GNU bug report logs -
#68606
[PATCH 0/2] Update GDAL and build Java bindings.
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(Sat, 20 Jan 2024 11:30:02 GMT)
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:
New bug report received and forwarded. Copy sent to
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(Sat, 20 Jan 2024 11:30:02 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
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
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(Sat, 20 Jan 2024 11:31:02 GMT)
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Message #8 received at 68606 <at> debbugs.gnu.org (full text, mbox):
* 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
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Message #11 received at 68606 <at> debbugs.gnu.org (full text, mbox):
* 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
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(Sun, 21 Jan 2024 13:55:01 GMT)
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Message #14 received at 68606 <at> debbugs.gnu.org (full text, mbox):
* 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
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(Sun, 21 Jan 2024 13:55:02 GMT)
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Message #17 received at 68606 <at> debbugs.gnu.org (full text, mbox):
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
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Message #20 received at 68606 <at> debbugs.gnu.org (full text, mbox):
* 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
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(Sun, 21 Jan 2024 13:55:03 GMT)
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Message #23 received at 68606 <at> debbugs.gnu.org (full text, mbox):
* 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
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(Wed, 24 Jan 2024 14:33:02 GMT)
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Message #26 received at 68606 <at> debbugs.gnu.org (full text, mbox):
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
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(Wed, 24 Jan 2024 19:23:02 GMT)
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Message #29 received at 68606 <at> debbugs.gnu.org (full text, mbox):
Hi Andreas,
Andreas Enge <andreas <at> enge.fr> 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 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).
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.
--
Thanks,
Maxim
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(Thu, 25 Jan 2024 10:19:02 GMT)
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Message #32 received at 68606 <at> debbugs.gnu.org (full text, mbox):
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
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(Mon, 24 Mar 2025 14:52:02 GMT)
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Message #35 received at 68606 <at> debbugs.gnu.org (full text, mbox):
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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(Tue, 25 Mar 2025 10:25:01 GMT)
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Message #38 received at 68606 <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
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 <at> enge.fr> 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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(Tue, 25 Mar 2025 11:27:02 GMT)
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Message #41 received at 68606 <at> debbugs.gnu.org (full text, mbox):
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
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(Wed, 26 Mar 2025 07:47:01 GMT)
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Message #44 received at 68606 <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
Hi Andreas,
Ok, then let's close it for now. I don't have a gdal use case at the moment.
Thanks
On Tue, Mar 25, 2025, 12:26 Andreas Enge <andreas <at> enge.fr> wrote:
> 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
>
>
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(Wed, 26 Mar 2025 08:25:02 GMT)
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bug acknowledged by developer.
(Wed, 26 Mar 2025 08:25:02 GMT)
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Message #49 received at 68606-done <at> debbugs.gnu.org (full text, mbox):
Am Wed, Mar 26, 2025 at 08:45:45AM +0100 schrieb Roman Scherer:
> Ok, then let's close it for now. I don't have a gdal use case at the moment.
Done!
Andreas
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(Wed, 26 Mar 2025 09:41:01 GMT)
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Message #52 received at 68606-done <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
Thank you Andreas
On Wed, Mar 26, 2025, 09:24 Andreas Enge <andreas <at> enge.fr> wrote:
> Am Wed, Mar 26, 2025 at 08:45:45AM +0100 schrieb Roman Scherer:
> > Ok, then let's close it for now. I don't have a gdal use case at the
> moment.
>
> Done!
>
> Andreas
>
>
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