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JooYoung Seo
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Sep 6, 2019
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,82 +1,84 @@ | ||
| # getting some useful batch files for processing R scripts and Rmarkdown files. | ||
| # Windows users only | ||
|
|
||
| MakeBatch = | ||
| function(file = NULL) { | ||
| if (interactive()) { | ||
| MakeBatch = function(file = NULL) { | ||
| if (interactive()) { | ||
| if (.Platform$OS.type == "windows") { | ||
| RHome = gsub("/", "\\\\", Sys.getenv("R_HOME")) | ||
| if (is.null(file)) { | ||
| # write a batch file for processing R scripts | ||
| cat(paste0(RHome, "\\bin\\R.exe CMD BATCH --vanilla --quiet %1\n"), | ||
| file = "RBatch.bat") | ||
| message("RBatch.bat created successfully.") | ||
| # write a batch file for processing a specific R markdown file | ||
| cat(paste0(RHome, | ||
| "\\bin\\RScript.exe --vanilla -e \"rmarkdown::render('%1')\"\n"), | ||
| file = "RmdBatch.bat") | ||
| message("RmdBatch.bat created successfully.") | ||
| # write a batch file for processing all R markdown files | ||
| cat(paste0(RHome, '\\bin\\Rscript.exe --vanilla -e "BrailleR::ProcessAllRmd()"\n'), | ||
| file = "ProcessAllRmd.bat") | ||
| message("ProcessAllRmd.bat created successfully.") | ||
| # write a batch file for processing all markdown files | ||
| cat(paste0(RHome, '\\bin\\Rscript.exe --vanilla -e "BrailleR::ProcessAllMd()"\n'), | ||
| file = "ProcessAllMd.bat") | ||
| message("ProcessAllMd.bat created successfully.") | ||
| message( | ||
| "These files need to be moved to a folder that is on your system path.") | ||
| # write a file to show the system path settings | ||
| cat(Sys.getenv("PATH"), file = "path.txt") | ||
| message("These details are saved in path.txt for reference.") | ||
| # write a test Rmd file | ||
| cat("# a test file | ||
| RHome = gsub("/", "\\\\", Sys.getenv("R_HOME")) | ||
| if (is.null(file)) { | ||
|
|
||
| # Assign path depending upon system architecture | ||
| R_architecture <- Sys.info()[["machine"]] | ||
|
|
||
| if (R_architecture == "x86-64") { | ||
| R_path <- paste0(RHome, "\\bin\\x64\\") | ||
| } else { | ||
| R_path <- paste0(RHome, "\\bin\\") | ||
| } | ||
|
|
||
| # write a batch file for processing R scripts | ||
| cat(paste0("@echo off\n", R_path, "R.exe CMD BATCH --vanilla --quiet %1\nstart %~dp1\\%~n1.Rout\n"), | ||
| file = "RBatch.bat") | ||
| message("RBatch.bat created successfully.") | ||
| # write a batch file for processing a specific R markdown file | ||
| cat(paste0("@echo off\nSET \"string=%1\"\n\n", R_path, "RScript.exe --vanilla -e \"lapply(rmarkdown::render('%string:\\=/%', output_format = 'all'), utils::browseURL)\"\n"), | ||
| file = "RmdBatch.bat") | ||
| message("RmdBatch.bat created successfully.") | ||
| # write a batch file for processing all R markdown files | ||
| cat(paste0("@echo off\n", R_path, "Rscript.exe --vanilla -e \"BrailleR::ProcessAllRmd()\"\n"), | ||
| file = "ProcessAllRmd.bat") | ||
| message("ProcessAllRmd.bat created successfully.") | ||
| # write a batch file for processing all markdown files | ||
| cat(paste0("@echo off\n", R_path, "Rscript.exe --vanilla -e \"BrailleR::ProcessAllMd()\"\n"), | ||
| file = "ProcessAllMd.bat") | ||
| message("ProcessAllMd.bat created successfully.") | ||
| message("These files need to be moved to a folder that is on your system path.") | ||
| # write a file to show the system path settings | ||
| cat(Sys.getenv("PATH"), file = "path.txt") | ||
| message("These details are saved in path.txt for reference.") | ||
