Validation Report - beautier@2.6.12
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 beautier
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 537 |
| has_vignettes | 19 |
| export_help | 537 |
| has_website | TRUE |
| has_maintainer | Richèl J.C. Bilderbeek rjcbilderbeek@gmail.com |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/ropensci/beautier |
| has_bug_reports_url | 1 |
| downloads_1yr | 6759 |
| reverse_dependencies | 5 |
| has_examples | 1 |
| dependencies | 6 |
| 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 | ape | Imports |
| 2 | rappdirs | Imports |
| 3 | purrr | Imports |
| 4 | rlang (>= 1.1.0) | Imports |
| 5 | seqinr | Imports |
| 6 | stringr | Imports |
Package dependencies
Reverse dependencies
Overall the package has 5 reverse dependencies:
babette, beastier, mauricer, mcbette, nodeSub
Namespace
Overall the package has 537 exported objects. 537 are documented:
alpha_parameter_to_xml
TRUE
are_clock_models
TRUE
are_equal_mcmcs
TRUE
are_equal_screenlogs
TRUE
are_equal_tracelogs
TRUE
are_equal_treelogs
TRUE
are_equal_xml_files
TRUE
are_equal_xml_lines
TRUE
are_equivalent_xml_files
TRUE
are_equivalent_xml_lines
TRUE
are_equivalent_xml_lines_all
TRUE
are_equivalent_xml_lines_loggers
TRUE
are_equivalent_xml_lines_operators
TRUE
are_equivalent_xml_lines_section
TRUE
are_fasta_filenames
TRUE
are_ids
TRUE
are_init_clock_models
TRUE
are_init_mrca_priors
TRUE
are_init_site_models
TRUE
are_init_tree_priors
TRUE
are_mrca_align_ids_in_fasta
TRUE
are_mrca_priors
TRUE
are_mrca_taxon_names_in_fasta
TRUE
are_rln_clock_models
TRUE
are_site_models
TRUE
are_tree_priors
TRUE
b_pop_sizes_param_to_xml
TRUE
b_pop_sizes_parameter_to_xml
TRUE
bd_tree_prior_to_xml_prior_distr
TRUE
beta_parameter_to_xml
TRUE
cbs_tree_prior_to_xml_prior_distr
TRUE
ccp_tree_prior_to_xml_prior_distr
TRUE
ccp_tree_prior_to_xml_state
TRUE
cep_tree_prior_to_xml_prior_distr
TRUE
check_alignment_id
TRUE
check_beauti_options
TRUE
check_clock_model
TRUE
check_clock_models
TRUE
check_empty_beautier_folder
TRUE
check_file_and_model_agree
TRUE
check_file_exists
TRUE
check_filename
TRUE
check_gamma_site_model
TRUE
check_gamma_site_model_names
TRUE
check_gtr_site_model
TRUE
check_gtr_site_model_names
TRUE
check_inference_model
TRUE
check_inference_models
TRUE
check_is_monophyletic
TRUE
check_log_mode
TRUE
check_log_sort
TRUE
check_mcmc
TRUE
check_mcmc_list_element_names
TRUE
check_mcmc_nested_sampling
TRUE
check_mcmc_values
TRUE
check_mrca_prior
TRUE
check_mrca_prior_name
TRUE
check_mrca_prior_names
TRUE
check_mrca_prior_taxa_names
TRUE
check_nested_sampling_mcmc
TRUE
check_ns_mcmc
TRUE
check_param
TRUE
check_param_names
TRUE
check_param_types
TRUE
check_phylogeny
TRUE
check_rename_fun
TRUE
check_rln_clock_model
TRUE
check_screenlog
TRUE
check_screenlog_names
TRUE
check_screenlog_values
TRUE
check_site_model
TRUE
check_site_model_names
TRUE
check_site_model_types
TRUE
check_site_models
TRUE
check_store_every
TRUE
check_strict_clock_model
TRUE
check_tn93_site_model
TRUE
check_tn93_site_model_names
TRUE
