Package: guix-patches;
Reported by: Andreas Enge <andreas <at> enge.fr>
Date: Wed, 26 Mar 2025 15:56:01 UTC
Severity: normal
Tags: patch
Done: Andreas Enge <andreas <at> enge.fr>
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andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Wed, 26 Mar 2025 15:56:01 GMT) Full text and rfc822 format available.Andreas Enge <andreas <at> enge.fr>:andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org.
(Wed, 26 Mar 2025 15:56:01 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: guix-patches <at> gnu.org Cc: Andreas Enge <andreas <at> enge.fr> Subject: [PATCH] gnu: hdf5: Make hdf <at> 1.14 the default version. Date: Wed, 26 Mar 2025 16:51:56 +0100
* gnu/packages/maths.scm (hdf5-1.14): Rename to...
(hdf5): ...this, which was previously defined as hdf5-1.10.
(hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names.
Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485
---
The following patch makes hdf5 <at> 1.14 the default, so that packages will
depend on this version instead of hdf5 <at> 1.10. We need to check which
dependents fail to build; for the time being, we can then replace their
inputs with hdf5 <at> 1.10. In the long run, this version of hdf5 should be
removed since it is not maintained any more, see
https://issues.guix.gnu.org/64448
This patch also does not update hdf-java.
gnu/packages/maths.scm | 14 +++++---------
1 file changed, 5 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 8baf3a0a7f..2fe2c6ddde 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1795,7 +1795,7 @@ (define-public hdf5-1.10
(base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00"))
(patches (search-patches "hdf5-config-date.patch"))))))
-(define-public hdf5-1.14
+(define-public hdf5
(package
(inherit hdf5-1.8)
(version "1.14.3")
@@ -1833,10 +1833,6 @@ (define-public hdf5-1.14
(("@UNAME_INFO@")
"Linux"))))))))))
-(define-public hdf5
- ;; Default version of HDF5.
- hdf5-1.10)
-
;; Keep this in sync with the current hdf5 package.
(define-public hdf-java
(package
@@ -2002,7 +1998,7 @@ (define-public hdf-eos5
(list autoconf automake gfortran libtool))
(build-system gnu-build-system)
(inputs
- (list hdf5-1.14 zlib gctp))
+ (list hdf5 zlib gctp))
(arguments
(list
#:configure-flags ''("--enable-install-include" "--enable-shared"
@@ -2037,13 +2033,13 @@ (define-public hdf-eos5
(license (license:non-copyleft home-page))))
(define-public hdf5-parallel-openmpi
- (package/inherit hdf5-1.14 ;use the latest
+ (package/inherit hdf5
(name "hdf5-parallel-openmpi")
(inputs
`(("mpi" ,openmpi)
,@(package-inputs hdf5)))
(arguments
- (substitute-keyword-arguments (package-arguments hdf5-1.14)
+ (substitute-keyword-arguments (package-arguments hdf5)
((#:configure-flags flags)
#~(cons "--enable-parallel"
(delete "--enable-cxx"
@@ -10588,7 +10584,7 @@ (define-public scilab
curl
fftw
gettext-minimal
- hdf5-1.14
+ hdf5
libarchive
libx11
libxml2
base-commit: ea41557c9f8bb8670e25a389a408d0112ea6aa34
--
2.49.0
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Wed, 26 Mar 2025 21:26:02 GMT) Full text and rfc822 format available.Message #8 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 77287 <at> debbugs.gnu.org Cc: andreas <at> enge.fr Subject: [PATCH] gnu: hdf5: Make hdf <at> 1.14 the default version. Date: Wed, 26 Mar 2025 21:25:04 +0000
[Message part 1 (text/plain, inline)]
Hi Andreas, Would like to wait QA to pick up this issue? I'll give it a go to build "guix build -P1 hdf5" mean while. -- Oleg
[signature.asc (application/pgp-signature, inline)]
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Wed, 26 Mar 2025 21:42:03 GMT) Full text and rfc822 format available.Message #11 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: Sharlatan Hellseher <sharlatanus <at> gmail.com> Cc: 77287 <at> debbugs.gnu.org Subject: Re: [PATCH] gnu: hdf5: Make hdf <at> 1.14 the default version. Date: Wed, 26 Mar 2025 22:40:48 +0100
Am Wed, Mar 26, 2025 at 09:25:04PM +0000 schrieb Sharlatan Hellseher: > Would like to wait QA to pick up this issue? Maybe. QA is working so poorly right now that I think it would make more sense to let it handle contributions by people who are not committers. > I'll give it a go to build "guix build -P1 hdf5" mean while. Hold back, I am doing it already, and replacing back hdf5-1.10 as input for packages that do not compile with hdf5 <at> 1.14. So far I have found fast5 and ncbi-vdb. I will keep you (and this issue) updated. The package that might need more work is hdf-java; I think we should update it to 1.14, preferably in the same commit series. It has a very long recipe, and in case we cannot simply update the source, but need to modify the code, I am afraid this will be quite time consuming. Andreas
