Skip to content

Commit

Permalink
Release today
Browse files Browse the repository at this point in the history
  • Loading branch information
richelbilderbeek committed Sep 10, 2019
1 parent 4a97b8c commit 09d9ad3
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion NEWS.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

Newest versions at top.

## beastier 2.0.21 (unreleased)
## beastier 2.0.21 (2019-09-10)

### NEW FEATURES

Expand Down

8 comments on commit 09d9ad3

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/check_beast2_options.R:67:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_data_types <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:110:1: style: Variable and function names should not be longer than 30 characters.

​check_beast2_options_filenames_differ <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:151:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'input_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:154:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_log_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:157:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_trees_filenames'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check_beast2_options.R:160:1: style: Lines should not be more than 80 characters.

​    stop("'beast2_working_dir' must be a different folder than the folder of 'output_state_filename'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:12:1: style: Lines should not be more than 80 characters.

​#'    get_alignment_ids_from_xml_filename(get_beastier_path("anthus_15_15.xml")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_alignment_ids.R:17:1: style: Variable and function names should not be longer than 30 characters.

​get_alignment_ids_from_xml_filename <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:27:11: warning: no visible global function definition for ‘create_beast2_version_cmd’

​  cmds <- create_beast2_version_cmd(beast2_path)
          ^~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:32:5: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    {
    ^

R/get_beast2_version.R:69:5: style: Commented code should be removed.

​  # ./beast -version
    ^~~~~~~~~~~~~~~~

R/get_beast2_version.R:74:1: style: Lines should not be more than 80 characters.

​  # [java, -Xms8g, -Xms256m, -Djava.library.path=/usr/local/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib, -cp, ::/home/richel/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/richel/.beast/2.5/NS/lib/NS.addon.jar:/home/richel/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/richel/.beast/2.5/BEAST/lib/beast.jar:/home/richel/.beast/2.5/BEAST/lib/beast.src.jar, beast.app.beastapp.BeastMain, -version]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/get_beast2_version.R:76:24: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                       ^

R/get_beast2_version.R:76:39: style: Do not place spaces around code in parentheses or square brackets.

​  last_lines <- output[ length(output) ]
                                      ^

R/run_beast2.R:34:1: style: functions should have cyclomatic complexity of less than 15, this has 26.

​run_beast2 <- function(
^

R/upgrade_beast2.R:29:3: warning: no visible global function definition for ‘uninstall_beast2’

​  uninstall_beast2()
  ^~~~~~~~~~~~~~~~

R/upgrade_beast2.R:30:3: warning: no visible global function definition for ‘install_beast2’

​  install_beast2()
  ^~~~~~~~~~~~~~

tests/testthat/test-create_beast2_options.R:48:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test-create_beast2_options.R:49:1: style: Trailing blank lines are superfluous.

​
^

Please sign in to comment.