NEWS.md
In richelbilderbeek/beautier: 'BEAUti' from R
News
Newest versions at top.
beautier v2.6.12 (2024-04-01)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Remove dependency on 'spelling'
BUG FIXES
DEPRECATED AND DEFUNCT
- None
beautier v2.6.11 (2023-11-02)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- CRAN version
- Improved documentation
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.10 (2023-11-02)
NEW FEATURES
- Remove dependency on 'assertive'
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.9 (2023-09-25)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use new CITATION style
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.8 (2023-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Did
usethis::use_package_doc()
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.8 (2023-08-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
create_strict_clock_model can also create a strict model from
only a string (conversion from a double was already supported)create_mean_param can also create a mean parameter from
only a string (conversion from a double was already supported)- Add
get_default_beast_namespace_v2_4 and get_default_beast_namespace_v2_6,
to work well with create_beauti_options_v2_4 and create_beauti_options_v2_6
respectively
BUG FIXES
- Strict clock model's clock rate can have a normal distribution, #138
DEPRECATED AND DEFUNCT
- None
beautier v2.6.7 (2023-04-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- The clock rate distribution of a strict clock model can be set
DEPRECATED AND DEFUNCT
- None
beautier v2.6.6 (2023-03-14)
NEW FEATURES
- Add
create_freq_param/create_param_freq for the GTR, HKY and TN93 site models
- Add
create_kappa_param/create_param_kappa for the HKY site model
- Add
is_freq_param for the GTR, HKY and TN93 site models
- Add
is_kappa_param for the HKY site model
- The clock rate of a strict clock model can be estimated
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
create_hky_site_model does not have kappa as an argument anymore:
use kappa_param instead. Using kappa gives a proper deprecation message
beautier v2.6.5 (2022-08-11)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Doc does not link to absent functions
- No tests take more than 5 seconds on CRAN infrastructure
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Removed functions that were deprecated in v2.6.4
beautier v2.6.4 (2022-06-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- There is no 'beautier' temporary folder created by the tests, not the
examples, to comply with CRAN policy
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.3 (2022-05-18)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- At the end of the tests, delete the 'beautier' temporary folder, thanks Brian Ripley
DEPRECATED AND DEFUNCT
- Filenames cannot have spaces
beautier v2.6.2 (2021-07-24)
NEW FEATURES
- None
MINOR IMPROVEMENTS
check_empty_beautier_folder works correctly on Windows
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.1 (2021-07-23)
NEW FEATURES
- Added
check_empty_beautier_folder to make sure
no temporary files are created
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Removed all deprecated functions and function arguments
that warn the user in the current CRAN version (v2.6)
- Internal functions
clock_model_to_xml_prior_distr,
tipdate_taxa_to_xml_tree, tree_priors_to_xml_operators
work with infererence_model,
deprecated other arguments
- Deprecated internal function
clock_models_to_xml_prior_distr,
redirect user to clock_model_to_xml_prior_distr
- Deprecated internal function
tree_priors_to_xml_operators,
redirect user to tree_prior_to_xml_operators
- Deprecated
clock_models_to_xml_state,
redirect user to clock_model_to_xml_state
- Deprecated
clock_models_to_xml_operators,
redirect user to clock_model_to_xml_operators
- Deprecated
clock_models_to_xml_tracelog,
redirect user to clock_model_to_xml_tracelog
- Deprecated
mrca_priors_to_xml_tracelog,
redirect user to mrca_prior_to_xml_tracelog
- Deprecated
tree_models_to_xml_tracelog,
redirect user to tree_model_to_tracelog_xml
beautier v2.6 (2021-05-22)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Make sure that no files are created in
~/.cache, fix #129
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.5.2 (2021-05-22)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Removed
LazyData: true from DESCRIPTION
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.5.1 (2021-05-22)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- GitHub Actions scheduler tests package once per week
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.5 (2021-05-14)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use GitHub Actions to check build
- Check more setups, thanks @GaryNapier
- Better synergy with
system2
BUG FIXES
- None
DEPRECATED AND DEFUNCT
phylo_to_xml_state removed site_models_to_xml_state gives a deprecation messagetree_priors_to_xml_state gives a deprecation messagemrca_priors_to_xml_state has the arguments mrca_prior