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:02 GMT) Full text and rfc822 format available.Message #14 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 0/8] Update default hdf5 to 1.14 Date: Sat, 29 Mar 2025 10:21:24 +0100
Hello, here is an updated patch series, mostly for reference. The main patch is "gnu: hdf5: Make hdf <at> 1.14 the default version.". The first patches correspond to packages that compiled neither with the previous, nor with the current hdf5; I have opened separate issues for removing them. If you want to test and apply them, then all first-level dependencies of hdf5 still build. Up to there, the hdf-java package is still at version 1.10. I did not manage to update it easily, the final patch is there just for reference. In fact the Makefile.am and Makefile.in files that are supposed to be modified in a phase have disappeared, and there is only a CMakeLists.txt file remaining. If someone else could work on this, it would be much appreciated. If not, I think that the "Make hdf5 <at> 1.14 the default version." patch can be pushed as is, leaving hdf-java at the 1.10 version (the package has no dependencies). (I just notice that there is a "5" missing in the commit message, I will correct this immediately.) Andreas Enge (8): gnu: Remove h5check. gnu: Remove shogun. gnu: Remove atlas. gnu: Remove variant-tools. gnu: Remove mia. gnu: Remove itk-snap. gnu: hdf5: Make hdf <at> 1.14 the default version. gnu: hdf-java: Update to 1.14.3. gnu/packages/bioinformatics.scm | 41 +------ gnu/packages/cran.scm | 2 +- gnu/packages/image-processing.scm | 187 ------------------------------ gnu/packages/image.scm | 2 +- gnu/packages/machine-learning.scm | 148 ----------------------- gnu/packages/maths.scm | 167 ++------------------------ 6 files changed, 11 insertions(+), 536 deletions(-) base-commit: c31662f7294b194663bc521358b01c3a7d7e4e27 -- 2.49.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:02 GMT) Full text and rfc822 format available.Message #17 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 1/8] gnu: Remove h5check. Date: Sat, 29 Mar 2025 10:21:25 +0100
* gnu/packages/maths.scm (h5check): Delete variable.
Change-Id: Ia7ced02059734cf8a5a2db39bbe0f1b38f67df12
---
gnu/packages/maths.scm | 20 --------------------
1 file changed, 20 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 3de5b7b8ae..0d56dd4410 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2144,26 +2144,6 @@ (define-public hdf5-blosc
Blosc-compressed datasets.")
(license license:expat)))
-(define-public h5check
- (package
- (name "h5check")
- (version "2.0.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
- "h5check/src/h5check-" version ".tar.gz"))
- (sha256
- (base32
- "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
- (build-system gnu-build-system)
- (inputs (list hdf5-1.8)) ;h5cc for tests
- (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
- (synopsis "HDF5 format checker")
- (description "@code{h5check} is a validation tool for verifying that an
-HDF5 file is encoded according to the HDF File Format Specification.")
- (license (license:x11-style "file://COPYING"))))
-
(define-public itex2mml
(package
(name "itex2mml")
--
2.49.0
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:03 GMT) Full text and rfc822 format available.Message #20 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 2/8] gnu: Remove shogun. Date: Sat, 29 Mar 2025 10:21:26 +0100
* gnu/packages/machine-learning.scm (shogun): Delete variable.
The package depends on atlas, which does not build any more. The ftp
server that is supposed to contain the source code has become private
and does not accept anonymous connections. The package has not been
updated since 2018. It has no dependent packages.
Change-Id: Ia2e1ef51180397a056410fd8d33ce2827623aaa0
---
gnu/packages/machine-learning.scm | 148 ------------------------------
1 file changed, 148 deletions(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 4ea05a7752..818e208a37 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1422,154 +1422,6 @@ (define-public python-spacy
model packaging, deployment and workflow management.")
(license license:expat)))
-(define-public shogun
- (package
- (name "shogun")
- (version "6.1.3")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "ftp://shogun-toolbox.org/shogun/releases/"
- (version-major+minor version)
- "/sources/shogun-" version ".tar.bz2"))
- (sha256
- (base32
- "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
- (modules '((guix build utils)
- (ice-9 rdelim)))
- (snippet
- '(begin
- ;; Remove non-free sources and files referencing them
- (for-each delete-file
- (find-files "src/shogun/classifier/svm/"
- "SVMLight\\.(cpp|h)"))
- (for-each delete-file
- (find-files "examples/undocumented/libshogun/"
- (string-append
- "(classifier_.*svmlight.*|"
- "evaluation_cross_validation_locked_comparison).cpp")))
- ;; Remove non-free functions.
