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Subject: [bug#77902] [PATCH science-team 0/2] Update SuiteSparse.
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The component suitesparse packages have no other dependents.

igraph has 26 dependent packages. Switch igraph to the suitesparse
dependency as the newer CXSparse breaks the build (igraph vendors
CXSparse from SuiteSparse 5.12.0).

Greg Hogan (2):
  gnu: Add %suitesparse-package-versions.
  gnu: igraph: Update to 0.10.15.

 gnu/local.mk                                  |  1 -
 gnu/packages/graph.scm                        |  7 +-
 gnu/packages/maths.scm                        | 64 +++++++++++--------
 gnu/packages/patches/gklib-suitesparse.patch  |  6 +-
 .../igraph-fix-varargs-integer-size.patch     | 39 -----------
 5 files changed, 45 insertions(+), 72 deletions(-)
 delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch

base-commit: ffc8a07ba45503014cc0647c5dd0613829999f98
-- 
2.49.0

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Subject: bug#77902: Acknowledgement ([PATCH science-team 0/2] Update
 SuiteSparse.)
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Subject: [bug#77902] [PATCH science-team 2/2] gnu: igraph: Update to 0.10.15.
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* gnu/packages/graph.scm (igraph): Update to 0.10.15.
[source]: Remove patches.
[inputs]: Replace suitesparse-cxsparse with suitesparse.
* gnu/packages/patches/igraph-fix-varargs-integer-size.patch: Delete.
* gnu/local.mk (dist_patch_DATA): Update accordingly.

Change-Id: Iffbfdc83b347f9abf82891f5b97954903d3df3dd
---
 gnu/local.mk                                  |  1 -
 gnu/packages/graph.scm                        |  7 ++--
 .../igraph-fix-varargs-integer-size.patch     | 39 -------------------
 3 files changed, 3 insertions(+), 44 deletions(-)
 delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 62cfe230bb..2828d8913f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1610,7 +1610,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
   %D%/packages/patches/id3lib-UTF16-writing-bug.patch			\
   %D%/packages/patches/idris-test-ffi008.patch			\
-  %D%/packages/patches/igraph-fix-varargs-integer-size.patch	\
   %D%/packages/patches/ilmbase-fix-tests.patch			\
   %D%/packages/patches/indent-CVE-2024-0911.patch	\
   %D%/packages/patches/inferno-fix-crash.patch		\
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 467a7f661b..af4943c281 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -106,7 +106,7 @@ (define-public plfit
 (define-public igraph
   (package
     (name "igraph")
-    (version "0.10.7")
+    (version "0.10.15")
     (source
      (origin
        (method git-fetch)
@@ -114,7 +114,6 @@ (define-public igraph
              (url "https://github.com/igraph/igraph")
              (commit version)))
        (file-name (git-file-name name version))
-       (patches (search-patches "igraph-fix-varargs-integer-size.patch"))
        (modules '((guix build utils)
                   (ice-9 ftw)
                   (srfi srfi-26)))
@@ -136,7 +135,7 @@ (define-public igraph
                      (("add_sub.*vendor.*") ""))))
        (sha256
         (base32
-         "025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn"))))
+         "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -201,7 +200,7 @@ (define-public igraph
            ;lapack
            openblas
            plfit
-           suitesparse-cxsparse))
+           suitesparse))
     ;; libxml2 is in the 'Requires.private' of igraph.pc.
     (propagated-inputs (list libxml2))
     (home-page "https://igraph.org")
diff --git a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch b/gnu/packages/patches/igraph-fix-varargs-integer-size.patch
deleted file mode 100644
index 2d7ffd7e68..0000000000
--- a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-If the size of int is different from IGRAPH_INTEGER_SIZE, the integer size
-passed to these vararg arguments is different from the assumed one,
-leading to undefined behavior.
-Submitted upstream: https://github.com/igraph/igraph/pull/2423
-
-
-diff -ur a/examples/simple/igraph_union.c b/examples/simple/igraph_union.c
---- a/examples/simple/igraph_union.c
-+++ b/examples/simple/igraph_union.c
-@@ -103,7 +103,7 @@
-     igraph_vector_ptr_init(&glist, 10);
-     for (i = 0; i < igraph_vector_ptr_size(&glist); i++) {
-         VECTOR(glist)[i] = calloc(1, sizeof(igraph_t));
--        igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1);
-+        igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1);
-         igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_DIRECTED);
-         igraph_vector_int_destroy(&v);
-     }
-@@ -123,7 +123,7 @@
-     igraph_vector_ptr_init(&glist, 10);
-     for (i = 0; i < igraph_vector_ptr_size(&glist); i++) {
-         VECTOR(glist)[i] = calloc(1, sizeof(igraph_t));
--        igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1);
-+        igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1);
-         igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_UNDIRECTED);
-         igraph_vector_int_destroy(&v);
-     }
-diff -ur a/src/core/matrix.pmt b/src/core/matrix.pmt
---- a/src/core/matrix.pmt
-+++ b/src/core/matrix.pmt
-@@ -1863,7 +1863,7 @@
- #ifdef FPRINTFUNC_ALIGNED
-             FPRINTFUNC_ALIGNED(file, VECTOR(column_width)[j], MATRIX(*m, i, j));
- #else
--            fprintf(file, format, VECTOR(column_width)[j], MATRIX(*m, i, j));
-+            fprintf(file, format, (int) VECTOR(column_width)[j], MATRIX(*m, i, j));
- #endif
-         }
-         fprintf(file, "\n");
-- 
2.49.0