and has_non_strict_clock_model replaced by inference_model
beautier v2.4 (2020-10-15)
NEW FEATURES
- Add
inference_models vignette
MINOR IMPROVEMENTS
- Added
create_ns_inference_model
- No
testthat tests in examples
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.7 (2020-08-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Internal functions have better names
- More internal functions use an
inference_model (instead of
multiple elements of it)
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.6 (2020-04-21)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Fix bug when using tipdating, thanks Katherine S. Walter, @ksw9
DEPRECATED AND DEFUNCT
- None
beautier v2.3.5 (2020-02-25)
NEW FEATURES
- Add
get_mcmc_filenames and get_inference_model_filenames
- Add
rename_mcmc_filenames and rename_inference_model_filenames
- Add rename functions
get_remove_dir_fun, get_remove_hex_fun and get_replace_dir_fun
MINOR IMPROVEMENTS
- Link to https of BEAST2
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.4 (2020-01-15)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Lost dependency on orphaned
geiger package
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Moved
fasta_to_phylo and fastas_to_phylos to repository at
https://github.com/richelbilderbeek/ribir to lose dependency on
orphaned geiger package
beautier v2.3.3 (2019-12-26)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Implemented all @lintr-bot's suggestions
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.2 (2019-11-30)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Remove files for CRAN submission
DEPRECATED AND DEFUNCT
- None
beautier v2.3.1 (2019-11-29)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use
testthat in documentation, instead of the less known testit
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3 (2019-10-27)
NEW FEATURES
- Added
create_tracelog, create_screenlog, create_treelog, that
indicate where BEAST2 will store its output file
create_mcmc has all elements that BEAUti has- Added testing functions, that use a short MCMC chain length and/or
a simple inference model:
create_test_mcmc, create_test_tracelog,
create_test_screenlog, create_test_treelog
and create_test_inference_model
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.4 (2019-10-15)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Added
create_beast2_input_from_model function
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.3 (2019-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Added
check_mcmc_nested_sampling function
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.2 (2019-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Exported and documented more
is_ functions
- Added
check_file_exists function
- Added
is_one_int and is_one_double functions
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.1 (2019-03-08)
NEW FEATURES
beautier has passed rOpenSci peer reviewbeautier is on CRAN
MINOR IMPROVEMENTS
- Exported multiple
is_x and check_x functions
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.15 (2018-11-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Correct BEAST2 files are created when using a RLN clock
model, with an MRCA prior with a distribution, thanks @rscherrer
and Jana Riederer
DEPRECATED AND DEFUNCT
- Support for multiple alignments, site models, clock models,
tree models has decreased
beautier 1.14.2 (2018-10-30)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Tested to build under macOS
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.14.1 (2018-10-29)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Documented the simplified interface for parameters better
- Use the simplified interface for parameters as defaults more often
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.14.0 (2018-10-26)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Simplified interface for parameters:
# Old
distr <- create_distr_poisson(id = 1, lambda = create_lambda_param(value = 1.2))
# Added
distr <- create_distr_poisson(id = 1, lambda = 1.2)
BUG FIXES
- When using MRCA priors with/without monophyly with/without
a distribution, resulted in incorrect BEAST2
.xml files
DEPRECATED AND DEFUNCT
- Cannot set parameters to be estimated, when the resulting
BEAST2
.xml would be incomplete
beautier 1.13.4 (2018-09-11)
NEW FEATURES
- Support for a Nested-Sampling MCMC run
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.13.3 (2018-05-17)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Tagged for the academic article about
babette
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.13.2 (2018-04-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Follow all rOpenSci packaging guidelines
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
richelbilderbeek/beautier documentation built on April 4, 2024, 12:33 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
News
Newest versions at top.
