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

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

[Roman Scherer]

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

[bug#68606] [PATCH 1/2] gnu: gdal: Update to 3.8.3.

[Roman Scherer]

* 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

[bug#68606] [PATCH 2/2] gnu: gdal: Build Java bindings.

[Roman Scherer]

* 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

[bug#68606] [PATCH v2 0/3] Update GDAL and build Java bindings.

[Roman Scherer]

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

[bug#68606] [PATCH v2 1/3] gnu: gdal: Update to 3.8.3.

[Roman Scherer]

* 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

[bug#68606] [PATCH v2 2/3] gnu: gdal: Build Java bindings.

[Roman Scherer]

* 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

[bug#68606] [PATCH v2 3/3] gnu: patchelf: Update to 0.18.0.

[Roman Scherer]

* 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