install.packages2 package:reposTools R Documentation _F_u_n_c_t_i_o_n_s _t_o _d_o_w_n_l_o_a_d, _i_n_s_t_a_l_l _a_n_d _m_a_n_i_p_u_l_a_t_e _l_o_c_a_l _p_a_c_k_a_g_e_s _D_e_s_c_r_i_p_t_i_o_n: These functions are designed to allow the user to install, update and download packages from R repositories, as well as remove packages from their local system. _U_s_a_g_e: install.packages2(pkgs = NULL, repEntry = NULL, lib, versions, type, method = "auto", theme= NULL, recurse = TRUE, searchOptions = FALSE, getNewest = TRUE, force = FALSE, versForce = TRUE, getAllDeps = FALSE, fileSelect = baseFileSelect, develOK=FALSE) update.packages2(pkgs = NULL, repEntry = NULL, theme = NULL, libs = reposToolsLibPaths(), type, method = "auto", prevRepos = TRUE, recurse = TRUE, searchOptions = FALSE, force = FALSE, versForce = TRUE, getAllDeps = FALSE, develOK=FALSE) remove.packages2(pkgs, lib, force=FALSE) _A_r_g_u_m_e_n_t_s: repEntry: A ReposEntry object specifying a particular repository pkgs: A character vector of package name(s) to act upon theme: A character vector of repository theme(s) to install versions: A character vector of version numbers for the packages lib: A path to install (or remove from) the package. If this directory does not exist, it will be created (if possible). If this directory is not in the user's current '.libPaths()', it will be added. libs: A set of library path(s) to search for packages to update prevRepos: Whether or not to update a package from the repository it was installed from force: Whether or not to ignore any dependencies fileSelect: Function to determine if a package needs updating or not recurse: Whether to search through subrepositories for desired packages type: The type of package to download/install/etc (e.g. Source, Win32, etc) searchOptions: Whether to search repositories listed in options("repositories") as well as specified repositories. Default is FALSE which means that if one specifies a repository, *only* that repository is used. If set to TRUE, and a user specifies a repository, then any repositories set in the user's options will also be used. versForce: Whether or not to override R version checking on binary packages getNewest: Whether or not to just get the newest available version of a package, or to provide alternate means (currently a menu selection) of obtaining a package install: Whether or not to install the downloaded package update: Whether to seek to update the package or simply install the requested version getAllDeps: Will automatically download all dependencies if TRUE, otherwise will prompt the user method: Defaults to "auto", identical to the same parameter used for 'download.file' develOK: Deprecated. If you wish to install development versions of Bioconductor packages, please install a development version of R. _D_e_t_a_i_l_s: If the user uses the 'versions' argument, the number of items in 'versions' must match the number of items in 'pkgs' and they are considered to be a one-to-one matching. For install.packages2, update.packages2, and remove.packages2, the system will by default check to insure that no dependencies from other packages are being broken. This can be overridden using 'force=TRUE'. Also for all packages, the 'type' parameter's default depends on the user's OS. If the user is using a windows machine, the default 'type' to download from a repository is 'Win32', otherwise it is 'Source'. 'install.packages2': User can specify a ReposEntry object, and/or a set of packages or a set of themes. If no package names or themes are specified, it is assumed the user wants everything available in the repository denoted by the ReposEntry. If a theme (or themes) are specified, then any package directives are ignored (installation of themes is an all or nothing event). Will install packages requested into the library directory specified. If recurse==TRUE, will also search through any of the repository's listed subrepositories to find packages. Likewise, if searchOptions==TRUE, will also look in the repositories listed by options("repositories") (So, if one specifies packages w/o a ReposEntry, it will only look here). For more information on themes, see the help page on 'repositoryThemes'. 'update.packages2': Used to update a user's packages. Much like 'install.packages2', can take (or not) a 'ReposEntry' object and also can be told to utilize the "repositories" option. A set of packages can be specified, the packages from one or more 'themes' can be requested, or alternatively all packages in the specified 'libs' parameter will be used. If prevRepos==TRUE, the system will attempt to ascertain where the package was actually installed from previously and will update from there instead. 'remove.packages2': Will remove packages specified by 'pkgs' from the libPath noted by 'lib' and reflect this change in the local library listing. For 'install.packages2' and 'update.packages2', an object of class 'pkgStatusList' is returned. This can be used to report (and by default, the 'show' method is invoked if this output is not assigned to a variable) what packages were donwloaded and from where. Also, the 'matchesList' slot of the object can be referenced to find any potential matches for packages were not found (in the case of mispellings and the like). _V_a_l_u_e: An object of class 'pkgStatusList' _A_u_t_h_o_r(_s): Jeff Gentry _S_e_e _A_l_s_o: 'syncLocalLibList','ReposEntry','genRepos','pkgInfo', 'download.packages2', 'repositoryThemes' _E_x_a_m_p_l_e_s: ## set up a temporary directory for use with these examples ## this directory will be used with the this-is-escaped-code{ ## parameter. For normal usage, most users will be okay with using ## the defaults of this-is-escaped-codenormal-bracket98bracket-normal and not need to specify manually tmpLib <- tempfile() dir.create(tmpLib) ## install a package from the standard repositories (listed by ## the command this-is-escaped-codenormal-bracket99bracket-normal install.packages2("hu6800",lib=tmpLib) ## and another one from CRAN install.packages2("abind",lib=tmpLib)