check_tracelog
TRUE
check_tracelog_names
TRUE
check_tracelog_values
TRUE
check_tree_prior
TRUE
check_tree_priors
TRUE
check_treelog
TRUE
check_treelog_names
TRUE
check_treelog_values
TRUE
clock_model_to_xml_operators
TRUE
clock_model_to_xml_prior_distr
TRUE
clock_model_to_xml_state
TRUE
clock_model_to_xml_tracelog
TRUE
clock_model_to_xml_treelogger
TRUE
clock_rate_param_to_xml
TRUE
compare_lines
TRUE
count_trailing_spaces
TRUE
create_alpha_param
TRUE
create_b_pop_sizes_param
TRUE
create_bd_tree_prior
TRUE
create_beast2_beast_xml
TRUE
create_beast2_input
TRUE
create_beast2_input_beast
TRUE
create_beast2_input_data
TRUE
create_beast2_input_data_sequences
TRUE
create_beast2_input_distr
TRUE
create_beast2_input_distr_lh
TRUE
create_beast2_input_distr_prior
TRUE
create_beast2_input_file
TRUE
create_beast2_input_file_from_model
TRUE
create_beast2_input_from_model
TRUE
create_beast2_input_init
TRUE
create_beast2_input_map
TRUE
create_beast2_input_operators
TRUE
create_beast2_input_run
TRUE
create_beast2_input_state
TRUE
create_beauti_options
TRUE
create_beauti_options_v2_4
TRUE
create_beauti_options_v2_6
TRUE
create_beautier_tempfolder
TRUE
create_beta_distr
TRUE
create_beta_param
TRUE
create_branch_rate_model_xml
TRUE
create_cbs_tree_prior
TRUE
create_ccp_tree_prior
TRUE
create_cep_tree_prior
TRUE
create_clock_model
TRUE
create_clock_model_from_name
TRUE
create_clock_model_rln
TRUE
create_clock_model_strict
TRUE
create_clock_models
TRUE
create_clock_models_from_names
TRUE
create_clock_rate_param
TRUE
create_clock_rate_state_node_parameter_xml
TRUE
create_data_xml
TRUE
create_distr
TRUE
create_distr_beta
TRUE
create_distr_exp
TRUE
create_distr_gamma
TRUE
create_distr_inv_gamma
TRUE
create_distr_laplace
TRUE
create_distr_log_normal
TRUE
create_distr_normal
TRUE
create_distr_one_div_x
TRUE
create_distr_poisson
TRUE
create_distr_uniform
TRUE
create_exp_distr
TRUE
create_freq_param
TRUE
create_gamma_distr
TRUE
create_gamma_site_model
TRUE
create_gtr_site_model
TRUE
create_gtr_subst_model_xml
TRUE
create_hky_site_model
TRUE
create_hky_subst_model_xml
TRUE
create_inference_model
TRUE
create_inv_gamma_distr
TRUE
create_jc69_site_model
TRUE
create_jc69_subst_model_xml
TRUE
create_kappa_1_param
TRUE
create_kappa_2_param
TRUE
create_kappa_param
TRUE
create_lambda_param
TRUE
create_laplace_distr
TRUE
create_log_normal_distr
TRUE
create_loggers_xml
TRUE
create_m_param
TRUE
create_mcmc
TRUE
create_mcmc_nested_sampling
TRUE
create_mean_param
TRUE
create_mrca_prior
TRUE
create_mu_param
TRUE
create_normal_distr
TRUE
create_ns_inference_model
TRUE
create_ns_mcmc
TRUE
create_one_div_x_distr
TRUE
create_param
TRUE
create_param_alpha
TRUE
create_param_b_pop_sizes
TRUE
create_param_beta
TRUE
create_param_clock_rate
TRUE
create_param_freq
TRUE
create_param_kappa
TRUE
create_param_kappa_1
TRUE
create_param_kappa_2
TRUE
create_param_lambda
TRUE
create_param_m
TRUE
create_param_mean
TRUE
create_param_mu
TRUE
create_param_rate_ac
TRUE
create_param_rate_ag
TRUE
create_param_rate_at
TRUE
create_param_rate_cg
TRUE
create_param_rate_ct
