02/02: gnu: pigx-sars-cov-2: Fix build.

[guix-commits]

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

commit cb115ba7220d7db12ccb761a1261a778ec583ae2
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Sun May 29 00:39:19 2022 +0200

    gnu: pigx-sars-cov-2: Fix build.
    
    * gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add
    'autoreconf phase to patch build system.
---
 gnu/packages/bioinformatics.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0945bddbe7..1d8397c1aa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11359,6 +11359,13 @@ based methods.")
      `(#:tests? #f ;requires huge kraken database
        #:phases
        (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             ;; https://github.com/BIMSBbioinfo/pigx_sars-cov-2/issues/123
+             (substitute* "m4/ax_r_package.m4"
+               (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
+                "if(system.file(package=\"PKG\") == \"\")"))
+             (invoke "autoreconf" "-vif")))
          (add-before 'configure 'set-PYTHONPATH
            (lambda _
              (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))