01/02: gnu: r-hpo-db: Avoid internet access during build.

[guix-commits]

rekado pushed a commit to branch r-updates
in repository guix.

commit 544e9b4a753b78c2099674293b64ee8442e8651e
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Nov 3 19:05:57 2023 +0100

    gnu: r-hpo-db: Avoid internet access during build.
    
    * gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Add phase 'set-HOME 
and
    'avoid-internet-access.
    
    Change-Id: I34b7c0e49ef01693a7977860dc8a831069a33675
---
 gnu/packages/bioconductor.scm | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 18d24784b2..a724f64f8a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -81,6 +81,21 @@
         (base32 "1brzrnafvyh76h8a663gk5lprhixxpi9xi65vwgxwf7jh6yw0was"))))
     (properties `((upstream-name . "HPO.db")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; Needed for annotationhub
+         (add-after 'unpack 'set-HOME
+           (lambda _
+             (setenv "HOME" "/tmp")))
+         (add-after 'unpack 'avoid-internet-access
+           (lambda _
+             (setenv "GUIX_BUILD" "yes")
+             (substitute* "R/zzz.R"
+               (("ah <- suppressMessages\\(AnnotationHub\\(\\)\\)" m)
+                (string-append
+                 "if (Sys.getenv(\"GUIX_BUILD\") == \"yes\") { return(TRUE); 
}; " m))))))))
     (propagated-inputs
      (list r-annotationdbi r-annotationhub r-biocfilecache r-dbi))
     (native-inputs (list r-knitr))