TRUE
create_param_rate_gt
TRUE
create_param_s
TRUE
create_param_scale
TRUE
create_param_sigma
TRUE
create_poisson_distr
TRUE
create_rate_ac_param
TRUE
create_rate_ag_param
TRUE
create_rate_at_param
TRUE
create_rate_categories_state_node_xml
TRUE
create_rate_cg_param
TRUE
create_rate_ct_param
TRUE
create_rate_gt_param
TRUE
create_rln_clock_branch_rate_model_xml
TRUE
create_rln_clock_model
TRUE
create_s_param
TRUE
create_scale_param
TRUE
create_screenlog
TRUE
create_screenlog_xml
TRUE
create_sigma_param
TRUE
create_site_model
TRUE
create_site_model_from_name
TRUE
create_site_model_gtr
TRUE
create_site_model_hky
TRUE
create_site_model_jc69
TRUE
create_site_model_parameters_xml
TRUE
create_site_model_tn93
TRUE
create_site_model_xml
TRUE
create_site_models
TRUE
create_site_models_from_names
TRUE
create_strict_clock_branch_rate_model_xml
TRUE
create_strict_clock_model
TRUE
create_strict_clock_rate_scaler_operator_xml
TRUE
create_subst_model_xml
TRUE
create_temp_screenlog_filename
TRUE
create_temp_tracelog_filename
TRUE
create_temp_treelog_filename
TRUE
create_test_inference_model
TRUE
create_test_mcmc
TRUE
create_test_ns_inference_model
TRUE
create_test_ns_mcmc
TRUE
create_test_screenlog
TRUE
create_test_tracelog
TRUE
create_test_treelog
TRUE
create_tn93_site_model
TRUE
create_tn93_subst_model_xml
TRUE
create_tracelog
TRUE
create_tracelog_xml
TRUE
create_trait_set_string
TRUE
create_tree_likelihood_distr_xml
TRUE
create_tree_prior
TRUE
create_tree_prior_bd
TRUE
create_tree_prior_cbs
TRUE
create_tree_prior_ccp
TRUE
create_tree_prior_cep
TRUE
create_tree_prior_yule
TRUE
create_tree_priors
TRUE
create_treelog
TRUE
create_treelog_xml
TRUE
create_ucld_mean_state_node_param_xml
TRUE
create_ucld_stdev_state_node_param_xml
TRUE
create_uniform_distr
TRUE
create_xml_declaration
TRUE
create_yule_tree_prior
TRUE
distr_to_xml
TRUE
distr_to_xml_beta
TRUE
distr_to_xml_exp
TRUE
distr_to_xml_inv_gamma
TRUE
distr_to_xml_laplace
TRUE
distr_to_xml_log_normal
TRUE
distr_to_xml_normal
TRUE
distr_to_xml_one_div_x
TRUE
distr_to_xml_poisson
TRUE
distr_to_xml_uniform
TRUE
extract_xml_loggers_from_lines
TRUE
extract_xml_operators_from_lines
TRUE
extract_xml_section_from_lines
TRUE
fasta_file_to_sequences
TRUE
find_clock_model
TRUE
find_first_regex_line
TRUE
find_first_xml_opening_tag_line
TRUE
find_last_regex_line
TRUE
find_last_xml_closing_tag_line
TRUE
freq_equilibrium_to_xml
TRUE
freq_param_to_xml
TRUE
gamma_distr_to_xml
TRUE
gamma_site_model_to_xml_prior_distr
TRUE
gamma_site_model_to_xml_state
TRUE
gamma_site_models_to_xml_prior_distr
TRUE
get_alignment_id
TRUE
get_alignment_ids
TRUE
get_alignment_ids_from_fasta_filenames
TRUE
get_beautier_folder
TRUE
get_beautier_path
TRUE
get_beautier_paths
TRUE
get_beautier_tempfilename
TRUE
get_clock_model_name
TRUE
get_clock_model_names
TRUE
get_clock_models_ids
TRUE
get_crown_age
TRUE
get_default_beast_namespace
TRUE
get_default_beast_namespace_v2_4
TRUE
get_default_beast_namespace_v2_6
TRUE
get_distr_n_params
TRUE
get_distr_names
TRUE
get_fasta_filename
TRUE
