Package binman. January 14, 2017
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1 Title A Binary Download Manager Version Package binman January 14, 2017 Tools and functions for managing the download of binary files. Binary repositories are defined in 'YAML' format. Defining new pre-download, download and post-download templates allow additional repositories to be added. Depends R (>= 3.3) License MIT + file LICENSE Encoding UTF-8 LazyData true Suggests testthat, covr, knitr, rmarkdown Imports rappdirs, yaml, httr, jsonlite, xml2, utils, stats, assertthat, semver URL URLNote BugReports RoxygenNote VignetteBuilder knitr NeedsCompilation no Author John Harrison [aut, cre] (R package binman) Maintainer John Harrison <johndharrison0@gmail.com> Repository CRAN Date/Publication :22:47 R topics documented: app_dir assign_directory binman
2 2 app_dir download_files list_versions noproc_dlfiles predl_bitbucket_downloads predl_github_assets predl_google_storage process_yaml rm_platform rm_version unziptar_dlfiles Index 13 app_dir Get application directory Get application directory app_dir(, check = TRUE) check A character string giving the name of the application check whether the app given by exists or not. A character string giving the path of the directory appdir <- app_dir("superduperapp", FALSE)
3 assign_directory 3 assign_directory Assign directory Assign directory to download list assign_directory(dllist, ) dllist A named list of data.frames. The name indicates the platform. The data.frame should contain the version, url and file to be processed. Name to give the app A named list of data.frames. The data.frame should contain the version, url and file to be processed, the directory to download the file to and whether the file already exists. tdata <- system.file("testdata", "test_dllist.rdata", package="binman") load(tdata) assign_directory(test_dllist, "myapp") binman binman. binman.
4 4 download_files download_files Download binaries Download binaries from repository download_files(dllist, overwrite = FALSE) dllist overwrite A named list of data.frames. The data.frame should contain the version, url and file to be processed, the directory to download the file to and whether the file already exists. Overwrite existing binaries. Default value of FALSE A data.frame indicating whether a file was downloaded for a platform. trdata <- system.file("testdata", "test_dlres.rdata", package="binman") tldata <- system.file("testdata", "test_dllist.rdata", package="binman") load(trdata) load(tldata) dllist <- assign_directory(test_dllist, "myapp") testthat::with_mock( httr::get = function(...){ test_llres }, base::dir.create = function(...){true}, dlfiles <- download_files(dllist) )
5 list_versions 5 list_versions List app versions List app versions by platform list_versions(, platform = c("all")) platform A character string giving the name of the application A character vector of platforms to list. Defaults to "ALL" A list of platforms with version directories appdir <- app_dir("superduperapp", FALSE) platforms <- LETTERS[1:4] versions <- LETTERS[5:7] mkdirs <- file.path(appdir, outer(platforms, versions, file.path)) chk <- vapply(mkdirs, dir.create, logical(1), recursive = TRUE) expect_true(all(chk)) res <- list_versions("superduperapp") unlink(appdir, recursive = TRUE) noproc_dlfiles Dont post process Dont post process dlfiles noproc_dlfiles(dlfiles)
6 6 predl_bitbucket_downloads dlfiles A data.frame of files by platform and indicating whether they were processed Returns a list of character vectors indicating files processed ymlfile <- system.file("exdata", "sampleapp4.yml", package="binman") trdata <- system.file("testdata", "test_dlres.rdata", package="binman") load(trdata) testthat::with_mock( httr::get = function(...){ test_llres }, base::dir.create = function(...){true}, procyml <- process_yaml(ymlfile) ) procyml predl_bitbucket_downloads Pre download bitbucket downloads Pre download bitbucket downloads template function predl_bitbucket_downloads(url, platform, history,, platformregex = platform, versionregex = "\\d+(?:\\.\\d+)+") url platform history platformregex versionregex A url giving the bitbucket download JSON for a project. As an example the phantomjs project has an asset JSON available at A character vector of platform names The maximum number of files to get for a platform Name of the app A filter for platforms. Defaults to the platform A regex for retrieving the version.
7 predl_github_assets 7 A named list of data.frames. The name indicates the platform. The data.frame should contain the version, url and file to be processed. Used as input for download_files or an equivalent. bbdata <- system.file("testdata", "test_bitbucketdl.json", package="binman") platform <- c("linux64", "linux32", "windows", "macosx") platformregex <- c("linux-x86_64", "linux-i686", "windows", "macosx") bbdllist <- predl_bitbucket_downloads(url = bbdata, platform, history = 3L, = "binman_chromedriver", platformregex) predl_github_assets Pre download Github assets Pre download Github assets template function predl_github_assets(url, platform, history,, platformregex = platform, versionregex = c("", "")) url platform history platformregex versionregex A url giving the github asset JSON for a project. As an example the geckodriver project has an asset JSON available at A character vector of platform names The maximum number of files to get for a platform Name of the app A filter for platforms. Defaults to the platform A regex for retrieving the version. A named list of data.frames. The name indicates the platform. The data.frame should contain the version, url and file to be processed. Used as input for download_files or an equivalent.
