diff --git a/.Rbuildignore b/.Rbuildignore index 94754f1..af59964 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -16,5 +16,6 @@ ^whirl.*\.tgz$ ^whirl\.Rcheck$ ^whirl\.Rproj$ +^înst/WORDLIST$ plot1.png summary.html diff --git a/DESCRIPTION b/DESCRIPTION index cdafabe..864ad01 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,7 @@ Authors@R: c( person("Vladimir", "Obucina", , email = "vlob@novonordisk.com", role = "aut"), person("Novo Nordisk A/S", role = "cph") ) -Description: Provides functionalities for running R scripts in batch, while simultanously creating logs for each script execution. +Description: Provides functionalities for running R scripts in batch, while simultaneously creating logs for each script execution. License: Apache License (>= 2) URL: https://novonordisk-opensource.github.io/whirl/, https://github.com/novonordisk-opensource/whirl Depends: diff --git a/R/options.R b/R/options.R index bde1593..91cda9a 100644 --- a/R/options.R +++ b/R/options.R @@ -11,7 +11,7 @@ NULL options::define_option( option = "out_formats", default = "html", - desc = "Which log format(s) to produce. Possiblities are `html`, `json`, and + desc = "Which log format(s) to produce. Possibilities are `html`, `json`, and markdown formats: `gfm`, `commonmark`, and `markua`." ) @@ -54,7 +54,7 @@ options::define_option( options::define_option( option = "track_files_keep", default = paste0("^", getwd()), - desc = "List of file naming patterns alway to be tracked when + desc = "List of file naming patterns always to be tracked when track_files = TRUE", envvar_fn = options::envvar_str_split(delim = ";") ) @@ -83,7 +83,7 @@ options::define_option( options::define_option( option = "n_workers", default = 1, - desc = "Number of simultanous workers used in the run function. + desc = "Number of simultaneous workers used in the run function. A maximum of 128 workers is allowed." ) @@ -91,7 +91,7 @@ options::define_option( option = "log_dir", default = dirname, desc = "The output directory of the log files. Default is the folder of the - excuted script. log_dir can be a path as a character or it can be a function + executed script. log_dir can be a path as a character or it can be a function that takes the script path as input and returns the log directory. For more information see the examples of `run()` or `vignette('whirl')`." ) @@ -100,7 +100,7 @@ options::define_option( option = "execute_dir", default = NULL, desc = "The working directory of the process executing each script. - Defeault us to execute R files from the working directory when calling `run()` + Default us to execute R files from the working directory when calling `run()` and all other functions from the directory of the script. To change provide a character path (used for all scripts) or a function that takes the script as input and returns the execution directory." diff --git a/inst/WORDLIST b/inst/WORDLIST index 8bb6690..141a446 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,5 +1,4 @@ Aksel -alway aut callr Cervan @@ -10,12 +9,9 @@ config Config cph cre -Defeault dev dir dplyr -exampel -excuted Falgreen Gakava getenv @@ -48,7 +44,6 @@ OpenSource overwritable PKGS pkgs -Possiblities pre purrr README @@ -63,8 +58,6 @@ RoxygenNote sessioninfo setenv sffl -simultanous -simultanously Steffen stringr Sys diff --git a/man/options.Rd b/man/options.Rd index 6741e55..56d31b2 100644 --- a/man/options.Rd +++ b/man/options.Rd @@ -21,7 +21,7 @@ options::opt(x, default, env = "whirl") \describe{ \item{out_formats}{\describe{ -Which log format(s) to produce. Possiblities are \code{html}, \code{json}, and +Which log format(s) to produce. Possibilities are \code{html}, \code{json}, and markdown formats: \code{gfm}, \code{commonmark}, and \code{markua}.