gnu: mash: Update to 2.3 and fix build with gcc-14.

* gnu/packages/bioinformatics.scm (mash): Update to 2.3.
[arguments]<#:phases>{fix-includes}: Add file to substitutions.
* gnu/packages/patches/mash-add-missing-headers.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register new file.

Fixes: guix/guix#2986
Change-Id: I6a37a6b65b0abe9b72663bcafbc034dac0cff0c0
Signed-off-by: Andreas Enge <andreas@enge.fr>

gnu/local.mk

@@ -1829,6 +1829,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/make-impure-dirs.patch			\
   %D%/packages/patches/makem-replace-git.patch			\
   %D%/packages/patches/marisa-fix-MARISA_WORD_SIZE.patch	\
+  %D%/packages/patches/mash-add-missing-headers.patch           \
   %D%/packages/patches/mathjax-disable-webpack.patch			\
   %D%/packages/patches/mathjax-no-a11y.patch			\
   %D%/packages/patches/mathjax-3.1.2-no-a11y.patch		\

gnu/packages/bioinformatics.scm

@@ -10463,7 +10463,7 @@ technology.  Its features include:
 (define-public mash
   (package
     (name "mash")
-    (version "2.1")
+    (version "2.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -10472,12 +10472,13 @@ technology.  Its features include:
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
+                "00x4pvxwp3isf0qign1qmxwxc9rwzn5b3igjw9hyn3vx17bsx92q"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled kseq.
                ;; TODO: Also delete bundled murmurhash and open bloom filter.
-               '(delete-file "src/mash/kseq.h"))))
+               '(delete-file "src/mash/kseq.h"))
+              (patches (search-patches "mash-add-missing-headers.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; No tests.
@@ -10496,7 +10497,8 @@ technology.  Its features include:
            (lambda _
              (substitute* '("src/mash/Sketch.cpp"
                             "src/mash/CommandFind.cpp"
-                            "src/mash/CommandScreen.cpp")
+                            "src/mash/CommandScreen.cpp"
+                            "src/mash/CommandTaxScreen.cpp")
                (("^#include \"kseq\\.h\"")
                 "#include \"htslib/kseq.h\""))))
          (add-after 'fix-includes 'use-c++14

gnu/packages/patches/mash-add-missing-headers.patch

@@ -0,0 +1,26 @@
+https://patch-diff.githubusercontent.com/raw/marbl/Mash/pull/181.diff
+
+Add missing includes to support newer compilers.
+---
+diff --git a/src/mash/robin_hood.h b/src/mash/robin_hood.h
+index 573607f..9141848 100644
+--- a/src/mash/robin_hood.h
++++ b/src/mash/robin_hood.h
+@@ -42,6 +42,7 @@
+ #include <cstdlib>
+ #include <cstring>
+ #include <functional>
++#include <limits>
+ #include <memory> // only to support hash of smart pointers
+ #include <stdexcept>
+ #include <string>
+--- a/src/mash/Command.cpp
++++ b/src/mash/Command.cpp
+@@ -8,6 +8,7 @@
+ #include <sys/ioctl.h>
+ #include <sstream>
+ #include <fstream>
++#include <cstdint>
+
+ #include "Command.h"
+ #include "version.h"