From 63bf0db41159b613bbcf96646e496b417897da1e Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Mon, 23 Mar 2026 08:48:26 +0100
Subject: Fixes to build

---
 gn/packages/bioinformatics.scm | 3 +++
 gn/packages/file-systems.scm   | 1 +
 gn/packages/maths.scm          | 4 ++++
 3 files changed, 8 insertions(+)

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index af7724d..6688084 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -221,6 +221,8 @@ Canu's consensus module.")
                  (substitute* "makefile"
                    (("-Icxxopts/include") (string-append "-I" cxxopts))
                    (("-Iconcurrentqueue") (string-append "-I" concurrentqueue))
+                   ;; Fix missing cstdint with newer GCC.
+                   (("CPPFLAGS=") "CPPFLAGS=-include cstdint ")
                    ;; No need to build statically.
                    (("-Wl,-Bstatic") "")
                    (("-static-libstdc\\+\\+") "")))))
@@ -545,6 +547,7 @@ format.")
     (build-system gnu-build-system)
     (arguments
      (list #:tests? #f
+           #:make-flags #~(list "CXXFLAGS=-include linux/types.h")
            #:phases
            #~(modify-phases %standard-phases
                (delete 'configure)
diff --git a/gn/packages/file-systems.scm b/gn/packages/file-systems.scm
index 9c5cd04..dbf79c3 100644
--- a/gn/packages/file-systems.scm
+++ b/gn/packages/file-systems.scm
@@ -5,6 +5,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages admin)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python))
diff --git a/gn/packages/maths.scm b/gn/packages/maths.scm
index acbf69d..865e053 100644
--- a/gn/packages/maths.scm
+++ b/gn/packages/maths.scm
@@ -99,6 +99,7 @@
        ((#:tests? _ #t) #f)
        ((#:phases phases #~%standard-phases)
         #~(modify-phases #$phases
+            (delete 'move-static-library)
             (add-after 'install 'remove-extra-files
               (lambda _
                 (delete-file-recursively (string-append #$output "/bin"))
@@ -124,6 +125,7 @@
        ((#:tests? _ #t) #f)
        ((#:phases phases #~%standard-phases)
         #~(modify-phases #$phases
+            (delete 'move-static-library)
             (add-after 'install 'remove-extra-files
               (lambda _
                 (delete-file-recursively (string-append #$output "/bin"))
@@ -150,6 +152,7 @@
        ((#:tests? _ #t) #f)
        ((#:phases phases #~%standard-phases)
         #~(modify-phases #$phases
+            (delete 'move-static-library)
             (add-after 'install 'remove-extra-files
               (lambda _
                 (delete-file-recursively (string-append #$output "/bin"))
@@ -167,6 +170,7 @@
      (substitute-keyword-arguments (package-arguments gsl)
        ((#:phases phases #~%standard-phases)
         #~(modify-phases #$phases
+            (delete 'move-static-library)
             (add-after 'install 'install-optimized-libraries
               (lambda* (#:key inputs outputs #:allow-other-keys)
                 (let ((hwcaps "/lib/glibc-hwcaps"))
-- 
cgit 1.4.1