- (define (delete-ifdefs file)
- (with-atomic-file-replacement file
- (lambda (in out)
- (let loop ((line (read-line in 'concat))
- (skipping? #f))
- (if (eof-object? line)
- #t
- (let ((skip-next?
- (or (and skipping?
- (not (string-prefix?
- "#endif //USE_SVMLIGHT" line)))
- (string-prefix?
- "#ifdef USE_SVMLIGHT" line))))
- (when (or (not skipping?)
- (and skipping? (not skip-next?)))
- (display line out))
- (loop (read-line in 'concat) skip-next?)))))))
- (for-each delete-ifdefs
- (append
- (find-files "src/shogun/classifier/mkl"
- "^MKLClassification\\.cpp")
- (find-files "src/shogun/classifier/svm"
- "^SVMLightOneClass\\.(cpp|h)")
- (find-files "src/shogun/multiclass"
- "^ScatterSVM\\.(cpp|h)")
- (find-files "src/shogun/kernel/"
- "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
- (find-files "src/shogun/regression/svr"
- "^(MKLRegression|SVRLight)\\.(cpp|h)")
- (find-files "src/shogun/transfer/domain_adaptation"
- "^DomainAdaptationSVM\\.(cpp|h)")))
- #t))))
- (build-system cmake-build-system)
- (arguments
- '(#:tests? #f ;no check target
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'delete-broken-symlinks
- (lambda _
- (for-each delete-file '("applications/arts/data"
- "applications/asp/data"
- "applications/easysvm/data"
- "applications/msplicer/data"
- "applications/ocr/data"
- "examples/meta/data"
- "examples/undocumented/data"))
- #t))
- (add-after 'unpack 'change-R-target-path
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("src/interfaces/r/CMakeLists.txt"
- "examples/meta/r/CMakeLists.txt")
- (("\\$\\{R_COMPONENT_LIB_PATH\\}")
- (string-append (assoc-ref outputs "out")
- "/lib/R/library/")))
- #t))
- (add-after 'unpack 'fix-octave-modules
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* "src/interfaces/octave/CMakeLists.txt"
- (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
- "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
- ;; change target directory
- (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
- (string-append (assoc-ref outputs "out")
- "/share/octave/packages")))
- (substitute* '("src/interfaces/octave/swig_typemaps.i"
- "src/interfaces/octave/sg_print_functions.cpp")
- ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
- (("octave/config\\.h") "octave/octave-config.h")
- (("octave/oct-obj.h") "octave/ovl.h"))
- #t))
- (add-after 'unpack 'move-rxcpp
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((rxcpp-dir "shogun/third-party/rxcpp"))
- (mkdir-p rxcpp-dir)
- (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
- #t)))
- (add-before 'build 'set-HOME
- ;; $HOME needs to be set at some point during the build phase
- (lambda _ (setenv "HOME" "/tmp") #t)))
- #:configure-flags
- (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
- "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
- "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
- ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
- ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
- ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
- ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
- "-DINTERFACE_OCTAVE=ON"
- "-DINTERFACE_PYTHON=ON"
- "-DINTERFACE_R=ON")))
- (inputs
- `(("python" ,python)
- ("numpy" ,python-numpy)
- ("r-minimal" ,r-minimal)
- ("octave" ,octave-cli)
- ("swig" ,swig)
- ("eigen" ,eigen)
- ("hdf5" ,hdf5)
- ("atlas" ,atlas)
- ("arpack" ,arpack-ng)
- ("openblas" ,openblas)
- ("glpk" ,glpk)
- ("libxml2" ,libxml2)
- ("lzo" ,lzo)
- ("zlib" ,zlib)))
- (native-inputs
- (list pkg-config rxcpp))
- ;; Non-portable SSE instructions are used so building fails on platforms
- ;; other than x86_64.
- (supported-systems '("x86_64-linux"))
- (home-page "https://shogun-toolbox.org/")
- (synopsis "Machine learning toolbox")
- (description
- "The Shogun Machine learning toolbox provides a wide range of unified and
-efficient Machine Learning (ML) methods. The toolbox seamlessly
-combines multiple data representations, algorithm classes, and general purpose
-tools. This enables both rapid prototyping of data pipelines and extensibility
-in terms of new algorithms.")
