Package: guix-patches;
Reported by: Andreas Enge <andreas <at> enge.fr>
Date: Thu, 27 Mar 2025 19:48:02 UTC
Severity: normal
Tags: patch
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andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#77321; Package guix-patches.
(Thu, 27 Mar 2025 19:48:02 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.
(Thu, 27 Mar 2025 19:48:02 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: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr>, sharlatanus <at> gmail.com, bavier <at> posteo.net Subject: [PATCH 0/2] Remove atlas and shogun Date: Thu, 27 Mar 2025 20:47:05 +0100
After updating the standard hdf5 package from 1.10 to 1.14, I noticed that atlas and its only dependency shogun do not build. But in fact they also did not build before. So I suggest to remove them on or after April 27, with more arguments given in each patch. Andreas Enge (2): gnu: Remove shogun. gnu: Remove atlas. gnu/packages/machine-learning.scm | 148 ------------------------------ gnu/packages/maths.scm | 129 -------------------------- 2 files changed, 277 deletions(-) base-commit: 0e79d96ad85d9b5bf5e0356917ed740092a87c80 -- 2.49.0
guix-patches <at> gnu.org:bug#77321; Package guix-patches.
(Thu, 27 Mar 2025 19:51:02 GMT) Full text and rfc822 format available.Message #8 received at 77321 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77321 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr>, sharlatanus <at> gmail.com, bavier <at> posteo.net Subject: [PATCH 1/2] gnu: Remove shogun. Date: Thu, 27 Mar 2025 20:49:43 +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#77321; Package guix-patches.
(Thu, 27 Mar 2025 19:51:02 GMT) Full text and rfc822 format available.Message #11 received at 77321 <at> debbugs.gnu.org (full text, mbox):
From: Andreas Enge <andreas <at> enge.fr> To: 77321 <at> debbugs.gnu.org Cc: rekado <at> elephly.net, Andreas Enge <andreas <at> enge.fr>, sharlatanus <at> gmail.com, bavier <at> posteo.net Subject: [PATCH 2/2] gnu: Remove atlas. Date: Thu, 27 Mar 2025 20:49:44 +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 f0d0bb8f97..49e4ee4171 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6991,135 +6991,6 @@ (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#77321; Package guix-patches.
(Fri, 28 Mar 2025 07:19:02 GMT) Full text and rfc822 format available.Message #14 received at 77321 <at> debbugs.gnu.org (full text, mbox):
From: Ricardo Wurmus <rekado <at> elephly.net> To: Andreas Enge <andreas <at> enge.fr> Cc: 77321 <at> debbugs.gnu.org, sharlatanus <at> gmail.com, bavier <at> posteo.net Subject: Re: [PATCH 1/2] gnu: Remove shogun. Date: Fri, 28 Mar 2025 08:18:44 +0100
Andreas Enge <andreas <at> enge.fr> writes: > * 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. This looks good to me. I agree with removing it. -- Ricardo
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