beautier v2.6.12 (2024-04-01)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Remove dependency on 'spelling'
BUG FIXES
DEPRECATED AND DEFUNCT
- None
beautier v2.6.11 (2023-11-02)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- CRAN version
- Improved documentation
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.10 (2023-11-02)
NEW FEATURES
- Remove dependency on 'assertive'
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.9 (2023-09-25)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use new CITATION style
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.8 (2023-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Did
usethis::use_package_doc()
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.8 (2023-08-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
create_strict_clock_modelcan also create a strict model from only a string (conversion from a double was already supported)create_mean_paramcan also create a mean parameter from only a string (conversion from a double was already supported)- Add
get_default_beast_namespace_v2_4andget_default_beast_namespace_v2_6, to work well withcreate_beauti_options_v2_4andcreate_beauti_options_v2_6respectively
BUG FIXES
- Strict clock model's clock rate can have a normal distribution, #138
DEPRECATED AND DEFUNCT
- None
beautier v2.6.7 (2023-04-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- The clock rate distribution of a strict clock model can be set
DEPRECATED AND DEFUNCT
- None
beautier v2.6.6 (2023-03-14)
NEW FEATURES
- Add
create_freq_param/create_param_freqfor the GTR, HKY and TN93 site models - Add
create_kappa_param/create_param_kappafor the HKY site model - Add
is_freq_paramfor the GTR, HKY and TN93 site models - Add
is_kappa_paramfor the HKY site model - The clock rate of a strict clock model can be estimated
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
create_hky_site_modeldoes not havekappaas an argument anymore: usekappa_paraminstead. Usingkappagives a proper deprecation message
beautier v2.6.5 (2022-08-11)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Doc does not link to absent functions
- No tests take more than 5 seconds on CRAN infrastructure
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Removed functions that were deprecated in v2.6.4
beautier v2.6.4 (2022-06-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- There is no 'beautier' temporary folder created by the tests, not the examples, to comply with CRAN policy
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.3 (2022-05-18)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- At the end of the tests, delete the 'beautier' temporary folder, thanks Brian Ripley
DEPRECATED AND DEFUNCT
- Filenames cannot have spaces
beautier v2.6.2 (2021-07-24)
NEW FEATURES
- None
MINOR IMPROVEMENTS
check_empty_beautier_folderworks correctly on Windows
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.6.1 (2021-07-23)
NEW FEATURES
- Added
check_empty_beautier_folderto make sure no temporary files are created
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Removed all deprecated functions and function arguments that warn the user in the current CRAN version (v2.6)
- Internal functions
clock_model_to_xml_prior_distr,tipdate_taxa_to_xml_tree,tree_priors_to_xml_operatorswork withinfererence_model, deprecated other arguments - Deprecated internal function
clock_models_to_xml_prior_distr, redirect user toclock_model_to_xml_prior_distr - Deprecated internal function
tree_priors_to_xml_operators, redirect user totree_prior_to_xml_operators - Deprecated
clock_models_to_xml_state, redirect user toclock_model_to_xml_state - Deprecated
clock_models_to_xml_operators, redirect user toclock_model_to_xml_operators - Deprecated
clock_models_to_xml_tracelog, redirect user toclock_model_to_xml_tracelog - Deprecated
mrca_priors_to_xml_tracelog, redirect user tomrca_prior_to_xml_tracelog - Deprecated
tree_models_to_xml_tracelog, redirect user totree_model_to_tracelog_xml
beautier v2.6 (2021-05-22)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Make sure that no files are created in
~/.cache, fix #129
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.5.2 (2021-05-22)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Removed
LazyData: truefrom DESCRIPTION
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.5.1 (2021-05-22)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- GitHub Actions scheduler tests package once per week
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.5 (2021-05-14)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use GitHub Actions to check build
- Check more setups, thanks @GaryNapier
- Better synergy with
system2
BUG FIXES
- None
DEPRECATED AND DEFUNCT
phylo_to_xml_stateremovedsite_models_to_xml_stategives a deprecation messagetree_priors_to_xml_stategives a deprecation messagemrca_priors_to_xml_statehas the argumentsmrca_priorandhas_non_strict_clock_modelreplaced byinference_model
