From 15ca1959793b5ed9ae8fb525493edf9bd3caf2b8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 6 Nov 2017 22:39:05 +0100
Subject: [PATCH] gnu: r-mzr: Remove bundled copy of boost.

* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
---
 gnu/packages/bioinformatics.scm | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2ad5f953e1..115af50eb4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8899,9 +8899,26 @@ proteomics packages.")
        (uri (bioconductor-uri "mzR" version))
        (sha256
         (base32
-         "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))))
+         "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (delete-file-recursively "src/boost")
+           #t))))
     (properties `((upstream-name . "mzR")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-boost
+           (lambda _
+             (substitute* "src/Makevars"
+               (("\\./boost/libs.*") "")
+               (("ARCH_OBJS=" line)
+                (string-append line
+                               "\nARCH_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+             #t)))))
     (inputs
      `(("boost" ,boost) ; use this instead of the bundled boost sources
        ("netcdf" ,netcdf)))