 120 (95.00 %).
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 06:41:32 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
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ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE
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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_REMOTE_REPO
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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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$add.smooth
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$bitmapType
[1] "cairo"
$browser
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$browserNLdisabled
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$callr.condition_handler_cli_message
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else {
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<bytecode: 0x55cf5d6fe910>
<environment: namespace:cli>
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<bytecode: 0x55cf5e836ea0>
<environment: namespace:knitr>
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$rl_word_breaks
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$rlang_trace_top_env
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$scipen
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$str$formatNum
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<environment: 0x55cf5cbd6520>
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$try.outFile
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can write "yes"
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