beautier v2.4 (2020-10-15)
NEW FEATURES
- Add
inference_modelsvignette
MINOR IMPROVEMENTS
- Added
create_ns_inference_model - No
testthattests in examples
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.7 (2020-08-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Internal functions have better names
- More internal functions use an
inference_model(instead of multiple elements of it)
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.6 (2020-04-21)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Fix bug when using tipdating, thanks Katherine S. Walter, @ksw9
DEPRECATED AND DEFUNCT
- None
beautier v2.3.5 (2020-02-25)
NEW FEATURES
- Add
get_mcmc_filenamesandget_inference_model_filenames - Add
rename_mcmc_filenamesandrename_inference_model_filenames - Add rename functions
get_remove_dir_fun,get_remove_hex_funandget_replace_dir_fun
MINOR IMPROVEMENTS
- Link to https of BEAST2
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.4 (2020-01-15)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Lost dependency on orphaned
geigerpackage
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- Moved
fasta_to_phyloandfastas_to_phylosto repository athttps://github.com/richelbilderbeek/ribirto lose dependency on orphanedgeigerpackage
beautier v2.3.3 (2019-12-26)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Implemented all @lintr-bot's suggestions
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3.2 (2019-11-30)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Remove files for CRAN submission
DEPRECATED AND DEFUNCT
- None
beautier v2.3.1 (2019-11-29)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Use
testthatin documentation, instead of the less knowntestit
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.3 (2019-10-27)
NEW FEATURES
- Added
create_tracelog,create_screenlog,create_treelog, that indicate where BEAST2 will store its output file create_mcmchas all elements that BEAUti has- Added testing functions, that use a short MCMC chain length and/or
a simple inference model:
create_test_mcmc,create_test_tracelog,create_test_screenlog,create_test_treelogandcreate_test_inference_model
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.4 (2019-10-15)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Added
create_beast2_input_from_modelfunction
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.3 (2019-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Added
check_mcmc_nested_samplingfunction
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.2 (2019-09-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Exported and documented more
is_functions - Added
check_file_existsfunction - Added
is_one_intandis_one_doublefunctions
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier v2.2.1 (2019-03-08)
NEW FEATURES
beautierhas passed rOpenSci peer reviewbeautieris on CRAN
MINOR IMPROVEMENTS
- Exported multiple
is_xandcheck_xfunctions
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.15 (2018-11-10)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- None
BUG FIXES
- Correct BEAST2 files are created when using a RLN clock model, with an MRCA prior with a distribution, thanks @rscherrer and Jana Riederer
DEPRECATED AND DEFUNCT
- Support for multiple alignments, site models, clock models, tree models has decreased
beautier 1.14.2 (2018-10-30)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Tested to build under macOS
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.14.1 (2018-10-29)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Documented the simplified interface for parameters better
- Use the simplified interface for parameters as defaults more often
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.14.0 (2018-10-26)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Simplified interface for parameters:
# Old
distr <- create_distr_poisson(id = 1, lambda = create_lambda_param(value = 1.2))
# Added
distr <- create_distr_poisson(id = 1, lambda = 1.2)
BUG FIXES
- When using MRCA priors with/without monophyly with/without
a distribution, resulted in incorrect BEAST2
.xmlfiles
DEPRECATED AND DEFUNCT
- Cannot set parameters to be estimated, when the resulting
BEAST2
.xmlwould be incomplete
beautier 1.13.4 (2018-09-11)
NEW FEATURES
- Support for a Nested-Sampling MCMC run
MINOR IMPROVEMENTS
- None
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.13.3 (2018-05-17)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Tagged for the academic article about
babette
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
beautier 1.13.2 (2018-04-05)
NEW FEATURES
- None
MINOR IMPROVEMENTS
- Follow all rOpenSci packaging guidelines
BUG FIXES
- None
DEPRECATED AND DEFUNCT
- None
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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