8 8 predl_google_storage gadata <- system.file("testdata", "test_gitassets.json", package="binman") platform <- c("linux64", "win64", "macos") gadllist <- predl_github_assets(url = gadata, platform, history = 3L, = "binman_chromedriver") predl_google_storage Pre-Download Google Storage Pre-Download Google Storage template function predl_google_storage(url, platform, history,, fileregex = "\\.zip$", platformregex = platform, versionregex = c(paste0("(.*)/.*", fileregex), "\\1")) url platform history fileregex platformregex versionregex A url giving the JSON bucket listings for a project. For example: lists the chromedriver files but is the JSON listings for the project. A character vector of platform names The maximum number of files to get for a platform Name of the app A filter for files A filter for platforms. Defaults to the platform names. A regex for retrieving the version. A named list of data.frames. The name indicates the platform. The data.frame should contain the version, url and file to be processed. Used as input for download_files or an equivalent.
9 process_yaml 9 gsdata <- system.file("testdata", "test_googstor.json", package="binman") platform <- c("linux64", "win32", "mac64") gsdllist <- predl_google_storage(url = gsdata, platform, history = 5L, = "binman_chromedriver") process_yaml Process a yaml file Process a yaml file. The file defines the pre-download function, the download function and the post download function. process_yaml(ymlfile, verbose = TRUE) ymlfile verbose A file in a YAML format defining the pre-download/ download and post download functions together with their arguments. If TRUE, include status messages (if any) A list of files processed (downloaded and post processed) ymlfile <- system.file("exdata", "sampleapp.yml", package="binman") trdata <- system.file("testdata", "test_dlres.rdata", package="binman") load(trdata) testthat::with_mock( httr::get = function(...){ test_llres }, base::dir.create = function(...){true}, utils::unzip = function(zipfile,...){zipfile}, procyml <- process_yaml(ymlfile) ) procyml
10 10 rm_version rm_platform Remove application platform Remove application files/directories for a given platform rm_platform(, platform = c("all")) platform A character string giving the name of the application A character vector indicating the platform to remove. Defaults to "ALL" Returns a logical vector indicating whether the removal of platform was successful. Return is invisible. appdir <- app_dir(, FALSE) platforms <- LETTERS[1:4] versions <- LETTERS[5:7] mkdirs <- file.path(appdir, outer(platforms, versions, file.path)) chk <- vapply(mkdirs, dir.create, logical(1), recursive = TRUE) appver <- list_versions() rm_platform(, platforms[2:3]) unlink(appdir, recursive = TRUE) rm_version Remove application version Remove application version for a given platform rm_version(, platform, version = c("all"))
11 unziptar_dlfiles 11 platform version A character string giving the name of the application A character string indicating the platform. A character vector of versions to remove. Defaults to "ALL" Returns a logical vector indicating whether the removal of version was successful. Return is invisible. appdir <- app_dir(, FALSE) platforms <- LETTERS[1:4] versions <- LETTERS[5:7] mkdirs <- file.path(appdir, outer(platforms, versions, file.path)) chk <- vapply(mkdirs, dir.create, logical(1), recursive = TRUE) appver <- list_versions() rm_version(, platforms[2], versions[1:2]) unlink(appdir, recursive = TRUE) unziptar_dlfiles Unzip/Untar downloaded files Unzip/Untar downloaded files. Keeps the original zip file unziptar_dlfiles(dlfiles, chmod = FALSE) dlfiles chmod A data.frame of files by platform and indicating whether they were processed change the mode of the unarchived file/files to "755" so they are executable on unix like systems. Returns a list of character vectors indicating files processed
12 12 unziptar_dlfiles ymlfile <- system.file("exdata", "sampleapp.yml", package="binman") trdata <- system.file("testdata", "test_dlres.rdata", package="binman") load(trdata) testthat::with_mock( httr::get = function(...){ test_llres }, base::dir.create = function(...){true}, utils::unzip = function(zipfile,...){zipfile}, procyml <- process_yaml(ymlfile) ) procyml
13 Index app_dir, 2 assign_directory, 3 binman, 3 binman-package (binman), 3 download_files, 4, 7, 8 list_versions, 5 noproc_dlfiles, 5 predl_bitbucket_downloads, 6 predl_github_assets, 7 predl_google_storage, 8 process_yaml, 9 rm_platform, 10 rm_version, 10 unziptar_dlfiles, 11 13
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Type Package Package oasis February 21, 2018 Title Multiple Sclerosis Lesion Segmentation using Magnetic Resonance Imaging (MRI) Version 3.0.4 Date 2018-02-20 Trains and makes predictions from the OASIS
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Type Package Title Read and Write 'MTrackJ Data Files' Version 0.2.0 Package mdftracks February 6, 2017 'MTrackJ' is an 'ImageJ' plugin for motion tracking and analysis (see ).
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Package bisect April 16, 2018 Title Estimating Cell Type Composition from Methylation Sequencing Data Version 0.9.0 Maintainer Eyal Fisher Author Eyal Fisher [aut, cre] An implementation
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Package barcoder October 26, 2018 Title Labelling, Tracking, and Collecting Data from Biological Samples Version 0.1.0 Maintainer Robert Colautti Tools to generate unique identifiers
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Package sfdct August 29, 2017 Title Constrained Triangulation for Simple Features Version 0.0.4 Build a constrained 'Delaunay' triangulation from simple features objects, applying constraints based on
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