branch r-updates updated: gnu: bedtools-2.18: Fix build with newer toolchain.

[guix-commits]

This is an automated email from the git hooks/post-receive script.

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

The following commit(s) were added to refs/heads/r-updates by this push:
     new bdb659b  gnu: bedtools-2.18: Fix build with newer toolchain.
bdb659b is described below

commit bdb659b8b2c72019f05710e67f662cba6c8da1bf
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Nov 3 08:14:56 2021 +0000

    gnu: bedtools-2.18: Fix build with newer toolchain.
    
    * gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Add phase
    'compatibility, fixing syntax quirks that are problematic with newer
    toolchains.
    [native-inputs]: Do not inherit.
    [inherit]: Do not inherit.
---
 gnu/packages/bioinformatics.scm | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fbcd571..a731b9a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -544,14 +544,26 @@ BED, GFF/GTF, VCF.")
      '(#:test-target "test"
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'compatibility
+           (lambda _
+             (substitute* "src/utils/fileType/FileRecordTypeChecker.h"
+               (("static const float PERCENTAGE")
+                "static constexpr float PERCENTAGE"))
+             (substitute* "src/utils/general/DualQueue.h"
+               (("template <class T, template<class T> class CompareFunc>")
+                "template <class T, template<class U> class CompareFunc>"))))
          (delete 'configure)
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
                (for-each (lambda (file)
                            (install-file file bin))
-                         (find-files "bin" ".*")))
-             #t)))))))
+                         (find-files "bin" ".*"))))))))
+    (native-inputs
+     `(("python" ,python-wrapper)))
+    (inputs
+     `(("samtools" ,samtools)
+       ("zlib" ,zlib)))))
 
 (define-public pbbam
   (package