Validation Report - castor@1.8.3
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 castor
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 138 |
| has_vignettes | 0 |
| export_help | 138 |
| has_website | FALSE |
| has_maintainer | Stilianos Louca louca.research@gmail.com |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_bug_reports_url | 0 |
| downloads_1yr | 21317 |
| reverse_dependencies | 7 |
| has_examples | 1 |
| dependencies | 9 |
| 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 | Rcpp (>= 0.12.10) | Depends |
| 2 | parallel | Imports |
| 3 | naturalsort | Imports |
| 4 | stats | Imports |
| 5 | Matrix | Imports |
| 6 | RSpectra | Imports |
| 7 | jsonlite | Imports |
| 8 | methods | Imports |
| 9 | Rcpp | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 7 reverse dependencies:
DAISIEprep, dispRity, LDM, nichevol, orthGS, phylosignalDB, treestats
Namespace
Overall the package has 138 exported objects. 138 are documented:
asr_empirical_probabilities asr_independent_contrasts
TRUE TRUE
asr_max_parsimony asr_mk_model
TRUE TRUE
asr_squared_change_parsimony asr_subtree_averaging
TRUE TRUE
clade_densities collapse_monofurcations
TRUE TRUE
collapse_tree_at_resolution congruent_divergence_times
TRUE TRUE
congruent_hbds_model consensus_taxonomies
TRUE TRUE
consentrait_depth correlate_phylo_geodistances
TRUE TRUE
count_lineages_through_time count_tips_per_node
TRUE TRUE
count_transitions_between_clades date_tree_red
TRUE TRUE
discrete_trait_depth evaluate_spline
TRUE TRUE
expanded_tree_from_jplace expanded_tree_from_jplace
TRUE TRUE
expected_distances_sbm exponentiate_matrix
TRUE TRUE
extend_tree_to_height extract_deep_frame
TRUE TRUE
extract_fasttree_constraints extract_tip_neighborhood
TRUE TRUE
extract_tip_radius find_farthest_tip_pair
TRUE TRUE
find_farthest_tips find_nearest_tips
TRUE TRUE
find_root find_root_of_monophyletic_tips
TRUE TRUE
fit_and_compare_bm_models fit_and_compare_sbm_const
TRUE TRUE
fit_bm_model fit_hbd_model_on_grid
TRUE TRUE
fit_hbd_model_parametric fit_hbd_pdr_on_best_grid_size
TRUE TRUE
fit_hbd_pdr_on_grid fit_hbd_pdr_parametric
TRUE TRUE
fit_hbd_psr_on_best_grid_size fit_hbd_psr_on_grid
TRUE TRUE
fit_hbd_psr_parametric fit_hbds_model_on_grid
TRUE TRUE
fit_hbds_model_parametric fit_mk
TRUE TRUE
fit_musse fit_sbm_const
TRUE TRUE
fit_sbm_geobiased_const fit_sbm_linear
TRUE TRUE
fit_sbm_on_grid fit_sbm_parametric
TRUE TRUE
fit_tree_model gamma_statistic
TRUE TRUE
generate_gene_tree_msc generate_gene_tree_msc_hgt_dl
TRUE TRUE
generate_random_tree generate_tree_hbd_reverse
TRUE TRUE
generate_tree_hbds generate_tree_with_evolving_rates
TRUE TRUE
geographic_acf get_all_distances_to_root
TRUE TRUE
get_all_distances_to_tip get_all_node_depths
TRUE TRUE
get_all_pairwise_distances get_ancestral_nodes
TRUE TRUE
get_clade_list get_independent_contrasts
TRUE TRUE
get_independent_sister_tips get_mrca_of_set
TRUE TRUE
get_pairwise_distances get_pairwise_mrcas
TRUE TRUE
get_random_diffusivity_matrix get_random_mk_transition_matrix
TRUE TRUE
get_reds get_stationary_distribution
TRUE TRUE
get_subtree_at_node get_subtree_with_tips
TRUE TRUE
get_subtrees_at_nodes get_tips_for_mrcas
TRUE TRUE
get_trait_acf get_trait_stats_over_time
TRUE TRUE
get_transition_index_matrix get_tree_span
TRUE TRUE
get_tree_traversal_root_to_tips hsp_binomial
TRUE TRUE
hsp_empirical_probabilities hsp_independent_contrasts
TRUE TRUE
hsp_max_parsimony hsp_mk_model
TRUE TRUE
hsp_nearest_neighbor hsp_squared_change_parsimony
TRUE TRUE
hsp_subtree_averaging is_bifurcating
TRUE TRUE
is_monophyletic join_rooted_trees
TRUE TRUE
loglikelihood_hbd map_to_state_space
TRUE TRUE
mean_abs_change_scalar_ou merge_nodes_to_multifurcations
TRUE TRUE
merge_short_edges model_adequacy_hbd
TRUE TRUE
model_adequacy_hbds multifurcations_to_bifurcations
TRUE TRUE
pick_random_tips place_tips_taxonomically
TRUE TRUE
read_fasta read_tree
TRUE TRUE
reconstruct_past_diversification reorder_tree_edges
TRUE TRUE
root_at_midpoint root_at_node
TRUE TRUE
root_in_edge root_via_outgroup
TRUE TRUE
root_via_rtt shift_clade_times
TRUE TRUE
simulate_bm_model simulate_deterministic_hbd
TRUE TRUE
simulate_deterministic_hbds simulate_diversification_model
TRUE TRUE
simulate_dsse simulate_mk_model
TRUE TRUE
simulate_musse simulate_ou_model
TRUE TRUE
simulate_rou_model simulate_sbm
TRUE TRUE
simulate_tdsse spline_coefficients
TRUE TRUE
split_tree_at_height tree_distance
TRUE TRUE
tree_from_branching_ages tree_from_sampling_branching_ages
TRUE TRUE
tree_from_taxa tree_imbalance
TRUE TRUE
trim_tree_at_height write_tree
TRUE TRUE Examples
There are 136 help pages with examples, from 136 (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 | 2025-02-16 03:45:37 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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ANT_HOME /usr/share/ant
AZURE_EXTENSION_DIR /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
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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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PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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YES
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QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
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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:
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$browser
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$callr.condition_handler_cli_message
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