- (license license:gpl3+)))
-
(define-public onnx
(package
(name "onnx")
--
2.49.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:04 GMT) Full text and rfc822 format available.Message #23 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 3/8] gnu: Remove atlas. Date: Sat, 29 Mar 2025 10:21:27 +0100
* gnu/packages/maths.scm (atlas): Delete variable.
The package does not build anymore. Its last release dates from 2016.
After the removal of shogun there are no other dependent packages.
Change-Id: Ibe988d33451b63ef7680b6c0a19cff6430a42a68
---
gnu/packages/maths.scm | 129 -----------------------------------------
1 file changed, 129 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0d56dd4410..017abecc00 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6995,135 +6995,6 @@ (define-public suitesparse
;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
(license (list license:gpl2+ license:lgpl2.1+))))
-(define-public atlas
- (package
- (name "atlas")
- (version "3.10.3")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
- version "/atlas" version ".tar.bz2"))
- (patches (search-patches "atlas-gfortran-compat.patch"))
- (sha256
- (base32
- "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
- (build-system gnu-build-system)
- (home-page "https://math-atlas.sourceforge.net/")
- (inputs `(("gfortran" ,gfortran)
- ("lapack-tar" ,(package-source lapack))))
- (outputs '("out" "doc"))
- ;; For the moment we drop support for MIPS at it fails to compile. See
- ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
- (supported-systems (delete "mips64el-linux" %supported-systems))
- (arguments
- `(#:parallel-build? #f
- #:parallel-tests? #f
-
- ;; ATLAS tunes itself for the machine it is built on, as explained at
- ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
- ;; For this reason, we want users to build it locally instead of using
- ;; substitutes.
- #:substitutable? #f
-
- #:modules ((srfi srfi-26)
- (guix build gnu-build-system)
- (guix build utils))
- #:configure-flags
- `(;; Generate position independent code suitable for dynamic libraries
- ;; and use WALL timer to get more accurate timing.
- "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
- ;; Set word width.
- "-b"
- ,,(if (string-match "64" (%current-system))
- "64"
- "32")
- ;; Disable parallel build as it gives errors: atlas_pthread.h is
- ;; needed to compile C files before it is generated.
- "-Ss" "pmake" "make -j 1"
- ;; Probe is failing for MIPS. We therefore define the system
- ;; architecture explicitly by setting (-A) MACHINETYPE = 49
- ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
- ,,@(if (string-prefix? "mips" (%current-system))
- (list "-A" "49" "-V" "1")
- (list))
- ;; Generate shared libraries.
- "--shared"
- ;; Build a full LAPACK library.
- ,(string-append "--with-netlib-lapack-tarfile="
- (assoc-ref %build-inputs "lapack-tar")))
- #:phases
- (modify-phases %standard-phases
- (add-after 'install 'install-doc
- (lambda* (#:key outputs inputs #:allow-other-keys)
- (let ((doc (string-append (assoc-ref outputs "doc")
- "/share/doc/atlas")))
- (mkdir-p doc)
- (for-each (cut install-file <> doc)
- (find-files "../ATLAS/doc" ".*"))
- #t)))
- (add-after 'check 'check-pt
- (lambda _ (invoke "make" "ptcheck")))
- ;; Fix files required to run configure.
- (add-before 'configure 'fix-/bin/sh
- (lambda _
- ;; Use `sh', not `/bin/sh'.
- (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
- (("/bin/sh")
- "sh"))
- #t))
- ;; Fix /bin/sh in generated make files.
- (add-after 'configure 'fix-/bin/sh-in-generated-files
- (lambda _
- (substitute* (find-files "." "^[Mm]ake\\.inc.*")
- (("/bin/sh")
- "sh"))
- #t))
- ;; ATLAS configure program does not accepts the default flags
- ;; passed by the 'gnu-build-system'.
- (replace 'configure
- (lambda* (#:key native-inputs inputs outputs
- (configure-flags '())
- #:allow-other-keys #:rest args)
- (let* ((prefix (assoc-ref outputs "out"))
- (bash (or (and=> (assoc-ref
- (or native-inputs inputs) "bash")
- (cut string-append <> "/bin/bash"))
- "/bin/sh"))
- (flags `(,(string-append "--prefix=" prefix)
- ,@configure-flags))
- (abs-srcdir (getcwd))
- (srcdir (string-append "../" (basename abs-srcdir))))
- (format #t "source directory: ~s (relative from build: ~s)~%"
- abs-srcdir srcdir)
- (mkdir "../build")
- (chdir "../build")
- (format #t "build directory: ~s~%" (getcwd))
- (format #t "configure flags: ~s~%" flags)
- (apply invoke bash
- (string-append srcdir "/configure")
- flags)))))))
- (synopsis "Automatically Tuned Linear Algebra Software")
- (description
- "ATLAS is an automatically tuned linear algebra software library
-providing C and Fortran77 interfaces to a portably efficient BLAS
-implementation, as well as a few routines from LAPACK.
