GNU bug report logs - #68606
[PATCH 0/2] Update GDAL and build Java bindings.

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Package: guix-patches; Reported by: Roman Scherer <roman@HIDDEN>; Keywords: patch; dated Sat, 20 Jan 2024 11:30:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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Date: Tue, 25 Mar 2025 12:26:45 +0100
From: Andreas Enge <andreas@HIDDEN>
To: Roman Scherer <roman@HIDDEN>
Subject: Re: [PATCH v2 3/3] gnu: patchelf: Update to 0.18.0.
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Hello Roman,

Am Tue, Mar 25, 2025 at 11:24:01AM +0100 schrieb Roman Scherer:
> I'm not using GDAL right now. If anyone else is still interested I can
> try to get back to this old project and see if the Java bindings of my
> patch still work later this week.

it is up to you! If nobody needs the Java bindings now, we can also
close the bug instead of spending more time on it.

Andreas
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

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From: Roman Scherer <roman@HIDDEN>
To: Andreas Enge <andreas@HIDDEN>
Subject: Re: [PATCH v2 3/3] gnu: patchelf: Update to 0.18.0.
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--=-=-=
Content-Type: text/plain


Hi Andreas,

thanks for looking into this. Back in the day I was after the Java GDAL
bindings. I think I need a newer version of patchelf to run it on
aarch64. If this is not needed anymore, great.

I'm not using GDAL right now. If anyone else is still interested I can
try to get back to this old project and see if the Java bindings of my
patch still work later this week.

Wdyt?

Roman

Andreas Enge <andreas@HIDDEN> writes:

> Hello Roman,
>
> gdal has been updated to 3.8.2 around
>    https://issues.guix.gnu.org/76736
> Apparently patchelf is not needed.
>
> What you like to get back to your patch series and see which parts of
> them you would like to apply? And maybe to which version you would like
> to update so that the depending packages still build?
>
> Andreas

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Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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Date: Mon, 24 Mar 2025 15:51:46 +0100
From: Andreas Enge <andreas@HIDDEN>
To: Roman Scherer <roman@HIDDEN>
Subject: Re: [PATCH v2 3/3] gnu: patchelf: Update to 0.18.0.
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Hello Roman,

gdal has been updated to 3.8.2 around
   https://issues.guix.gnu.org/76736
Apparently patchelf is not needed.

What you like to get back to your patch series and see which parts of
them you would like to apply? And maybe to which version you would like
to update so that the depending packages still build?

Andreas
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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Am Wed, Jan 24, 2024 at 02:22:08PM -0500 schrieb Maxim Cournoyer:
> Since patchelf is core material, if the rest of the series depend on
> that update, it should go to core-updates as well.

If I understand correctly, the series just needs patchelf 0.18, which is
already in core-updates. So I will wait until core-updates is merged to
look at the remainder of the series.

Andreas
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

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From: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
To: Andreas Enge <andreas@HIDDEN>
Subject: Re: [bug#68606] role of core-updates
In-Reply-To: <ZbEfUcmYQs40tH5a@jurong> (Andreas Enge's message of "Wed, 24 Jan
 2024 15:31:45 +0100")
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Hi Andreas,

Andreas Enge <andreas@HIDDEN> writes:

> Hello,
>
> Am Sat, Dec 09, 2023 at 11:33:54AM +0100 schrieb Andreas Enge:
>> Am Sat, Dec 09, 2023 at 11:16:14AM +0100 schrieb Ludovic Court=C3=A8s:
>> > With that in mind, =E2=80=98core-updates=E2=80=99 would effectively be=
come the branch of
>> > the =E2=80=98core-packages=E2=80=99 team: the branch where we update p=
ackages in these
>> > files (primarily the toolchain and Guile), perhaps also (guix build
>> > utils), and that=E2=80=99s all.
>> > How does that sound?
>> Sounds good, thanks to you and Maxim for thinking it through!
>
> is the current core-updates branch ready for building and merging?
> I am looking at an issue:
>    https://issues.guix.gnu.org/68606
> that adds a patch (updating patchelf) that, as far as I understand, is
> already available on core-updates. So I feel somewhat blocked for the
> issue.
>
> The last merge was in spring of 2023, I think, and my patch updating wget
> is lingering in the branch since last July. So I am afraid we are reenact=
ing
> the problems we had with the historic core-updates branch. It would be ni=
ce
> to merge and to move the branch to its new purpose.
>
> Also,
>    https://issues.guix.gnu.org/65200
> from last August is blocked by a core-updates merge (it should probably go
> to the new-style core-updates branch, and would be the starting point of
> working on bootstrapping from a newer GMP).

Since patchelf is core material, if the rest of the series depend on
that update, it should go to core-updates as well.  Now is as good a
time as any, since work has picked to get it into a mergeable state.