get_file_base_sans_ext
TRUE
get_freq_equilibrium_names
TRUE
get_gamma_site_model_n_distrs
TRUE
get_gamma_site_model_n_params
TRUE
get_has_non_strict_clock_model
TRUE
get_inference_model_filenames
TRUE
get_log_modes
TRUE
get_log_sorts
TRUE
get_mcmc_filenames
TRUE
get_n_taxa
TRUE
get_operator_id_pre
TRUE
get_param_names
TRUE
get_remove_dir_fun
TRUE
get_remove_hex_fun
TRUE
get_replace_dir_fun
TRUE
get_site_model_n_distrs
TRUE
get_site_model_n_params
TRUE
get_site_model_names
TRUE
get_site_models_n_distrs
TRUE
get_site_models_n_params
TRUE
get_taxa_names
TRUE
get_tree_prior_n_distrs
TRUE
get_tree_prior_n_params
TRUE
get_tree_prior_names
TRUE
get_tree_priors_n_distrs
TRUE
get_tree_priors_n_params
TRUE
get_xml_closing_tag
TRUE
get_xml_opening_tag
TRUE
gtr_site_model_to_xml_prior_distr
TRUE
gtr_site_model_to_xml_state
TRUE
has_mrca_prior
TRUE
has_mrca_prior_with_distr
TRUE
has_rln_clock_model
TRUE
has_strict_clock_model
TRUE
has_tip_dating
TRUE
has_xml_closing_tag
TRUE
has_xml_opening_tag
TRUE
has_xml_short_closing_tag
TRUE
hky_site_model_to_xml_prior_distr
TRUE
hky_site_model_to_xml_state
TRUE
indent
TRUE
init_bd_tree_prior
TRUE
init_beta_distr
TRUE
init_ccp_tree_prior
TRUE
init_cep_tree_prior
TRUE
init_clock_models
TRUE
init_distr
TRUE
init_exp_distr
TRUE
init_gamma_distr
TRUE
init_gamma_site_model
TRUE
init_gtr_site_model
TRUE
init_hky_site_model
TRUE
init_inference_model
TRUE
init_inv_gamma_distr
TRUE
init_jc69_site_model
TRUE
init_laplace_distr
TRUE
init_log_normal_distr
TRUE
init_mrca_prior
TRUE
init_mrca_priors
TRUE
init_normal_distr
TRUE
init_one_div_x_distr
TRUE
init_param
TRUE
init_poisson_distr
TRUE
init_rln_clock_model
TRUE
init_site_models
TRUE
init_strict_clock_model
TRUE
init_tn93_site_model
TRUE
init_tree_priors
TRUE
init_uniform_distr
TRUE
init_yule_tree_prior
TRUE
interspace
TRUE
is_alpha_param
TRUE
is_b_pop_sizes_param
TRUE
is_bd_tree_prior
TRUE
is_beauti_options
TRUE
is_beta_distr
TRUE
is_beta_param
TRUE
is_cbs_tree_prior
TRUE
is_ccp_tree_prior
TRUE
is_cep_tree_prior
TRUE
is_clock_model
TRUE
is_clock_model_name
TRUE
is_clock_rate_param
TRUE
is_default_mcmc
TRUE
is_distr
TRUE
is_distr_name
TRUE
is_exp_distr
TRUE
is_freq_equilibrium_name
TRUE
is_freq_param
TRUE
is_gamma_distr
TRUE
is_gamma_site_model
TRUE
is_gtr_site_model
TRUE
is_hky_site_model
TRUE
is_id
TRUE
is_in_patterns
TRUE
is_inference_model
TRUE
is_init_bd_tree_prior
TRUE
is_init_beta_distr
TRUE
is_init_cbs_tree_prior
TRUE
is_init_ccp_tree_prior
TRUE
is_init_cep_tree_prior
TRUE
is_init_clock_model
TRUE
is_init_distr
TRUE
is_init_exp_distr
TRUE
is_init_gamma_distr
TRUE
is_init_gamma_site_model
TRUE
is_init_gtr_site_model
TRUE
is_init_hky_site_model
TRUE
is_init_inv_gamma_distr
TRUE
is_init_jc69_site_model
TRUE
is_init_laplace_distr
TRUE
is_init_log_normal_distr
TRUE
is_init_mrca_prior
TRUE
is_init_normal_distr
TRUE
is_init_one_div_x_distr
TRUE
is_init_param
TRUE
is_init_poisson_distr
TRUE
is_init_rln_clock_model
TRUE
is_init_site_model
TRUE
is_init_strict_clock_model
TRUE
is_init_tn93_site_model
TRUE
is_init_tree_prior
TRUE