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Subject: [bug#77902] [PATCH science-team 1/2] gnu: Add %suitesparse-package-versions.
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* gnu/packages/maths.scm (%suitesparse-package-versions): New variable.
(suitesparse-version): Update to 7.10.2.
(suitesparse-source)[origin]: Update deletion list.
(suitesparse-amd, suitesparse-btf, suitesparse-camd, suitesparse-colamd,
suitesparse-ccolamd, suitesparse-cholmod, suitesparse-cxsparse,
suitesparse-klu, suitesparse-ldl, suitesparse-rbio, suitesparse-monUse
goose,
suitesparse-spex, suitesparse-spqr, suitesparse-umfpack)
[version]: Use %suitesparse-package-versions.
(suitesparse-cholmod)[arguments]<#:phases>('install-license-files):
Update paths.
(suitesparse-klu)[arguments]<#:phases>('build-doc): Update paths.
(suitesparse-spex)[native-inputs]: Add texlive-fncychap.
(suitesparse-spqr)[native-inputs]: Add texlive-etoolbox.
* gnu/packages/patches/gklib-suitesparse.patch: Update version and path.

Change-Id: I14a9bfeddb37330c88a2e94b0992c2f1afbc5310
---
 gnu/packages/maths.scm                       | 64 ++++++++++++--------
 gnu/packages/patches/gklib-suitesparse.patch |  6 +-
 2 files changed, 42 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4be9e71320..4cfcd5ba9e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6060,9 +6060,25 @@ (define-public openspecfun
     ;; public domain software.
     (license (list license:expat license:public-domain))))
 