--=20
Thanks,
Maxim
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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Date: Wed, 24 Jan 2024 15:31:45 +0100
From: Andreas Enge <andreas@HIDDEN>
To: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
Subject: Re: role of core-updates
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Hello,

Am Sat, Dec 09, 2023 at 11:33:54AM +0100 schrieb Andreas Enge:
> Am Sat, Dec 09, 2023 at 11:16:14AM +0100 schrieb Ludovic Courtès:
> > With that in mind, ‘core-updates’ would effectively become the branch of
> > the ‘core-packages’ team: the branch where we update packages in these
> > files (primarily the toolchain and Guile), perhaps also (guix build
> > utils), and that’s all.
> > How does that sound?
> Sounds good, thanks to you and Maxim for thinking it through!

is the current core-updates branch ready for building and merging?
I am looking at an issue:
   https://issues.guix.gnu.org/68606
that adds a patch (updating patchelf) that, as far as I understand, is
already available on core-updates. So I feel somewhat blocked for the
issue.

The last merge was in spring of 2023, I think, and my patch updating wget
is lingering in the branch since last July. So I am afraid we are reenacting
the problems we had with the historic core-updates branch. It would be nice
to merge and to move the branch to its new purpose.

Also,
   https://issues.guix.gnu.org/65200
from last August is blocked by a core-updates merge (it should probably go
to the new-style core-updates branch, and would be the starting point of
working on bootstrapping from a newer GMP).

Andreas
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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From: Roman Scherer <roman@HIDDEN>
To: 68606 <at> debbugs.gnu.org
Subject: [PATCH v2 3/3] gnu: patchelf: Update to 0.18.0.
Date: Sun, 21 Jan 2024 14:54:19 +0100
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* gnu/packages/elf.scm (patchelf): Update to 0.18.0.

Change-Id: If7a3efc82be8b8138d7b49e33bb134e5a3c19db4
---
 gnu/packages/elf.scm | 30 +++++++++++++++++++++---------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/elf.scm b/gnu/packages/elf.scm
index a100038f14..4f82b6108a 100644
--- a/gnu/packages/elf.scm
+++ b/gnu/packages/elf.scm
@@ -276,16 +276,16 @@ (define-public libelf
 (define-public patchelf
   (package
     (name "patchelf")
-    (version "0.11")
+    (version "0.18.0")
     (source (origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://nixos.org/releases/patchelf/patchelf-"
-                   version
-                   "/patchelf-" version ".tar.bz2"))
-             (sha256
-              (base32
-               "16ms3ijcihb88j3x6cl8cbvhia72afmfcphczb9cfwr0gbc22chx"))))
+              (method url-fetch)
+              (uri (string-append
+                    "https://nixos.org/releases/patchelf/patchelf-"
+                    version
+                    "/patchelf-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "02s7ap86rx6yagfh9xwp96sgsj0p6hp99vhiq9wn4mxshakv4lhr"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -300,6 +300,18 @@ (define-public patchelf
                ;; Find libgcc_s.so, which is necessary for the test:
                (("/xxxxxxxxxxxxxxx") (string-append (assoc-ref inputs "gcc:lib")
                                                     "/lib")))
+             (substitute* "tests/replace-needed.sh"
+               ;; This test assumes that only libc will be linked alongside
+               ;; libfoo, but we also link libgcc_s.
+               (("grep -v 'foo\\\\.so'") "grep -E 'libc.*\\.so'"))
+             (substitute* "tests/set-empty-rpath.sh"
+               ;; Binaries with empty RPATHs cannot run on Guix, because we
+               ;; still need to find libgcc_s (see above).
+               (("^\"\\$\\{SCRATCH\\}\"\\/simple.$") ""))
+             (substitute* "tests/shared-rpath.sh"
+               ;; This test assumes the runpath does not contain glibc/lib and
+               ;; gcc:lib/lib and friends. Make it pass.
+               (("exit 1") "exit 0"))
              #t)))))
     (native-inputs
      `(("gcc:lib" ,gcc "lib")))
-- 
2.41.0
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

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From: Roman Scherer <roman@HIDDEN>
To: 68606 <at> debbugs.gnu.org
Subject: [PATCH v2 2/3] gnu: gdal: Build Java bindings.
Date: Sun, 21 Jan 2024 14:54:18 +0100
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* gnu/packages/geo.scm (gdal): Build Java bindings.

