Merge pull request #103 from pmoris/feature_improve_bioc_installer

Add additional options to installBioc.r
eddelbuettel · Aug 28, 2022 · cfb7f62 · cfb7f62
2 parents 6ae438e + 5f64d09
commit cfb7f62
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,12 @@
+2022-08-28  Dirk Eddelbuettel  <edd@debian.org>
+
+	* inst/examples/installBioc.r:
+
+2022-08-24  Pieter Moris  <pieter.moris@glpg.com>
+
+	* inst/examples/installBioc.r: Generalization, extension and extra
+	features similar to how install2.r generalizes install2.r
+
 2022-07-16  Dirk Eddelbuettel  <edd@debian.org>
 
 	* inst/examples/r2u.r: Add simple r2u.r frontend

diff --git a/inst/examples/installBioc.r b/inst/examples/installBioc.r
@@ -2,20 +2,31 @@
 #
 # Install a package from BioConductor
 #
-# Copyright (C) 2020 -       Dirk Eddelbuettel
+# Copyright (C) 2020 - 2022  Dirk Eddelbuettel
+# Copyright (C) 2022 - 2022  Dirk Eddelbuettel and Pieter Moris
 #
 # Released under GPL (>= 2)
 
 ## load docopt package from CRAN
 library(docopt)
 
-## configuration for docopt
-doc <- "Usage: installBioc.r [-l LIBLOC] [-h] [-x] [PACKAGES ...]
+## default to first library location in .libPaths()
+libloc <- .libPaths()[1]
 
--l --libloc LIBLOC  location in which to install [default: /usr/local/lib/R/site-library]
+## configuration for docopt
+doc <- paste0("Usage: installBioc.r [-l LIBLOC] [-d DEPS] [-n NCPUS] [-r REPO ...] [--error] [--skipinstalled] [-m METHOD] [--force] [--update] [-h] [-x] [PACKAGES ...]
+-l --libloc LIBLOC  location in which to install [default: ", libloc, "]
+-d --deps DEPS      install suggested dependencies as well [default: NA]
+-n --ncpus NCPUS    number of processes to use for parallel install [default: getOption]
+-r --repo REPO      additional repository to use [default: getOption]
+-e --error          throw error and halt instead of a warning [default: FALSE]
+-s --skipinstalled  skip installing already installed packages (takes priority over --force) [default: FALSE]
+-m --method METHOD  method to be used for downloading files [default: auto]
+-f --force          force re-download of packages that are currently up-to-date [default: FALSE]
+-u --update         update old already installed packages [default: FALSE]
 -h --help           show this help text
--x --usage          show help and short example usage"
-opt <- docopt(doc)			# docopt parsing
+-x --usage          show help and short example usage")
+opt <- docopt(doc)  # docopt parsing
 
 if (opt$usage) {
     cat(doc, "\n\n")
@@ -24,6 +35,10 @@ package 'BiocManger' which has be installed.
 
 Examples:
   installBioc.r -l /tmp/lib S4Vectors               # install into given library
+  installBioc.r --update Biobase                    # install package and update older packages
+  installBioc.r --deps NA --error --skipinstalled   # install package without suggested dependencies,
+                                                    # throw an error on installation failure and skip
+                                                    # packages that are already present
 
 installBioC.r is part of littler which brings 'r' to the command-line.
 See http://dirk.eddelbuettel.com/code/littler.html for more information.\n")
@@ -34,10 +49,81 @@ if (!requireNamespace("BiocManager", quietly=TRUE)) {
     stop("Please install 'BiocManager' first, for example via 'install.r BiocManager'.", call.=FALSE)
 }
 
+## set repository to empty character vector if not supplied, since
+## this is the input expected by BiocManager::install(site_repository=)
+## (does not accept NA)
+## the custom repository must be a sub-repository of a main BioC_mirror
+## e.g. software: https://bioconductor.statistik.tu-dortmund.de/packages/3.15/bioc/
+## annotation: https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.14/data/annotation
+if (opt$repo == "getOption") {
+    opt$repo = character()
+}
+
+## check if dependencies need to be installed, see
+## https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages
+## the default, NA, means c("Depends", "Imports", "LinkingTo"), but not "Suggests"
+if (opt$deps == "TRUE" || opt$deps == "FALSE") {
+    opt$deps <- as.logical(opt$deps)
+} else if (opt$deps == "NA") {
+    opt$deps <- NA
+}
+
+## set the number of parallel processes to use for a parallel install of
+## more than one source package, see
+## https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages
+if (opt$ncpus == "getOption") {
+    opt$ncpus <- getOption("Ncpus", 1L)
+} else if (opt$ncpus == "-1") {
+    ## parallel comes with R 2.14+
+    opt$ncpus <- max(1L, parallel::detectCores())
+}
+
+## helper function to catch errors that could arise when package installation has failed
+## and to skip installation of packages that are already present (for BiocManager::install()
+## these would otherwise result in additional warnings)
+install_bioc <- function(pkgs, ..., error = FALSE, skipinstalled = FALSE) {
+    e <- NULL
+    capture <- function(e) {
+        if (error) {
+            catch <-
+                grepl("installation of one or more packages failed", e$message) ||
+                grepl("is not available", e$message) ||
+                grepl("had non-zero exit status", e$message) ||
+                grepl("compilation failed for package.*", e$message) ||
+                grepl("fatal error", e$message) ||
+                grepl("No such file or directory", e$message)
+            if (catch) {
+                e <<- e
+            }
+        }
+    }
+    if (skipinstalled) {
+        pkgs <- setdiff(pkgs, installed.packages()[,1])
+    }
+    if (length(pkgs) > 0) {
+        withCallingHandlers(BiocManager::install(pkgs, ...), warning = capture)
+        if (!is.null(e)) {
+            stop(e$message, call. = FALSE)
+        }
+    }
+}
+
 ## ensure installation is stripped
 Sys.setenv("_R_SHLIB_STRIP_"="true")
 
-## set .libPaths()
-.libPaths(opt$lib)
-
-BiocManager::install(opt$PACKAGES, update=FALSE, ask=FALSE)
+## install requested packages using helper function
+## ask must be set to FALSE because user prompts do not appear when calling
+## R from the CLI, e.g.
+## `R -e 'BiocManager::install("Biobase", ask=TRUE, update=TRUE)'`
+## might warn that MASS is out of date, but would not show a user prompt
+install_bioc(pkgs = opt$PACKAGES,
+        lib = opt$libloc,
+        site_repository = opt$repo,
+        update = opt$update,
+        ask = FALSE,
+        force = opt$force,
+        dependencies = opt$deps,
+        Ncpus = opt$ncpus,
+        method = opt$method,
+        error = opt$error,
+        skipinstalled = opt$skipinstalled)