Merge branch 'master' into core-updates

2 files changed, 30 insertions, 18 deletions

diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index ec2b7e6029..49e5d2d358 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -128,9 +128,9 @@ package definition."
 (define %cran-url "http://cran.r-project.org/web/packages/")
 (define %bioconductor-url "https://bioconductor.org/packages/")
 
-;; The latest Bioconductor release is 3.6.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.7.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.6")
+(define %bioconductor-version "3.7")
 
 (define %bioconductor-packages-list-url
   (string-append "https://bioconductor.org/packages/"
diff --git a/guix/self.scm b/guix/self.scm
index 3503fbda43..a24e9c6147 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -171,7 +171,8 @@ must be present in the search path."
          (source (imported-files (string-append name "-source")
                                  (append module-files extra-files))))
     (node name modules source dependencies
-          (compiled-modules name source modules
+          (compiled-modules name source
+                            (map car module-files)
                             (map node-source dependencies)
                             (map node-compiled dependencies)
                             #:extensions extensions
@@ -313,7 +314,12 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                        *extra-modules* *core-modules*)
                  #:extensions dependencies
                  #:extra-files
-                 (file-imports source "gnu/system/examples" (const #t))
+                 (append (file-imports source "gnu/system/examples"
+                                       (const #t))
+
+                         ;; Build-side code that we don't build.  Some of
+                         ;; these depend on guile-rsvg, the Shepherd, etc.
+                         (file-imports source "gnu/build" (const #t)))
                  #:guile-for-build
                  guile-for-build))
 
@@ -481,6 +487,11 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
 (define (imported-files name files)
   ;; This is a non-monadic, simplified version of 'imported-files' from (guix
   ;; gexp).
+  (define same-target?
+    (match-lambda*
+      (((file1 . _) (file2 . _))
+       (string=? file1 file2))))
+
   (define build
     (with-imported-modules (source-module-closure
                             '((guix build utils)))
@@ -497,14 +508,15 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                        ;; symlinks, as this makes a difference for
                        ;; 'add-to-store'.
                        (copy-file store-path final-path)))
-                    '#$files))))
+                    '#$(delete-duplicates files same-target?)))))
 
   ;; We're just copying files around, no need to substitute or offload it.
   (computed-file name build
                  #:options '(#:local-build? #t
-                             #:substitutable? #f)))
+                             #:substitutable? #f
+                             #:env-vars (("COLUMNS" . "200")))))
 
-(define* (compiled-modules name module-tree modules
+(define* (compiled-modules name module-tree module-files
                            #:optional
                            (dependencies '())
                            (dependencies-compiled '())
@@ -512,6 +524,9 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                            (extensions '())       ;full-blown Guile packages
                            parallel?
                            guile-for-build)
+  "Build all the MODULE-FILES from MODULE-TREE.  MODULE-FILES must be a list
+like '(\"guix/foo.scm\" \"gnu/bar.scm\") and MODULE-TREE is the directory
+containing MODULE-FILES and possibly other files as well."
   ;; This is a non-monadic, enhanced version of 'compiled-file' from (guix
   ;; gexp).
   (define build
@@ -542,16 +557,13 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                     (* 100. (/ completed total)) total)
             (force-output))
 
-          (define (process-directory directory output)
-            (let ((files  (find-files directory "\\.scm$"))
-                  (prefix (+ 1 (string-length directory))))
-              ;; Hide compilation warnings.
-              (parameterize ((current-warning-port (%make-void-port "w")))
-                (compile-files directory #$output
-                               (map (cut string-drop <> prefix) files)
-                               #:workers (parallel-job-count)
-                               #:report-load report-load
-                               #:report-compilation report-compilation))))
+          (define (process-directory directory files output)
+            ;; Hide compilation warnings.
+            (parameterize ((current-warning-port (%make-void-port "w")))
+              (compile-files directory #$output files
+                             #:workers (parallel-job-count)
+                             #:report-load report-load
+                             #:report-compilation report-compilation)))
 
           (setvbuf (current-output-port) _IONBF)
           (setvbuf (current-error-port) _IONBF)
@@ -579,7 +591,7 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
 
           (mkdir #$output)
           (chdir #+module-tree)
-          (process-directory "." #$output)
+          (process-directory "." '#+module-files #$output)
           (newline))))
 
   (computed-file name build