Validation Report - Claddis@0.7.0
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 Claddis
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 88 |
| has_vignettes | 0 |
| export_help | 88 |
| has_website | FALSE |
| has_maintainer | Graeme T. Lloyd graemetlloyd@gmail.com |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_bug_reports_url | 0 |
| downloads_1yr | 6414 |
| reverse_dependencies | 1 |
| has_examples | 0.967033 |
| dependencies | 12 |
| 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 | Depends |
| 2 | phytools | Depends |
| 3 | strap | Depends |
| 4 | clipr | Imports |
| 5 | geoscale | Imports |
| 6 | graphics | Imports |
| 7 | grDevices | Imports |
| 8 | methods | Imports |
| 9 | multicool | Imports |
| 10 | partitions | Imports |
| 11 | stats | Imports |
| 12 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 1 reverse dependencies:
dispRity
Namespace
Overall the package has 88 exported objects. 88 are documented:
add_polymorphisms_to_costmatrix add_uncertainties_to_costmatrix
TRUE TRUE
align_matrix_block assign_taxa_to_bins
TRUE TRUE
bin_changes bin_character_completeness
TRUE TRUE
bin_edge_lengths build_cladistic_matrix
TRUE TRUE
calculate_g calculate_gmax
TRUE TRUE
calculate_kardashian_index calculate_morphological_distances
TRUE TRUE
calculate_MPD calculate_tree_length
TRUE TRUE
calculate_WMPD check_cladisticMatrix
TRUE TRUE
check_costMatrix check_stateGraph
TRUE TRUE
check_taxonGroups check_timeBins
TRUE TRUE
classify_costmatrix compactify_cladistic_matrix
TRUE TRUE
convert_adjacency_matrix_to_costmatrix convert_costmatrix_to_stategraph
TRUE TRUE
convert_state_tree_to_adjacency_matrix convert_stategraph_to_costmatrix
TRUE TRUE
count_cherries date_nodes
TRUE TRUE
drop_time_tip estimate_ancestral_states
TRUE TRUE
estimate_squared_change_ancestors find_costmatrix_minimum_span
TRUE TRUE
find_descendant_edges find_linked_edges
TRUE TRUE
find_minimum_spanning_edges find_mrca
TRUE TRUE
find_shortest_costmatrix_path find_stategraph_minimum_span
TRUE TRUE
find_time_bin_midpoints find_unique_trees
TRUE TRUE
fix_costmatrix fix_root_time
TRUE TRUE
is_graph_connected is.cladisticMatrix
TRUE TRUE
is.costMatrix is.stateGraph
TRUE TRUE
is.taxonGroups is.timeBins
TRUE TRUE
locate_bracket_positions make_costmatrix
TRUE TRUE
make_labels map_dollo_changes
TRUE TRUE
match_tree_edges ordinate_cladistic_matrix
TRUE TRUE
partition_time_bins permute_all_polymorphisms
TRUE TRUE
permute_all_treeshape_labellings permute_all_uncertainties
TRUE TRUE
permute_connected_graphs permute_costmatrices
TRUE TRUE
permute_graph_splits permute_restricted_compositions
TRUE TRUE
permute_tipstates permute_treeshapes
TRUE TRUE
plot_changes_on_tree plot_chronophylomorphospace
TRUE TRUE
plot_morphospace plot_morphospace_stack
TRUE TRUE
plot_multi_morphospace plot_rates_character
TRUE TRUE
plot_rates_time plot_rates_tree
TRUE TRUE
print.cladisticMatrix print.costMatrix
TRUE TRUE
print.stateGraph print.taxonGroups
TRUE TRUE
print.timeBins prune_cladistic_matrix
TRUE TRUE
read_nexus_matrix reconstruct_ancestral_states
TRUE TRUE
safe_taxonomic_reduction safe_taxonomic_reinsertion
TRUE TRUE
split_out_subgraphs test_rates
TRUE TRUE
trim_marginal_whitespace trim_matrix
TRUE TRUE
write_nexus_matrix write_tnt_matrix
TRUE TRUE Examples
There are 88 help pages with examples, from 91 (96.70 %).
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 | 2025-02-16 04:25:29 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_1.8.9
[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
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xz
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libdeflate
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PCRE
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ICU
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TRE
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iconv
"glibc 2.39"
readline
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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
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double.neg.ulp.digits double.exponent double.min.exp
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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
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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
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PHARMAPKGS_EXCLUDED_METRICS
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TZ UTC
USER runner
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XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
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$callr.condition_handler_cli_message
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<bytecode: 0x5652e40be910>
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