is_init_uniform_distr
TRUE
is_init_yule_tree_prior
TRUE
is_inv_gamma_distr
TRUE
is_jc69_site_model
TRUE
is_kappa_1_param
TRUE
is_kappa_2_param
TRUE
is_kappa_param
TRUE
is_lambda_param
TRUE
is_laplace_distr
TRUE
is_log_normal_distr
TRUE
is_m_param
TRUE
is_mcmc
TRUE
is_mcmc_nested_sampling
TRUE
is_mean_param
TRUE
is_mrca_align_id_in_fasta
TRUE
is_mrca_align_ids_in_fastas
TRUE
is_mrca_prior
TRUE
is_mrca_prior_with_distr
TRUE
is_mu_param
TRUE
is_nested_sampling_mcmc
TRUE
is_normal_distr
TRUE
is_on_appveyor
TRUE
is_on_ci
TRUE
is_on_github_actions
TRUE
is_on_travis
TRUE
is_one_bool
TRUE
is_one_div_x_distr
TRUE
is_one_double
TRUE
is_one_empty_string
TRUE
is_one_int
TRUE
is_one_na
TRUE
is_one_string
TRUE
is_one_string_that_is_a_number
TRUE
is_param
TRUE
is_param_name
TRUE
is_phylo
TRUE
is_poisson_distr
TRUE
is_rate_ac_param
TRUE
is_rate_ag_param
TRUE
is_rate_at_param
TRUE
is_rate_cg_param
TRUE
is_rate_ct_param
TRUE
is_rate_gt_param
TRUE
is_rln_clock_model
TRUE
is_s_param
TRUE
is_scale_param
TRUE
is_sigma_param
TRUE
is_site_model
TRUE
is_site_model_name
TRUE
is_strict_clock_model
TRUE
is_tn93_site_model
TRUE
is_tree_prior
TRUE
is_tree_prior_name
TRUE
is_uniform_distr
TRUE
is_xml
TRUE
is_yule_tree_prior
TRUE
jc69_site_model_to_xml_state
TRUE
kappa_param_to_xml
TRUE
m_param_to_xml
TRUE
mcmc_to_xml_run
TRUE
mcmc_to_xml_run_default
TRUE
mcmc_to_xml_run_nested_sampling
TRUE
mrca_prior_to_xml_prior_distr
TRUE
mrca_prior_to_xml_state
TRUE
mrca_prior_to_xml_taxonset
TRUE
mrca_prior_to_xml_tracelog
TRUE
mrca_priors_to_xml_prior_distr
TRUE
no_taxa_to_xml_tree
TRUE
parameter_to_xml
TRUE
parameter_to_xml_kappa_1
TRUE
parameter_to_xml_kappa_2
TRUE
parameter_to_xml_lambda
TRUE
parameter_to_xml_mean
TRUE
parameter_to_xml_mu
TRUE
parameter_to_xml_rate_ac
TRUE
parameter_to_xml_rate_ag
TRUE
parameter_to_xml_rate_at
TRUE
parameter_to_xml_rate_cg
TRUE
parameter_to_xml_rate_ct
TRUE
parameter_to_xml_rate_gt
TRUE
parameter_to_xml_scale
TRUE
parameter_to_xml_sigma
TRUE
remove_beautier_folder
TRUE
remove_empty_lines
TRUE
remove_multiline
TRUE
rename_inference_model_filenames
TRUE
rename_mcmc_filenames
TRUE
rln_clock_model_to_xml_mean_rate_prior
TRUE
rln_clock_model_to_xml_operators
TRUE
rln_clock_model_to_xml_prior_distr
TRUE
rln_clock_model_to_xml_state
TRUE
rln_clock_model_to_xml_tracelog
TRUE
rnd_phylo_to_xml_init
TRUE
s_parameter_to_xml
TRUE
site_model_to_xml_operators
TRUE
site_model_to_xml_prior_distr
TRUE
site_model_to_xml_state
TRUE
site_model_to_xml_tracelog
TRUE
site_models_to_xml_operators
TRUE
site_models_to_xml_prior_distr
TRUE
site_models_to_xml_tracelog
TRUE
strict_clock_model_to_xml_operators
TRUE
strict_clock_model_to_xml_prior_distr
TRUE
strict_clock_model_to_xml_state
TRUE
strict_clock_model_to_xml_tracelog
TRUE
taxa_to_xml_tree
TRUE
tipdate_taxa_to_xml_trait
TRUE
tipdate_taxa_to_xml_tree
TRUE
tn93_site_model_to_xml_prior_distr
TRUE
tn93_site_model_to_xml_state
TRUE
tree_model_to_tracelog_xml
TRUE
tree_prior_to_xml_operators
TRUE
tree_prior_to_xml_prior_distr
TRUE
tree_prior_to_xml_state
TRUE