-
-Optimization occurs at build time. For this reason, the library is built on
-the machine where it is installed, without resorting to pre-built substitutes.
-
-Before building the library, CPU throttling should be disabled. This can be
-done in the BIOS, or, on GNU/Linux, with the following command:
-
-@example
-# cpupower --governor performance
-@end example
-
-Failure to do so will result in a library with poor performance.")
- ;; The test suite is notoriously lengthy and routinely exceeds the default
- ;; timeout of 21600 seconds on the not unbeefy berlin build nodes.
- (properties '((timeout . 86400))) ; 1 day
- (license license:bsd-3)))
-
(define-public cglm
(package
(name "cglm")
--
2.49.0
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:05 GMT) Full text and rfc822 format available.Message #26 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 5/8] gnu: Remove mia. Date: Sat, 29 Mar 2025 10:21:29 +0100
The package has no dependent packages. It does not build any more since
May 2023, and has not seen a newer release since the currently packaged
release from 2020.
* gnu/packages/image-processing.scm (mia): Delete variable.
Change-Id: I62556d2690903b6171b5ff752094310fb989fc03
---
gnu/packages/image-processing.scm | 56 -------------------------------
1 file changed, 56 deletions(-)
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index c4eb028877..4ddb01f450 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -206,62 +206,6 @@ (define-public dcmtk
"A union of the Apache 2.0 licence and various non-copyleft
licences similar to the Modified BSD licence."))))
-(define-public mia
- (package
- (name "mia")
- (version "2.4.7")
- (source (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/mia/mia/"
- (version-major+minor version)
- "/mia-" version ".tar.xz"))
- (sha256
- (base32
- "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1"))
- (patches (search-patches "mia-fix-boost-headers.patch"
- "mia-vtk9.patch"
- "mia-vtk92.patch"
- "mia-vtk-version.patch"))))
- (build-system cmake-build-system)
- (arguments
- `(#:configure-flags
- (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF"
- "-DCMAKE_CXX_FLAGS=-fpermissive")))
- (inputs
- (list boost
- dcmtk
- doxygen
- eigen
- fftw
- fftwf
- gsl
- gts
- hdf5
- itpp
- libjpeg-turbo
- libpng
- libtiff
- libxml2
- libxml++
- maxflow
- niftilib
- nlopt
- openexr-2
- python-lxml
- vtk))
- (native-inputs
- (list pkg-config
- python-wrapper))
- (home-page "https://mia.sourceforge.net")
- (synopsis "Toolkit for gray scale medical image analysis")
- (description "MIA provides a combination of command line tools, plug-ins,
-and libraries that make it possible run image processing tasks interactively
-in a command shell and to prototype using the shell's scripting language. It
-is built around a plug-in structure that makes it easy to add functionality
-without compromising the original code base and it makes use of a wide variety
-of external libraries that provide additional functionality.")
- (license license:gpl3+)))
-
(define-public opencolorio
(package
(name "opencolorio")
--
2.49.0
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:06 GMT) Full text and rfc822 format available.Message #29 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 4/8] gnu: Remove variant-tools. Date: Sat, 29 Mar 2025 10:21:28 +0100
* gnu/packages/bioinformatics.scm (variant-tools): Delete variable.
The package does not compile any more and has no dependent packages.
The last release dates from 2020; there is an additional commit in 2022;
the git repository has been archived in 2023.
Change-Id: Idb5df024121c5085f764f179d31ac67cff3fc5c7
---
gnu/packages/bioinformatics.scm | 37 ---------------------------------
1 file changed, 37 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0825fbb6ef..e8b585e495 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15248,43 +15248,6 @@ (define-public multiqc
common bioinformatics tools.")
(license license:gpl3+)))
-(define-public variant-tools
- (package
- (name "variant-tools")
- (version "3.1.2")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/vatlab/varianttools")
- ;; There is no tag corresponding to version 3.1.2
- (commit "813ae4a90d25b69abc8a40f4f70441fe09015249")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g"))))
- (build-system python-build-system)
- (inputs
- (list boost
- c-blosc
- gsl
- hdf5
- hdf5-blosc
- python-cython
- zlib))
- (propagated-inputs
- (list python-numpy python-pycurl python-pyzmq python-scipy
- python-tables))
- (home-page "https://vatlab.github.io/vat-docs/")
- (synopsis "Analyze genetic variants from Next-Gen sequencing studies")
- (description
- "Variant tools is a tool for the manipulation, annotation,
-selection, simulation, and analysis of variants in the context of next-gen
-sequencing analysis. Unlike some other tools used for next-gen sequencing
-analysis, variant tools is project based and provides a whole set of tools to
-manipulate and analyze genetic variants.")