\item{default: }{\preformatted{"html"}} \item{option: }{whirl.out_formats} \item{envvar: }{R_WHIRL_OUT_FORMATS (evaluated if possible, raw string otherwise)} @@ -48,7 +48,7 @@ List of file naming patterns not be tracked when track_files = TRUE\item{default }} \item{track_files_keep}{\describe{ -List of file naming patterns alway to be tracked when +List of file naming patterns always to be tracked when track_files = TRUE\item{default: }{\preformatted{paste0("^", getwd())}} \item{option: }{whirl.track_files_keep} \item{envvar: }{R_WHIRL_TRACK_FILES_KEEP (as character vector, split on ';' delimiter)} @@ -74,7 +74,7 @@ Approved URL library packages\item{default: }{\preformatted{NULL}} }} \item{n_workers}{\describe{ -Number of simultanous workers used in the run function. +Number of simultaneous workers used in the run function. A maximum of 128 workers is allowed.\item{default: }{\preformatted{1}} \item{option: }{whirl.n_workers} \item{envvar: }{R_WHIRL_N_WORKERS (evaluated if possible, raw string otherwise)} @@ -82,7 +82,7 @@ A maximum of 128 workers is allowed.\item{default: }{\preformatted{1}} \item{log_dir}{\describe{ The output directory of the log files. Default is the folder of the -excuted script. log_dir can be a path as a character or it can be a function +executed script. log_dir can be a path as a character or it can be a function that takes the script path as input and returns the log directory. For more information see the examples of \code{run()} or \code{vignette('whirl')}.\item{default: }{\preformatted{dirname}} \item{option: }{whirl.log_dir} @@ -91,7 +91,7 @@ For more information see the examples of \code{run()} or \code{vignette('whirl') \item{execute_dir}{\describe{ The working directory of the process executing each script. -Defeault us to execute R files from the working directory when calling \code{run()} +Default us to execute R files from the working directory when calling \code{run()} and all other functions from the directory of the script. To change provide a character path (used for all scripts) or a function that takes the script as input and returns the execution directory.\item{default: }{\preformatted{NULL}} diff --git a/man/options_params.Rd b/man/options_params.Rd index d9f35fe..99a89ba 100644 --- a/man/options_params.Rd +++ b/man/options_params.Rd @@ -8,15 +8,15 @@ \code{quiet}, \code{minimal} and \code{verbose}. (Defaults to \code{"verbose"}, overwritable using option 'whirl.verbosity_level' or environment variable 'R_WHIRL_VERBOSITY_LEVEL')} \item{log_dir}{The output directory of the log files. Default is the folder of the -excuted script. log_dir can be a path as a character or it can be a function +executed script. log_dir can be a path as a character or it can be a function that takes the script path as input and returns the log directory. For more information see the examples of \code{run()} or \code{vignette('whirl')}. (Defaults to \code{dirname}, overwritable using option 'whirl.log_dir' or environment variable 'R_WHIRL_LOG_DIR')} -\item{n_workers}{Number of simultanous workers used in the run function. +\item{n_workers}{Number of simultaneous workers used in the run function. A maximum of 128 workers is allowed. (Defaults to \code{1}, overwritable using option 'whirl.n_workers' or environment variable 'R_WHIRL_N_WORKERS')} \item{execute_dir}{The working directory of the process executing each script. -Defeault us to execute R files from the working directory when calling \code{run()} +Default us to execute R files from the working directory when calling \code{run()} and all other functions from the directory of the script. To change provide a character path (used for all scripts) or a function that takes the script as input and returns the execution directory. (Defaults to \code{NULL}, overwritable using option 'whirl.execute_dir' or environment variable 'R_WHIRL_EXECUTE_DIR')} @@ -26,14 +26,14 @@ as input and returns the execution directory. (Defaults to \code{NULL}, overwrit \item{track_files}{Should files read and written be tracked? Currently only supported on Linux. (Defaults to \code{FALSE}, overwritable using option 'whirl.track_files' or environment variable 'R_WHIRL_TRACK_FILES')} -\item{out_formats}{Which log format(s) to produce. Possiblities are \code{html}, \code{json}, and +\item{out_formats}{Which log format(s) to produce. Possibilities are \code{html}, \code{json}, and markdown formats: \code{gfm}, \code{commonmark}, and \code{markua}. (Defaults to \code{"html"}, overwritable using option 'whirl.out_formats' or environment variable 'R_WHIRL_OUT_FORMATS')} \item{approved_pkgs_folder}{Approved folder library packages (Defaults to \code{NULL}, overwritable using option 'whirl.approved_pkgs_folder' or environment variable 'R_WHIRL_APPROVED_PKGS_FOLDER')} \item{check_renv}{Should the projects renv status be checked? (Defaults to \code{FALSE}, overwritable using option 'whirl.check_renv' or environment variable 'R_WHIRL_CHECK_RENV')} -\item{track_files_keep}{List of file naming patterns alway to be tracked when +\item{track_files_keep}{List of file naming patterns always to be tracked when track_files = TRUE (Defaults to \code{paste0("^", getwd())}, overwritable using option 'whirl.track_files_keep' or environment variable 'R_WHIRL_TRACK_FILES_KEEP')} \item{approved_pkgs_url}{Approved URL library packages (Defaults to \code{NULL}, overwritable using option 'whirl.approved_pkgs_url' or environment variable 'R_WHIRL_APPROVED_PKGS_URL')} diff --git a/man/run.Rd b/man/run.Rd index f785d60..fa67137 100644 --- a/man/run.Rd +++ b/man/run.Rd @@ -31,7 +31,7 @@ then all steps listed in the config file will be executed.} \item{summary_file}{A character string specifying the file path where the summary log will be stored.} -\item{n_workers}{Number of simultanous workers used in the run function. +\item{n_workers}{Number of simultaneous workers used in the run function. A maximum of 128 workers is allowed. (Defaults to \code{1}, overwritable using option 'whirl.n_workers' or environment variable 'R_WHIRL_N_WORKERS')} \item{check_renv}{Should the projects renv status be checked? (Defaults to \code{FALSE}, overwritable using option 'whirl.check_renv' or environment variable 'R_WHIRL_CHECK_RENV')} @@ -42,11 +42,11 @@ A maximum of 128 workers is allowed. (Defaults to \code{1}, overwritable using o \item{track_files}{Should files read and written be tracked? Currently only supported on Linux. (Defaults to \code{FALSE}, overwritable using option 'whirl.track_files' or environment variable 'R_WHIRL_TRACK_FILES')} -\item{out_formats}{Which log format(s) to produce. Possiblities are \code{html}, \code{json}, and +\item{out_formats}{Which log format(s) to produce. Possibilities are \code{html}, \code{json}, and markdown formats: \code{gfm}, \code{commonmark}, and \code{markua}. (Defaults to \code{"html"}, overwritable using option 'whirl.out_formats' or environment variable 'R_WHIRL_OUT_FORMATS')} \item{log_dir}{The output directory of the log files. Default is the folder of the -excuted script. log_dir can be a path as a character or it can be a function +executed script. log_dir can be a path as a character or it can be a function that takes the script path as input and returns the log directory. For more information see the examples of \code{run()} or \code{vignette('whirl')}. (Defaults to \code{dirname}, overwritable using option 'whirl.log_dir' or environment variable 'R_WHIRL_LOG_DIR')} } diff --git a/man/whirl-package.Rd b/man/whirl-package.Rd index 782e7a3..9d4fecb 100644 --- a/man/whirl-package.Rd +++ b/man/whirl-package.Rd @@ -8,7 +8,7 @@ \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} -Provides functionalities for running R scripts in batch, while simultanously creating logs for each script execution. +Provides functionalities for running R scripts in batch, while simultaneously creating logs for each script execution. } \seealso{ Useful links: diff --git a/vignettes/whirl.Rmd b/vignettes/whirl.Rmd index a7a4dae..f73f88d 100644 --- a/vignettes/whirl.Rmd +++ b/vignettes/whirl.Rmd @@ -166,6 +166,6 @@ run( ) ``` -In this exampel the log of script1.R will be stored in **path/to/dir1/logs** and the log of script2.R will be stored in **path/to/dir2/logs**. +In this example the log of script1.R will be stored in **path/to/dir1/logs** and the log of script2.R will be stored in **path/to/dir2/logs**. Note that **x** refer to the path of the script that is being executed.