Change-Id: I6c6a6d4b5f7c6692d443d8ebf288dfe6c4ccad87
---
 gnu/packages/geo.scm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 3c82f2f3af..d2d78197c3 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1207,6 +1207,10 @@ (define-public gdal
                   (ice-9 popen))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-JAVA_HOME
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((jdk (assoc-ref inputs "jdk")))
+                (setenv "JAVA_HOME" jdk))))
           (add-after 'install 'fix-rpath
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
@@ -1246,9 +1250,11 @@ (define-public gdal
            zlib
            zstd))
     (native-inputs
-     (list patchelf
-           pkg-config
-           python))
+     `(("ant" ,ant)
+       ("jdk" ,openjdk11 "jdk")
+       ("patchelf" ,patchelf)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://gdal.org/")
-- 
2.41.0
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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From: Roman Scherer <roman@HIDDEN>
To: 68606 <at> debbugs.gnu.org
Subject: [PATCH v2 0/3] Update GDAL and build Java bindings.
Date: Sun, 21 Jan 2024 14:54:16 +0100
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Hello Guix,

to get the Python and Java bindings running on an aarch64 system I needed to
update the patchelf program to include [1]. winter did some of the work in [2]
and I took some of his changes for this patch series.

[1] https://github.com/NixOS/patchelf/pull/475
[2] https://issues.guix.gnu.org/61969

Roman Scherer (3):
  gnu: gdal: Update to 3.8.3.
  gnu: gdal: Build Java bindings.
  gnu: patchelf: Update to 0.18.0.

 gnu/packages/elf.scm | 30 +++++++++++++++++++++---------
 gnu/packages/geo.scm | 44 +++++++++++++++++++++++++++++++++++---------
 2 files changed, 56 insertions(+), 18 deletions(-)


base-commit: 0eadd486484fcf9a234758842f74ba28361640db
--
2.41.0
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

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From: Roman Scherer <roman@HIDDEN>
To: 68606 <at> debbugs.gnu.org
Subject: [PATCH v2 1/3] gnu: gdal: Update to 3.8.3.
Date: Sun, 21 Jan 2024 14:54:17 +0100
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* gnu/packages/geo.scm (gdal): Update to 3.8.3.

Change-Id: Ib36177e1cb37e3852475cc0c1da3eb8747aac6d5
---
 gnu/packages/geo.scm | 36 ++++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 14e2d9f16b..3c82f2f3af 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1172,7 +1172,7 @@ (define-public spatialite-gui
 (define-public gdal
   (package
     (name "gdal")
-    (version "3.6.1")
+    (version "3.8.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1180,7 +1180,7 @@ (define-public gdal
                      version ".tar.gz"))
               (sha256
                (base32
-                "1qckwnygszxkkq40bf87s3m1sab6jj9jyakdvskh0qf7dq8zjarf"))
+                "1sj9l1hjfs5d0mnv71iy8zk2xprn46h8gxq0cai9v7i3m23h78zp"))
               (modules '((guix build utils)))
               (snippet
                 `(begin
@@ -1193,14 +1193,33 @@ (define-public gdal
                        "frmts/jpeg/libjpeg12"
                        "frmts/gtiff/libtiff"
                        "frmts/gtiff/libgeotiff"
-                       "frmts/zlib"
                        "ogr/ogrsf_frmts/geojson/libjson"))))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f
-       #:configure-flags
-       (list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL"
-             "-DGDAL_USE_JPEG12_INTERNAL=OFF")))
+     (list
+      #:tests? #f
+      #:configure-flags
+      #~(list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL"
+              "-DGDAL_USE_JPEG12_INTERNAL=OFF")
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  (ice-9 rdelim)
+                  (ice-9 popen))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'fix-rpath
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
+                (for-each
+                 (lambda (file)
+                   (let* ((pipe (open-pipe* OPEN_READ "patchelf"
+                                            "--print-rpath" file))
+                          (line (read-line pipe)))
+                     (and (zero? (close-pipe pipe))
+                          (invoke "patchelf" "--set-rpath"
+                                  (string-append libdir ":" line)
+                                  file))))
+                 (find-files libdir ".*\\.so$"))))))))
     (inputs
      (list curl
            expat
@@ -1227,7 +1246,8 @@ (define-public gdal
            zlib
            zstd))
     (native-inputs
-     (list pkg-config
+     (list patchelf
+           pkg-config
            python))
     (propagated-inputs
      (list python-numpy))
-- 
2.41.0
Information forwarded to guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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From: Roman Scherer <roman@HIDDEN>
To: 68606 <at> debbugs.gnu.org
Subject: [PATCH 2/2] gnu: gdal: Build Java bindings.
Date: Sat, 20 Jan 2024 12:30:26 +0100
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* gnu/packages/geo.scm (gdal): Build Java bindings.