- (license license:gpl3+)))
-
(define-public r-chromvarmotifs
(let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076")
(revision "1"))
--
2.49.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:07 GMT) Full text and rfc822 format available.Message #32 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 8/8] gnu: hdf-java: Update to 1.14.3. Date: Sat, 29 Mar 2025 10:21:32 +0100
* gnu/packages/maths.scm (hdf-java): Update to 1.14.3.
[inputs]: Remove hdf5-1.10; add hdf5.
Change-Id: I43db316c3a83f5ddac14b0c670430811dcac6bdc
---
gnu/packages/maths.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index f851937a7c..c9a00c4b94 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1876,7 +1876,7 @@ (define-public hdf5
(define-public hdf-java
(package
(name "hdf-java")
- (version "1.10.9")
+ (version "1.14.3")
(source
(origin
(method git-fetch)
@@ -1888,7 +1888,7 @@ (define-public hdf-java
version)))))
(file-name (git-file-name name version))
(sha256
- (base32 "1sjdcnafvzsy99vqhybkps8rnwmxb6fsvmkw89wb2mrrp4vi5z9v"))
+ (base32 "0lw9f62zxyjiv7vx9nvnashjj39i44j8d626i7b788zkxw58csvs"))
(modules '((guix build utils)))
(snippet ; Make sure we don't use the bundled sources and binaries.
'(for-each delete-file
@@ -1959,7 +1959,7 @@ (define-public hdf-java
java-slf4j-simple))
(inputs
(list hdf4
- hdf5-1.10
+ hdf5
java-slf4j-api
libjpeg-turbo
zlib))
--
2.49.0
andreas <at> enge.fr, bavier <at> posteo.net, laurent.gatto <at> gmail.com, rekado <at> elephly.net, sharlatanus <at> gmail.com, zimon.toutoune <at> gmail.com, guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:07 GMT) Full text and rfc822 format available.Message #35 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 7/8] gnu: hdf5: Make hdf <at> 1.14 the default version. Date: Sat, 29 Mar 2025 10:21:31 +0100
This replaces all inputs hdf5 <at> 1.10 by hdf5 <at> 1.14 unless explicitly
specified otherwise.
* gnu/packages/maths.scm (hdf5-1.14): Rename to...
(hdf5): ...this, which was previously defined as hdf5-1.10.
(hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names.
(hdf-java)[inputs]: Keep hdf5-1.10.
* gnu/packages/bioinformatics.scm (fast5, ncbi-vdb),
gnu/packages/cran.scm (r-h5), gnu/packages/image.scm (vigra)[inputs]:
Keep hdf5-1.10.
Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485
---
gnu/packages/bioinformatics.scm | 4 ++--
gnu/packages/cran.scm | 2 +-
gnu/packages/image.scm | 2 +-
gnu/packages/maths.scm | 16 ++++++----------
4 files changed, 10 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e8b585e495..8fd7789028 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7941,7 +7941,7 @@ (define-public fast5
(add-after 'unpack 'chdir
(lambda _
(chdir "python"))))))
- (inputs (list hdf5))
+ (inputs (list hdf5-1.10))
(propagated-inputs
(list python-dateutil))
(native-inputs
@@ -11349,7 +11349,7 @@ (define-public ncbi-vdb
(install-file "libs/kfg/default.kfg" target)
(install-file "libs/kfg/certs.kfg" target)))))))
(inputs
- (list file hdf5 java-ngs libxml2 ngs-sdk ))
+ (list file hdf5-1.10 java-ngs libxml2 ngs-sdk ))
(native-inputs (list perl))
;; NCBI-VDB requires SSE capability.
