Try binary installation of build-only deps for source packages (#82)

* additional step to pull build-only deps for src packages

* some refactoring

* don't pass dots down to installed.packages

* add tests for hard_deps

* bump version, update NEWS

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bspm
 Type: Package
 Title: Bridge to System Package Manager
-Version: 0.5.5.1
+Version: 0.5.6
 Authors@R: c(
     person("Iñaki", "Ucar", email="iucar@fedoraproject.org",
       role=c("aut", "cph", "cre"), comment=c(ORCID="0000-0001-6403-5550")))

NEWS.md

@@ -1,6 +1,8 @@
-# bspm 0.5.5.1
+# bspm 0.5.6
 
 - Move to cran4linux org on GitHub, update URLs.
+- Try binary installation of build-only dependencies for source packages
+  (#82 addressing #81).
 
 # bspm 0.5.5
 

R/integration.R

@@ -87,18 +87,19 @@ utils::globalVariables("contrib.url") # argument
 # install binaries with checks for newer versions from source
 install_both <- function(pkgs, contriburl, method, dependencies, ...) {
   db <- utils::available.packages(contriburl=contriburl, method=method, ...)
-  pkgs <- pkg_deps(pkgs, dependencies, db, ..., all=TRUE)
+  pkgs <- pkg_deps(pkgs, dependencies, db, all=TRUE)
   pkgs <- check_versions(pkgs, db)
-  later <- ask_user(pkgs$later, pkgs$bins, pkgs$binvers, pkgs$srcvers)
-  pkgs <- c(install_sys(pkgs$bins[!later]), pkgs$bins[later], pkgs$srcs)
+  mask <- ask_user(pkgs$later, pkgs$bins, pkgs$binvers, pkgs$srcvers)
+  hard <- hard_deps(pkgs, db, mask)
+  pkgs <- c(install_sys(c(pkgs$bins[!mask], hard)), pkgs$bins[mask], pkgs$srcs)
   pkgs
 }
 
 # install as many binaries as possible and fallback to source
 install_fast <- function(pkgs, contriburl, method, ...) {
   if (length(pkgs <- install_sys(pkgs))) {
     db <- utils::available.packages(contriburl=contriburl, method=method, ...)
-    install_sys(pkg_deps(pkgs, NA, db=db, ..., all=FALSE))
+    install_sys(pkg_deps(pkgs, NA, db=db, all=FALSE))
   }
   pkgs
 }

R/utils.R

@@ -53,27 +53,38 @@ shadowed_packages <- function(lib.loc=NULL) {
   shadow
 }
 
+list_inst <- function() {
+  libs <- unique(c(.Library.site, .Library))
+  inst <- unique(row.names(utils::installed.packages(libs)))
+  inst
+}
+
+list_deps <- function(packages, db, which, recursive) {
+  deps <- tools::package_dependencies(packages, db, which, recursive)
+  deps <- unique(unlist(deps, use.names=FALSE))
+  deps
+}
+
 # get package dependencies
-pkg_deps <- function(pkgs, dependencies, db, ..., all=TRUE) {
+pkg_deps <- function(pkgs, dependencies, db, all=TRUE) {
   pkgs <- unique(pkgs)
-  libs <- unique(c(.Library.site, .Library))
-  inst <- row.names(utils::installed.packages(libs, ...))
-  deps <- tools::package_dependencies(pkgs, db, c("Depends", "Imports"), recursive=TRUE)
-  deps <- unlist(deps, use.names=FALSE)
-  if (!all) {
-    hard <- tools::package_dependencies(pkgs, db, "LinkingTo", recursive=FALSE)
-    deps <- c(deps, unlist(hard, use.names=FALSE))
-  }
-  if (isTRUE(dependencies) || "Suggests" %in% dependencies) {
-    soft <- tools::package_dependencies(pkgs, db, "Suggests", recursive=FALSE)
-    deps <- c(deps, unlist(soft, use.names=FALSE))
-  }
-  if ("Enhances" %in% dependencies) {
-    enha <- tools::package_dependencies(pkgs, db, "Enhances", recursive=FALSE)
-    deps <- c(deps, unlist(enha, use.names=FALSE))
-  }
-  pkgs <- unique(c(setdiff(deps, inst), if (all) pkgs))
-  pkgs
+  deps <- list_deps(pkgs, db, c("Depends", "Imports"), recursive=TRUE)
+  if (!all)
+    deps <- c(deps, list_deps(pkgs, db, "LinkingTo", recursive=FALSE))
+  if (isTRUE(dependencies) || "Suggests" %in% dependencies)
+    deps <- c(deps, list_deps(pkgs, db, "Suggests", recursive=FALSE))
+  if ("Enhances" %in% dependencies)
+    deps <- c(deps, list_deps(pkgs, db, "Enhances", recursive=FALSE))
+  deps <- unique(c(setdiff(deps, list_inst()), if (all) pkgs))
+  deps
+}
+
+# get LinkingTo-only dependencies for src packages
+hard_deps <- function(pkgs, db, mask) {
+  srcs <- c(pkgs$bins[mask], pkgs$srcs)
+  deps <- list_deps(srcs, db, "LinkingTo", recursive=FALSE)
+  deps <- setdiff(deps, c(list_inst(), pkgs$bins, pkgs$srcs))
+  deps
 }
 
 # adapted from install.packages

cran-comments.md

@@ -1,5 +1,5 @@
 ## Patch release
-Fix test involving numeric_version per CRAN request.
+Minor fixes.
 
 ## Test environments
 - local up-to-date R installation

inst/tinytest/test_utils.R

@@ -8,7 +8,7 @@ expect_equal(colnames(df), c("Package", "LibPath", "Version",
                              "Shadow.LibPath", "Shadow.Version", "Shadow.Newer"))
 expect_equal(df$Version < df$Shadow.Version, df$Shadow.Newer)
 
-# pkg_deps ----
+# pkg_deps, hard_deps ----
 
 mock("installed.packages", pkg="utils", function(...)
   matrix(1:2, dimnames=list(c("codetools", "rticles"), NULL)))
@@ -24,6 +24,10 @@ deps <- c(deps, "simmer.plot", "parallel", "testthat", "knitr", "rmarkdown")
 expect_equal(sort(bspm:::pkg_deps(pkgs, TRUE, db, all=TRUE)), sort(deps))
 expect_equal(sort(bspm:::pkg_deps(pkgs, "Suggests", db, all=TRUE)), sort(deps))
 
+deps <- bspm:::pkg_deps(pkgs, NA, db, all=TRUE)
+expect_equal(bspm:::hard_deps(list(bins=deps), db, FALSE), NULL)
+expect_equal(bspm:::hard_deps(list(bins=deps), db, TRUE), "BH")
+
 unmock_all()
 
 # check_versions ----