+(define %suitesparse-package-versions
+  '(("AMD" . "3.3.3")
+    ("BTF" . "2.3.2")
+    ("CAMD" . "3.3.3")
+    ("CCOLAMD" . "3.3.4")
+    ("CHOLMOD" . "5.3.2")
+    ("COLAMD" . "3.3.4")
+    ("CXSparse" . "4.4.1")
+    ("KLU" . "2.3.5")
+    ("LDL" . "3.3.2")
+    ("SuiteSparse_Mongoose" . "3.3.4")
+    ("RBio" . "4.3.4")
+    ("SPEX" . "3.2.3")
+    ("SPQR" . "4.3.4")
+    ("UMFPACK" . "6.3.5")))
+
 ;; Source for the modular SuiteSparse packages. When updating, also update the
 ;; (different) versions of the subpackages.
-(define suitesparse-version "7.2.0")
+(define suitesparse-version "7.10.2")
 (define suitesparse-source
   (origin
     (method git-fetch)
@@ -6072,10 +6088,12 @@ (define suitesparse-source
     (file-name (git-file-name "suitesparse" suitesparse-version))
     (sha256
      (base32
-      "1draljn8i46862drc6008cnb2zjpklf74j8c34jirjazzpf53kaa"))
+      "1ndwx2cp5zxrikq4xdrzjrxk1b5ps7lyi6qw34m8jpfpa0ba01ln"))
     (modules '((guix build utils)))
     (snippet
      #~(begin
+         ;; Empty except for a .gitignore.
+         (delete-file-recursively "build")
          ;; Delete autogenerated and bundled files
          (for-each delete-file (find-files "." "\\.pdf$"))
          ;; ssget
@@ -6086,19 +6104,13 @@ (define suitesparse-source
          (delete-file-recursively "CHOLMOD/SuiteSparse_metis")
          ; GraphBLAS
          (delete-file "GraphBLAS/README.md")
-         (delete-file "GraphBLAS/Config/GB_config.h")
          (delete-file "GraphBLAS/Config/GB_prejit.c")
          (delete-file-recursively "GraphBLAS/cpu_features")
-         (delete-file "GraphBLAS/CUDA/GB_cuda_common_jitFactory.hpp")
-         (delete-file "GraphBLAS/JITpackage/GB_JITpackage.c")
          (delete-file-recursively "GraphBLAS/lz4/lz4.c")
          (delete-file-recursively "GraphBLAS/lz4/lz4.h")
          (delete-file-recursively "GraphBLAS/lz4/lz4hc.c")
          (delete-file-recursively "GraphBLAS/lz4/lz4hc.h")
-         (delete-file "GraphBLAS/GraphBLAS/Config/GB_config.h")
          (delete-file "GraphBLAS/Tcov/PreJIT/GB_prejit.c")
-         (delete-file-recursively "GraphBLAS/Source/FactoryKernels")
-         (delete-file "GraphBLAS/Source/GB_AxB__include1.h")
          (delete-file "GraphBLAS/xxHash/xxhash.h")
          (delete-file-recursively "GraphBLAS/zstd/zstd_subset")
          ;; KLU
@@ -6144,7 +6156,7 @@ (define-public suitesparse-config
 (define-public suitesparse-amd
   (package
     (name "suitesparse-amd")
-    (version "3.2.0")
+    (version (assoc-ref %suitesparse-package-versions "AMD"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6192,7 +6204,7 @@ (define-public suitesparse-amd
 (define-public suitesparse-btf
   (package
     (name "suitesparse-btf")
-    (version "2.2.0")
+    (version (assoc-ref %suitesparse-package-versions "BTF"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6225,7 +6237,7 @@ (define-public suitesparse-btf
 (define-public suitesparse-camd
   (package
     (name "suitesparse-camd")
-    (version "3.2.0")
+    (version (assoc-ref %suitesparse-package-versions "CAMD"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6270,7 +6282,7 @@ (define-public suitesparse-camd
 (define-public suitesparse-colamd
   (package
     (name "suitesparse-colamd")
-    (version "3.2.0")
+    (version (assoc-ref %suitesparse-package-versions "COLAMD"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6303,7 +6315,7 @@ (define-public suitesparse-colamd
 (define-public suitesparse-ccolamd
   (package
     (name "suitesparse-ccolamd")
-    (version "3.2.0")
+    (version (assoc-ref %suitesparse-package-versions "CCOLAMD"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6386,7 +6398,7 @@ (define-public metis-suitesparse
 (define-public suitesparse-cholmod
   (package
     (name "suitesparse-cholmod")
-    (version "4.2.0")
+    (version (assoc-ref %suitesparse-package-versions "CHOLMOD"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6448,7 +6460,7 @@ (define-public suitesparse-cholmod
               (let ((out (string-append #$output