| # write a test Rmd file | ||
| cat("# a test file | ||
| ## created by the BrailleR package | ||
| My R version is `r version$major`.`r version$minor` and is being used to create this test file | ||
| It will then be used to process the test file later once the necessary actions are taken in Windows Explorer. \n", | ||
| file = "test1.Rmd") | ||
| message("test1.Rmd created successfully.") | ||
| MakeBatch("test1.Rmd") | ||
| # write a test R script | ||
| cat("# a test file | ||
| It will then be used to process the test file later once the necessary actions are taken in Windows Explorer. \n", | ||
| file = "test1.Rmd") | ||
| message("test1.Rmd created successfully.") | ||
| MakeBatch("test1.Rmd") | ||
| # write a test R script | ||
| cat("# a test file | ||
| ## created by the BrailleR package | ||
| MySample=sample(100, 10) | ||
| MySample | ||
| mean(MySample) \n", | ||
| file = "test2.R") | ||
| cat("test2.R created successfully.\n") | ||
| MakeBatch("test2.R") | ||
| message( | ||
| "Consult the help page for guidance on using these files in Windows Explorer.") | ||
| } else { | ||
| if (!file.exists(file)) | ||
| warning(paste0('The specified file "', file, | ||
| '" does not currently exist.\n')) | ||
| FullFile = unlist(strsplit(file, split = ".", fixed = TRUE)) | ||
| if (endsWith(file, ".R") | endsWith(file, ".r")) { | ||
| # write a batch file for processing the R script | ||
| cat(paste0(RHome, "\\bin\\R.exe CMD BATCH --vanilla --quiet ", | ||
| FullFile[1], ".R\n"), | ||
| file = paste0(FullFile[1], ".bat")) | ||
| message(FullFile[1], ".bat created successfully.") | ||
| mean(MySample) \n", | ||
| file = "test2.R") | ||
| cat("test2.R created successfully.\n") | ||
| MakeBatch("test2.R") | ||
| message("Consult the help page for guidance on using these files in Windows Explorer.") | ||
| } else { | ||
| if (!file.exists(file)) | ||
| warning(paste0("The specified file \"", file, "\" does not currently exist.\n")) | ||
| FullFile = unlist(strsplit(file, split = ".", fixed = TRUE)) | ||
| if (endsWith(file, ".R") | endsWith(file, ".r")) { | ||
| # write a batch file for processing the R script | ||
| cat(paste0(RHome, "\\bin\\R.exe CMD BATCH --vanilla --quiet ", | ||
| FullFile[1], ".R\n"), file = paste0(FullFile[1], ".bat")) | ||
| message(FullFile[1], ".bat created successfully.") | ||
| } | ||
| if (endsWith(file, ".Rmd") | endsWith(file, ".rmd")) { | ||
|
|
||
| # write a batch file for processing the R markdown file | ||
| cat(paste0(RHome, "\\bin\\RScript.exe -e \"rmarkdown::render('", | ||
| FullFile[1], ".Rmd')\"\n"), file = paste0(FullFile[1], ".bat")) | ||
| message(FullFile[1], ".bat created successfully.") | ||
| } | ||
| } | ||
| if (endsWith(file, ".Rmd") | endsWith(file, ".rmd")) { | ||
|
|
||
| # write a batch file for processing the R markdown file | ||
| cat(paste0(RHome, "\\bin\\RScript.exe -e \"rmarkdown::render('", | ||
| FullFile[1], ".Rmd')\"\n"), | ||
| file = paste0(FullFile[1], ".bat")) | ||
| message(FullFile[1], ".bat created successfully.") | ||
| } | ||
| } | ||
| } else { | ||
| warning( | ||
| "This function is for users running R under the Windows operating system.\n") | ||
| warning("This function is for users running R under the Windows operating system.\n") | ||
| } | ||
| } else { | ||
| } else { | ||
| warning("This function is meant for use in interactive mode only.\n") | ||
| } | ||
| return(invisible(NULL)) | ||
| } | ||
| return(invisible(NULL)) | ||
| } |
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@ajrgodfrey, please read the notes above.