(supported-systems '("i686-linux" "x86_64-linux"))
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8522eb07a5..4e96d70849 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -14934,7 +14934,7 @@ (define-public r-h5
"14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
(build-system r-build-system)
(inputs
- (list zlib hdf5))
+ (list zlib hdf5-1.10))
(native-inputs
(list r-knitr r-testthat which))
(propagated-inputs
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 89e7ef83e6..83b694b409 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -1389,7 +1389,7 @@ (define-public vigra
`(("boost" ,boost)
("fftw" ,fftw)
("fftwf" ,fftwf)
- ("hdf5" ,hdf5)
+ ("hdf5" ,hdf5-1.10)
("ilmbase" ,ilmbase) ; propagated by openexr, but needed explicitly
; to create a configure-flag
("libjpeg" ,libjpeg-turbo)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 017abecc00..f851937a7c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1834,7 +1834,7 @@ (define-public hdf5-1.10
(base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00"))
(patches (search-patches "hdf5-config-date.patch"))))))
-(define-public hdf5-1.14
+(define-public hdf5
(package
(inherit hdf5-1.8)
(version "1.14.3")
@@ -1872,10 +1872,6 @@ (define-public hdf5-1.14
(("@UNAME_INFO@")
"Linux"))))))))))
-(define-public hdf5
- ;; Default version of HDF5.
- hdf5-1.10)
-
;; Keep this in sync with the current hdf5 package.
(define-public hdf-java
(package
@@ -1963,7 +1959,7 @@ (define-public hdf-java
java-slf4j-simple))
(inputs
(list hdf4
- hdf5
+ hdf5-1.10
java-slf4j-api
libjpeg-turbo
zlib))
@@ -2041,7 +2037,7 @@ (define-public hdf-eos5
(list autoconf automake gfortran libtool))
(build-system gnu-build-system)
(inputs
- (list hdf5-1.14 zlib gctp))
+ (list hdf5 zlib gctp))
(arguments
(list
#:configure-flags ''("--enable-install-include" "--enable-shared"
@@ -2076,13 +2072,13 @@ (define-public hdf-eos5
(license (license:non-copyleft home-page))))
(define-public hdf5-parallel-openmpi
- (package/inherit hdf5-1.14 ;use the latest
+ (package/inherit hdf5
(name "hdf5-parallel-openmpi")
(inputs
`(("mpi" ,openmpi)
,@(package-inputs hdf5)))
(arguments
- (substitute-keyword-arguments (package-arguments hdf5-1.14)
+ (substitute-keyword-arguments (package-arguments hdf5)
((#:configure-flags flags)
#~(cons "--enable-parallel"
(delete "--enable-cxx"
@@ -10481,7 +10477,7 @@ (define-public scilab
curl
fftw
gettext-minimal
- hdf5-1.14
+ hdf5
libarchive
libx11
libxml2
--
2.49.0
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sat, 29 Mar 2025 09:30:08 GMT) Full text and rfc822 format available.Message #38 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: [PATCH v2 6/8] gnu: Remove itk-snap. Date: Sat, 29 Mar 2025 10:21:30 +0100
TODO: So far this is only for testing purposes.
* gnu/packages/image-processing.scm (itk-snap): Delete variable.
Change-Id: Iccdc5c60987fec57ee11ca190b43effb19675165
---
gnu/packages/image-processing.scm | 131 ------------------------------
1 file changed, 131 deletions(-)
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 4ddb01f450..a89874fc06 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1386,137 +1386,6 @@ (define-public insight-toolkit-4.12
;; error: ISO C++17 does not allow dynamic exception specifications
#~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
-(define-public itk-snap
- (package
- (name "itk-snap")
- (version "3.8.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://git.code.sf.net/p/itk-snap/src")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q"))
- (patches (search-patches "itk-snap-alt-glibc-compat.patch"))))
- (build-system cmake-build-system)
- (arguments
- `(#:configure-flags
- (list "-DSNAP_VERSION_GIT_SHA1=release"
- "-DSNAP_VERSION_GIT_BRANCH=release"
- "-DSNAP_VERSION_GIT_TIMESTAMP=0"
- "-DSNAP_PACKAGE_QT_PLUGINS=OFF"
- "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
- #:phases
- (modify-phases %standard-phases
- ;; During the installation phase all libraries provided by all
- ;; dependencies will be copied to the lib directory. That's insane,
- ;; so we disable this.
- (add-after 'unpack 'do-not-copy-dependencies
- (lambda _
- (substitute* "CMakeLists.txt"
- (("install_qt5_executable\
-\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)")
- ""))))
- (add-after 'unpack 'disable-gui-tests
- (lambda _
- ;; The GUI tests just time out.
