Merged origin/main into eeholmes-main

gaborcsardi · gaborcsardi · commit fa7655ca09c3 · 2025-01-09T14:47:00.000+01:00
diff --git a/NAMESPACE b/NAMESPACE
@@ -104,5 +104,6 @@ importFrom(tools,file_ext)
 importFrom(utils,available.packages)
 importFrom(utils,compareVersion)
 importFrom(utils,contrib.url)
+importFrom(utils,download.file)
 importFrom(utils,install.packages)
 importFrom(utils,read.delim)
diff --git a/R/bioc-standalone.R b/R/bioc-standalone.R
@@ -74,6 +74,7 @@
 #' @noRd
 NULL
 
+#' @importFrom utils download.file
 
 bioconductor <- local({
 
@@ -113,7 +114,8 @@ bioconductor <- local({
     "4.0"  = package_version("3.12"),
     "4.1"  = package_version("3.14"),
     "4.2"  = package_version("3.16"),
-    "4.3"  = package_version("3.18")
+    "4.3"  = package_version("3.18"),
+    "4.4"  = package_version("3.20")
     # Do not include R 4.4 <-> Bioc 3.19, because R 4.4 will use
     # Bioc 3.20 eventually.
   )
diff --git a/inst/install-github.R b/inst/install-github.R
diff --git a/install-github.R b/install-github.R
diff --git a/tests/testthat/test-bioc.R b/tests/testthat/test-bioc.R
@@ -36,7 +36,7 @@ test_that("internal map is current", {
   skip_if_offline()
   expect_equal(
     bioconductor$get_release_version(),
-    package_version("3.18"))
+    package_version("3.20"))
 })
 
 test_that("set of repos are correct", {
diff --git a/tests/testthat/test-system_requirements.R b/tests/testthat/test-system_requirements.R
@@ -136,15 +136,15 @@ test_that("system_requirements return the system requirements if 2nd order depen
 
   expect_equal(
     system_requirements("ubuntu", "16.04", pkg),
-    c("apt-get install -y libcurl4-openssl-dev",
-      "apt-get install -y libssl-dev"
+    c("apt-get install -y libssl-dev",
+      "apt-get install -y libcurl4-openssl-dev"
     )
   )
 
   expect_equal(
     system_requirements("redhat", "7", pkg),
-    c("yum install -y libcurl-devel",
-      "yum install -y openssl-devel"
+    c("yum install -y openssl-devel",
+      "yum install -y libcurl-devel"
     )
   )
 })
@@ -186,8 +186,7 @@ test_that("system_requirements work with vector package arguments", {
 
     sort(c("apt-get install -y software-properties-common",
       "add-apt-repository -y ppa:cran/libgit2",  "apt-get update",
-      "apt-get install -y libgit2-dev", "apt-get install -y libssh2-1-dev",
-      "apt-get install -y libssl-dev", "apt-get install -y zlib1g-dev",
+      "apt-get install -y libgit2-dev", "apt-get install -y libssl-dev", 
       "apt-get install -y libcurl4-openssl-dev"
     ))
   )

Original file line number	Diff line number	Diff line change
`@@ -136,15 +136,15 @@ test_that("system_requirements return the system requirements if 2nd order depen`
`136`	`136`
`137`	`137`	`expect_equal(`
`138`	`138`	`system_requirements("ubuntu", "16.04", pkg),`
`139`		`- c("apt-get install -y libcurl4-openssl-dev",`
`140`		`- "apt-get install -y libssl-dev"`
	`139`	`+ c("apt-get install -y libssl-dev",`
	`140`	`+ "apt-get install -y libcurl4-openssl-dev"`
`141`	`141`	`)`
`142`	`142`	`)`
`143`	`143`
`144`	`144`	`expect_equal(`
`145`	`145`	`system_requirements("redhat", "7", pkg),`
`146`		`- c("yum install -y libcurl-devel",`
`147`		`- "yum install -y openssl-devel"`
	`146`	`+ c("yum install -y openssl-devel",`
	`147`	`+ "yum install -y libcurl-devel"`
`148`	`148`	`)`
`149`	`149`	`)`
`150`	`150`	`})`
`@@ -186,8 +186,7 @@ test_that("system_requirements work with vector package arguments", {`
`186`	`186`
`187`	`187`	`sort(c("apt-get install -y software-properties-common",`
`188`	`188`	`"add-apt-repository -y ppa:cran/libgit2", "apt-get update",`
`189`		`- "apt-get install -y libgit2-dev", "apt-get install -y libssh2-1-dev",`
`190`		`- "apt-get install -y libssl-dev", "apt-get install -y zlib1g-dev",`
	`189`	`+ "apt-get install -y libgit2-dev", "apt-get install -y libssl-dev",`
`191`	`190`	`"apt-get install -y libcurl4-openssl-dev"`
`192`	`191`	`))`
`193`	`192`	`)`