tree_prior_to_xml_tracelog
TRUE
tree_priors_to_xml_prior_distr
TRUE
tree_priors_to_xml_tracelog
TRUE
unindent
TRUE
yule_tree_prior_to_xml_operators
TRUE
yule_tree_prior_to_xml_prior_distr
TRUE Examples
There are 493 help pages with examples, from 493 (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 | 2025-02-15 03:50:40 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
/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
/usr/local/lib/android/sdk/ndk/27.2.12479018
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
0
DOTNET_NOLOGO 1
DOTNET_SKIP_FIRST_TIME_EXPERIENCE
1
EDGEWEBDRIVER /usr/local/share/edge_driver
EDITOR vi
GECKOWEBDRIVER /usr/local/share/gecko_driver
GHCUP_INSTALL_BASE_PREFIX
/usr/local
GITHUB_ACTION __run
GITHUB_ACTION_REF
GITHUB_ACTION_REPOSITORY
GITHUB_ACTIONS true
GITHUB_ACTOR llrs-roche
GITHUB_ACTOR_ID 185338939
GITHUB_API_URL https://api.github.com
GITHUB_BASE_REF
GITHUB_ENV /home/runner/work/_temp/_runner_file_commands/set_env_f8c509ad-0cb5-478b-b30f-5ae6b6902174
GITHUB_EVENT_NAME schedule
GITHUB_EVENT_PATH /home/runner/work/_temp/_github_workflow/event.json
GITHUB_GRAPHQL_URL https://api.github.com/graphql
GITHUB_HEAD_REF
GITHUB_JOB main
GITHUB_OUTPUT /home/runner/work/_temp/_runner_file_commands/set_output_f8c509ad-0cb5-478b-b30f-5ae6b6902174
GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_f8c509ad-0cb5-478b-b30f-5ae6b6902174
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
42115094
GITHUB_RETENTION_DAYS 90
GITHUB_RUN_ATTEMPT 1
GITHUB_RUN_ID 13341233413
GITHUB_RUN_NUMBER 92
GITHUB_SERVER_URL https://github.com
GITHUB_SHA 0c0fc0bc0d98c42191882830260da9dad887eea6
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_f8c509ad-0cb5-478b-b30f-5ae6b6902174
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_f8c509ad-0cb5-478b-b30f-5ae6b6902174
GITHUB_TRIGGERING_ACTOR
llrs-roche
GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA 0c0fc0bc0d98c42191882830260da9dad887eea6
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
3650
HOMEBREW_NO_AUTO_UPDATE
1
ImageOS ubuntu24
ImageVersion 20250209.1.0
INVOCATION_ID 5c7bed78c97148e29cb0b195c5a78088
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 8:8239
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 1000
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/Rtmpxlc1zI
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1ccd8857a93_1739591435
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/RtmpXA1w2A
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 8
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_4fe491a9-475c-47ca-863f-ba9d90fd5980
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 830
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: 0x563f54a49910>
<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: 0x563f54a79c98>
<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: 0x563f53f21520>
$str.dendrogram.last
[1] "`"
$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
[1] "validation_report_beautier_v2.6.12-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