Refactor R package installation (#1381)

* Support installing R environment in DEB822 format Signed-off-by: Botong Ou <[email protected]> * Support installing R environment in DEB822 format Signed-off-by: Botong Ou <[email protected]> * Support installing R environment in DEB822 format Signed-off-by: Botong Ou <[email protected]> * Support installing R environment in DEB822 format Signed-off-by: Botong Ou <[email protected]> * Temporarily removed return error from installRLang Signed-off-by: Botong Ou <[email protected]> * Append to apt.conf Signed-off-by: Botong Ou <[email protected]> * Move apt configuration to a separate file /etc/apt/apt.conf.d/DEB822.conf Signed-off-by: Botong Ou <[email protected]> * Add comments and change some typos Signed-off-by: Botong Ou <[email protected]> * Adjust comments Signed-off-by: Botong Ou <[email protected]> * Adjust comments Signed-off-by: Botong Ou <[email protected]> * Fix typo Signed-off-by: Botong Ou <[email protected]> * Change to const Signed-off-by: Botong Ou <[email protected]> * Change to const Signed-off-by: Botong Ou <[email protected]> * Change internal message when install R environment Signed-off-by: Botong Ou <[email protected]> * Add e2e test for R language environment Signed-off-by: Botong Ou <[email protected]> * Format rlang/build.envd Signed-off-by: Botong Ou <[email protected]> * remove incorrect user-switching Signed-off-by: Botong Ou <[email protected]> * Discard the changes in main Signed-off-by: Botong Ou <[email protected]> * add install.r_packages() Signed-off-by: Botong Ou <[email protected]> * update e2e test Signed-off-by: Botong Ou <[email protected]> * update e2e test Signed-off-by: Botong Ou <[email protected]> * update e2e test Signed-off-by: Botong Ou <[email protected]> * switched to small library for e2e test Signed-off-by: Botong Ou <[email protected]> * refactor R packcages installation Signed-off-by: Botong Ou <[email protected]> * refactor R packcages installation Signed-off-by: Botong Ou <[email protected]> * update R packages installation Signed-off-by: Botong Ou <[email protected]> * update R packages installation Signed-off-by: Botong Ou <[email protected]> * fix lint Signed-off-by: Botong Ou <[email protected]> * udpate R packages installation Signed-off-by: Botong Ou <[email protected]> * udpate R packages installation Signed-off-by: Botong Ou <[email protected]> Signed-off-by: Botong Ou <[email protected]>
tensorchord · Jan 9, 2023 · 3f7d699 · 3f7d699
1 parent aab7f53
commit 3f7d699
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Showing 5 changed files with 28 additions and 19 deletions.
diff --git a/pkg/lang/frontend/starlark/v1/install/install.go b/pkg/lang/frontend/starlark/v1/install/install.go
@@ -136,9 +136,9 @@ func ruleFuncRPackage(thread *starlark.Thread, _ *starlark.Builtin,
 	}
 
 	logger.Debugf("rule `%s` is invoked, name=%v", ruleRPackage, nameList)
-	ir.RPackage(nameList)
+	err = ir.RPackage(nameList)
 
-	return starlark.None, nil
+	return starlark.None, err
 }
 
 func ruleFuncJuliaPackage(thread *starlark.Thread, _ *starlark.Builtin,

diff --git a/pkg/lang/ir/v1/compile.go b/pkg/lang/ir/v1/compile.go
@@ -53,7 +53,7 @@ func NewGraph() ir.Graph {
 		NumGPUs:  0,
 
 		PyPIPackages:    [][]string{},
-		RPackages:       []string{},
+		RPackages:       [][]string{},
 		JuliaPackages:   []string{},
 		SystemPackages:  []string{},
 		Exec:            []ir.RunBuildCommand{},

diff --git a/pkg/lang/ir/v1/interface.go b/pkg/lang/ir/v1/interface.go
@@ -89,10 +89,17 @@ func PyPIPackage(deps []string, requirementsFile string, wheels []string) error
 	return nil
 }
 
-func RPackage(deps []string) {
+func RPackage(deps []string) error {
+
+	if len(deps) == 0 {
+		return errors.New("Can not install empty R package")
+	}
+
 	g := DefaultGraph.(*generalGraph)
 
-	g.RPackages = append(g.RPackages, deps...)
+	g.RPackages = append(g.RPackages, deps)
+
+	return nil
 }
 
 func JuliaPackage(deps []string) {

diff --git a/pkg/lang/ir/v1/r.go b/pkg/lang/ir/v1/r.go
@@ -31,26 +31,28 @@ func (g generalGraph) installRLang(root llb.State) llb.State {
 }
 
 func (g generalGraph) installRPackages(root llb.State) llb.State {
+
 	if len(g.RPackages) == 0 {
 		return root
 	}
-	// TODO(terrytangyuan): Support different CRAN mirrors
-	var sb strings.Builder
+
 	mirrorURL := "https://cran.rstudio.com"
 	if g.CRANMirrorURL != nil {
 		mirrorURL = *g.CRANMirrorURL
 	}
-	sb.WriteString(fmt.Sprintf(`R -e 'options(repos = c(CRAN = "%s")); install.packages(c(`, mirrorURL))
-	for i, pkg := range g.RPackages {
-		sb.WriteString(fmt.Sprintf(`"%s"`, pkg))
-		if i != len(g.RPackages)-1 {
-			sb.WriteString(", ")
-		}
+
+	lib := "/usr/local/lib/R/site-library/"
+
+	root = root.
+		Run(llb.Shlexf("chmod 777 %s", lib), llb.WithCustomNamef("[internal] setting execute permision for default R package library for envd users")).Root()
+
+	for _, packages := range g.RPackages {
+		command := fmt.Sprintf(`R -e 'options(repos = "%s"); install.packages(c("%s"), lib = "%s")'`, mirrorURL, strings.Join(packages, `","`), lib)
+		run := root.
+			Run(llb.Shlex(command), llb.WithCustomNamef("[internal] installing R pacakges: %s", strings.Join(packages, " ")))
+		root = run.Root()
+
 	}
-	sb.WriteString(`))'`)
 
-	// TODO(terrytangyuan): Support cache.
-	cmd := sb.String()
-	run := root.Run(llb.Shlex(cmd), llb.WithCustomNamef("install R packages"))
-	return run.Root()
+	return root
 }
diff --git a/pkg/lang/ir/v1/types.go b/pkg/lang/ir/v1/types.go
@@ -49,7 +49,7 @@ type generalGraph struct {
 	PyPIPackages     [][]string
 	RequirementsFile *string
 	PythonWheels     []string
-	RPackages        []string
+	RPackages        [][]string
 	JuliaPackages    []string
 	SystemPackages   []string