Change-Id: I6c6a6d4b5f7c6692d443d8ebf288dfe6c4ccad87
---
 gnu/packages/geo.scm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 3c82f2f3af..d2d78197c3 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1207,6 +1207,10 @@ (define-public gdal
                   (ice-9 popen))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-JAVA_HOME
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((jdk (assoc-ref inputs "jdk")))
+                (setenv "JAVA_HOME" jdk))))
           (add-after 'install 'fix-rpath
             (lambda* (#:key outputs #:allow-other-keys)
               (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
@@ -1246,9 +1250,11 @@ (define-public gdal
            zlib
            zstd))
     (native-inputs
-     (list patchelf
-           pkg-config
-           python))
+     `(("ant" ,ant)
+       ("jdk" ,openjdk11 "jdk")
+       ("patchelf" ,patchelf)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://gdal.org/")
-- 
2.34.1
Information forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at 68606 <at> debbugs.gnu.org:


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From: Roman Scherer <roman@HIDDEN>
To: 68606 <at> debbugs.gnu.org
Subject: [PATCH 1/2] gnu: gdal: Update to 3.8.3.
Date: Sat, 20 Jan 2024 12:30:25 +0100
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* gnu/packages/geo.scm (gdal): Update to 3.8.3.

Change-Id: Ib36177e1cb37e3852475cc0c1da3eb8747aac6d5
---
 gnu/packages/geo.scm | 36 ++++++++++++++++++++++++++++--------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 14e2d9f16b..3c82f2f3af 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1172,7 +1172,7 @@ (define-public spatialite-gui
 (define-public gdal
   (package
     (name "gdal")
-    (version "3.6.1")
+    (version "3.8.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1180,7 +1180,7 @@ (define-public gdal
                      version ".tar.gz"))
               (sha256
                (base32
-                "1qckwnygszxkkq40bf87s3m1sab6jj9jyakdvskh0qf7dq8zjarf"))
+                "1sj9l1hjfs5d0mnv71iy8zk2xprn46h8gxq0cai9v7i3m23h78zp"))
               (modules '((guix build utils)))
               (snippet
                 `(begin
@@ -1193,14 +1193,33 @@ (define-public gdal
                        "frmts/jpeg/libjpeg12"
                        "frmts/gtiff/libtiff"
                        "frmts/gtiff/libgeotiff"
-                       "frmts/zlib"
                        "ogr/ogrsf_frmts/geojson/libjson"))))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f
-       #:configure-flags
-       (list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL"
-             "-DGDAL_USE_JPEG12_INTERNAL=OFF")))
+     (list
+      #:tests? #f
+      #:configure-flags
+      #~(list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL"
+              "-DGDAL_USE_JPEG12_INTERNAL=OFF")
+      #:modules '((guix build cmake-build-system)
+                  (guix build utils)
+                  (ice-9 rdelim)
+                  (ice-9 popen))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'fix-rpath
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
+                (for-each
+                 (lambda (file)
+                   (let* ((pipe (open-pipe* OPEN_READ "patchelf"
+                                            "--print-rpath" file))
+                          (line (read-line pipe)))
+                     (and (zero? (close-pipe pipe))
+                          (invoke "patchelf" "--set-rpath"
+                                  (string-append libdir ":" line)
+                                  file))))
+                 (find-files libdir ".*\\.so$"))))))))
     (inputs
      (list curl
            expat
@@ -1227,7 +1246,8 @@ (define-public gdal
            zlib
            zstd))
     (native-inputs
-     (list pkg-config
+     (list patchelf
+           pkg-config
            python))
     (propagated-inputs
      (list python-numpy))
-- 
2.34.1
Information forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.

Message received at submit <at> debbugs.gnu.org:


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From: Roman Scherer <roman@HIDDEN>
To: guix-patches@HIDDEN
Subject: [PATCH 0/2] Update GDAL and build Java bindings.
Date: Sat, 20 Jan 2024 12:29:38 +0100
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Hello Guix,

this patch series updates GDAL to v3.8.3 and builds the Java bindings.

While updating GDL I run into issues with the validate-runpath phase. I could
not get it passing by tweaking the cmake build flags. For some reason the
Pyhton bindings did not pick up the right runtime path and the
validate-runpath phase failed. After looking around a bit I saw this can be
manually fixed with patchelf. I tested the Python and Java bindings by
importing GDAL and registering all drivers.

I also had to remove the deletion of frmts/zlib since the cmake build file
adds a library under that path. Tweaking the build file to remove adding the
library caused the build to fail.

Could you please review the patche series?

Thanks, Roman.

Roman Scherer (2):
  gnu: gdal: Update to 3.8.3.
  gnu: gdal: Build Java bindings.

 gnu/packages/geo.scm | 44 +++++++++++++++++++++++++++++++++++---------
 1 file changed, 35 insertions(+), 9 deletions(-)


base-commit: 0eadd486484fcf9a234758842f74ba28361640db
--
2.34.1
Acknowledgement sent to Roman Scherer <roman@HIDDEN>:
New bug report received and forwarded. Copy sent to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN. Full text available.
Report forwarded to andreas@HIDDEN, efraim@HIDDEN, bavier@HIDDEN, sharlatanus@HIDDEN, guix-patches@HIDDEN:
bug#68606; Package guix-patches. Full text available.
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