- (substitute* "CMakeLists.txt"
- ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\
-|RandomForest|RandomForestBailOut)")
- ""))))
- (add-after 'unpack 'make-reproducible
- (lambda _
- (substitute* "CMakeLists.txt"
- (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)")
- "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")"))))
- (add-after 'unpack 'prepare-submodules
- (lambda* (#:key inputs #:allow-other-keys)
- (rmdir "Submodules/c3d")
- (copy-recursively (assoc-ref inputs "c3d-src")
- "Submodules/c3d")
- (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx"
- "Submodules/c3d/adapters/ApplyMetric.cxx")
- (("vcl_") "std::"))
- (rmdir "Submodules/greedy")
- (symlink (assoc-ref inputs "greedy-src")
- "Submodules/greedy")))
- (add-after 'unpack 'fix-includes
- (lambda _
- (substitute* "GUI/Model/RegistrationModel.cxx"
- (("<vnl_symmetric_eigensystem.h>")
- "<vnl/algo/vnl_symmetric_eigensystem.h>"))))
- (add-before 'check 'prepare-tests
- (lambda _
- ;; Needed by at least one test.
- (setenv "HOME" "/tmp")))
- (add-after 'install 'wrap-executable
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/itksnap")
- `("QT_PLUGIN_PATH" ":" prefix
- ,(map (lambda (label)
- (string-append (assoc-ref inputs label)
- "/lib/qt5/plugins"))
- '("qtbase" "qtdeclarative-5"))))))))))
- (inputs
- (list bash-minimal
- curl
- fftw
- fftwf
- glu
- hdf5
- mesa-opencl
- ;; This package does not build with either insight-toolkit 5.0.0
- ;; and not with 4.13. It really needs to be 4.12.
- insight-toolkit-4.12
- vtk-7
- qtbase-5
- qtdeclarative-5
- vxl-1
- zlib))
- (native-inputs
- `(("googletest" ,googletest)
- ("qttools-5" ,qttools-5)
- ("pkg-config" ,pkg-config)
- ("c3d-src"
- ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3")
- (revision "1")
- (version (git-version "0" revision commit)))
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pyushkevich/c3d")
- (commit commit)))
- (file-name (git-file-name "c3d" version))
- (sha256
- (base32
- "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3")))))
- ;; We are using an arbitrary commit from 2017 because the latest
- ;; version breaks the build...
- ("greedy-src"
- ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3")
- (revision "1")
- (version (git-version "0" revision commit)))
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pyushkevich/greedy")
- (commit commit)))
- (file-name (git-file-name "greedy" version))
- (sha256
- (base32
- "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab")))))))
- (home-page "https://sourceforge.net/p/itk-snap/")
- (synopsis "Medical image segmentation")
- (description "ITK-SNAP is a tool for segmenting anatomical structures in
-medical images. It provides an automatic active contour segmentation
-pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a
-full-featured UI aimed at clinical researchers.")
- ;; This includes the submodules greedy and c3d.
- (license license:gpl3+)))
-
(define-public metapixel
;; Follow stable branch.
(let ((commit "98ee9daa093b6c334941242e63f90b1c2876eb4f"))
--
2.49.0
guix-patches <at> gnu.org:bug#77287; Package guix-patches.
(Sun, 30 Mar 2025 14:46:01 GMT) Full text and rfc822 format available.Message #41 received at 77287 <at> debbugs.gnu.org (full text, mbox):
From: David Elsing <david.elsing <at> posteo.net> To: Andreas Enge <andreas <at> enge.fr>, 77287 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr> Subject: Re: [PATCH v2 0/8] Update default hdf5 to 1.14 Date: Sun, 30 Mar 2025 14:45:17 +0000
Hello, Andreas Enge <andreas <at> enge.fr> writes: > Up to there, the hdf-java package is still at version 1.10. I did not > manage to update it easily, the final patch is there just for reference. > In fact the Makefile.am and Makefile.in files that are supposed to be > modified in a phase have disappeared, and there is only a CMakeLists.txt > file remaining. If someone else could work on this, it would be much > appreciated. When adjusting the versions in the 'unbundle phase, the build succeeds: https://issues.guix.gnu.org/77385 Cheers, David
Andreas Enge <andreas <at> enge.fr>:Andreas Enge <andreas <at> enge.fr>:Message #46 received at 77287-done <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: David Elsing <david.elsing <at> posteo.net> Cc: rekado <at> elephly.net, 77287-done <at> debbugs.gnu.org Subject: Re: [PATCH v2 0/8] Update default hdf5 to 1.14 Date: Mon, 31 Mar 2025 10:35:13 +0200
Am Sun, Mar 30, 2025 at 02:45:17PM +0000 schrieb David Elsing: > When adjusting the versions in the 'unbundle phase, the build succeeds: > https://issues.guix.gnu.org/77385 Ah, excellent, thanks a lot for your help! I have pushed your patch as well as my patch updating hdf5, which makes all direct dependencies of hdf5 build except for those that also did not build before. So I am closing this, and will wait for the 1 month period until (probably) removing the non-building dependencies; if you want to comment on them, I have opened specific issues for each of them. Andreas
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