Package: W4MRUtils 1.0.0

W4MRUtils: Utils List for W4M - Workflow for Metabolomics

Provides a set of utility function to prevent the spread of utilities script in W4M (Workflow4Metabolomics) scripts, and centralize them in a single package. Some are meant to be replaced by real packages in a near future, like the parse_args() function: it is here only to prepare the ground for more global changes in W4M scripts and tools.

Authors:Lain Pavot [aut, cre], Melanie Petera [aut]

W4MRUtils_1.0.0.tar.gz
W4MRUtils_1.0.0.zip(r-4.5)W4MRUtils_1.0.0.zip(r-4.4)W4MRUtils_1.0.0.zip(r-4.3)
W4MRUtils_1.0.0.tgz(r-4.4-any)W4MRUtils_1.0.0.tgz(r-4.3-any)
W4MRUtils_1.0.0.tar.gz(r-4.5-noble)W4MRUtils_1.0.0.tar.gz(r-4.4-noble)
W4MRUtils_1.0.0.tgz(r-4.4-emscripten)W4MRUtils_1.0.0.tgz(r-4.3-emscripten)
W4MRUtils.pdf |W4MRUtils.html✨
W4MRUtils/json (API)

# Install 'W4MRUtils' in R:
install.packages('W4MRUtils', repos = c('https://lain-inrae.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.18 score 7 scripts 167 downloads 48 exports 1 dependencies

Last updated 1 years agofrom:d1533f3f57. Checks:OK: 3 ERROR: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winERRORNov 01 2024
R-4.5-linuxERRORNov 01 2024
R-4.4-winERRORNov 01 2024
R-4.4-macOKNov 01 2024
R-4.3-winERRORNov 01 2024
R-4.3-macOKNov 01 2024

Exports:check_errcheck_one_charactercheck_one_complexcheck_one_integercheck_one_logicalcheck_one_numericcheck_param_type_n_lengthcheck_parameter_lengthcheck_parameter_typecollapsecollapse_linesconvert_parametersdf_force_numericdf_isdf_read_tableget_base_dirget_loggerget_r_envimport2import3in_galaxy_envmatch2match3optparse_characteroptparse_flagoptparse_integeroptparse_listoptparse_numericoptparse_parametersparse_argsprintfprintfpprintpreproduce_idrun_galaxy_functionrun_galaxy_processingshow_galaxy_footershow_galaxy_headershow_sysshy_libsource_localstock_idstopastestopaste0stopfunmangle_galaxy_paramunmangle_galaxy_stringW4MLogger

Dependencies:rlang

logging

Rendered fromlogging.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-09-08
Started: 2023-09-08

parse_arguments

Rendered fromparse_arguments.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-09-08
Started: 2022-12-15

W4MRUtils

Rendered fromW4MRUtils.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-09-08
Started: 2022-12-15

Readme and manuals

Help Manual

Help pageTopics
Check Errorscheck_err
check_one_charactercheck_one_character
check_one_complexcheck_one_complex
check_one_integercheck_one_integer
check_one_logicalcheck_one_logical
check_one_numericcheck_one_numeric
check_param_type_n_length - to check parameterscheck_param_type_n_length
check_parameter_length - validate parameter's lengthcheck_parameter_length
check_parameter_type - validate parameter's typecheck_parameter_type
collapse - to paste strings with collapse = ""collapse
collapse_lines - to paste strings with collapse = "\n"collapse_lines
Convert Parametersconvert_parameters
Convert data frame to numeric.df_force_numeric
Test type of a data frame.df_is
Data frame loading from a file.df_read_table
get_base_dir - to get... the base directoryget_base_dir
Instantiate a Loggerget_logger
get_r_env - provides env vars begining with R_*get_r_env
Import two W4M tablesimport2
Import the three W4M tablesimport3
in_galaxy_env - check if the script has been run by galaxyin_galaxy_env
Table match check functionsmatch2
match3match3
Mini tools for Galaxy scriptingmini_tools
optparse_character - define a command parameter as stringoptparse_character
optparse_flag - define a command parameter as a triggeroptparse_flag
optparse_integer - define a command parameter as an integeroptparse_integer
optparse_list - define a command parameter as a list of objectsoptparse_list
optparse_numeric - define a command parameter as an numericoptparse_numeric
optparse_parameters - parse easily the command line parametersoptparse_parameters
Parse Command argumentsparse_args
printf - to format a string and print itprintf
printfp - to paste, format and print a stringprintfp
printp - to format a string and print itprintp
Reproduce IDreproduce_id
run_galaxy_function - automate running functions in galaxyrun_galaxy_function
run_galaxy_processing - automate running code in galaxyrun_galaxy_processing
show_galaxy_footer - shows the footer for glaxy toolsshow_galaxy_footer
show_galaxy_header - shows the header for glaxy toolsshow_galaxy_header
show_sys - prints env variables related to Rshow_sys
Shy Libshy_lib
source_local - source file, from absolute or relative pathsource_local
Stock IDstock_id
stopaste - to paste string to a message and stopstopaste
stopaste0 - to paste string to a message and stopstopaste0
stopf - to stop and format messagestopf
unmangle_galaxy_param - revert effects of galaxy manglings.unmangle_galaxy_param
unmangle_galaxy_string - revert effects of galaxy manglingunmangle_galaxy_string
The W4MLogger ClassW4MLogger
W4MLogger_.message__W4MLogger_.message__
Log info/warning/error/debug/verbose messagesW4MLogger$debug W4MLogger$error W4MLogger$info W4MLogger$verbose W4MLogger$warning W4MLogger_[info,warning,error,debug,verbose]
Adds a file where logs are duplicatedW4MLogger_add_out_paths
W4MLogger_finalizeW4MLogger_finalize
W4MLogger$set_debugW4MLogger_set_debug
W4MLogger$set_errorW4MLogger_set_error
W4MLogger$set_infoW4MLogger_set_info
Defines in which file logs are duplicatedW4MLogger_set_out_paths
W4MLogger$set_verboseW4MLogger_set_verbose
W4MLogger$set_warningW4MLogger_set_warning