                                         "/share/doc/" #$name "-" #$version)))
                 (install-file "../CHOLMOD/Doc/License.txt" out)
-                (install-file "../CHOLMOD/Core/lesser.txt" out)
+                (install-file "../CHOLMOD/Check/lesser.txt" out)
                 (install-file "../CHOLMOD/MatrixOps/gpl.txt" out)))))))
     (inputs
      (list gklib-suitesparse
@@ -6471,7 +6483,7 @@ (define-public suitesparse-cholmod
 (define-public suitesparse-cxsparse
   (package
     (name "suitesparse-cxsparse")
-    (version "4.2.0")
+    (version (assoc-ref %suitesparse-package-versions "CXSparse"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6505,7 +6517,7 @@ (define-public suitesparse-cxsparse
 (define-public suitesparse-klu
   (package
     (name "suitesparse-klu")
-    (version "2.2.0")
+    (version (assoc-ref %suitesparse-package-versions "KLU"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6537,7 +6549,7 @@ (define-public suitesparse-klu
             (lambda _
               (substitute* "../KLU/Doc/Makefile"
                 (("\\.\\./\\.\\./BTF/Include/btf.h")
-                 (string-append #$suitesparse-btf "/include/btf.h")))
+                 (string-append #$suitesparse-btf "/include/suitesparse/btf.h")))
               (with-directory-excursion "../KLU/Doc"
                 (invoke "make"))))
           (add-after 'install 'install-doc
@@ -6569,7 +6581,7 @@ (define-public suitesparse-klu
 (define-public suitesparse-ldl
   (package
     (name "suitesparse-ldl")
-    (version "3.2.0")
+    (version (assoc-ref %suitesparse-package-versions "LDL"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6622,7 +6634,7 @@ (define-public suitesparse-ldl
 (define-public suitesparse-rbio
   (package
     (name "suitesparse-rbio")
-    (version "4.2.0")
+    (version (assoc-ref %suitesparse-package-versions "RBio"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6660,7 +6672,7 @@ (define-public suitesparse-rbio
 (define-public suitesparse-mongoose
   (package
     (name "suitesparse-mongoose")
-    (version "3.2.0")
+    (version (assoc-ref %suitesparse-package-versions "SuiteSparse_Mongoose"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6735,7 +6747,7 @@ (define-public suitesparse-mongoose
 (define-public suitesparse-spex
   (package
     (name "suitesparse-spex")
-    (version "2.2.0")
+    (version (assoc-ref %suitesparse-package-versions "SPEX"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6778,6 +6790,7 @@ (define-public suitesparse-spex
                   texlive-soul
                   texlive-multirow
                   texlive-algorithms
+                  texlive-fncychap
                   texlive-float
                   texlive-algorithmicx
                   texlive-cprotect
@@ -6801,7 +6814,7 @@ (define-public suitesparse-spex
 (define-public suitesparse-spqr
   (package
     (name "suitesparse-spqr")
-    (version "4.2.0")
+    (version (assoc-ref %suitesparse-package-versions "SPQR"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
@@ -6851,7 +6864,8 @@ (define-public suitesparse-spqr
     (propagated-inputs (list suitesparse-cholmod))
     (native-inputs
      (list (texlive-updmap.cfg
-            (list texlive-epsf))))
+            (list texlive-epsf
+                  texlive-etoolbox))))
     (home-page "https://people.engr.tamu.edu/davis/suitesparse.html")
     (synopsis "Sparse QR factorization method")
     (description "The SPQR (SuiteSparseQR) package provides sparse QR
@@ -6862,7 +6876,7 @@ (define-public suitesparse-spqr
 (define-public suitesparse-umfpack
   (package
     (name "suitesparse-umfpack")
-    (version "6.2.0")
+    (version (assoc-ref %suitesparse-package-versions "UMFPACK"))
     (source suitesparse-source)
     (build-system cmake-build-system)
     (arguments
diff --git a/gnu/packages/patches/gklib-suitesparse.patch b/gnu/packages/patches/gklib-suitesparse.patch
index 8b6c708b6a..d207f080b1 100644
--- a/gnu/packages/patches/gklib-suitesparse.patch
+++ b/gnu/packages/patches/gklib-suitesparse.patch
@@ -1,5 +1,5 @@
 This patch contains the relevant changes to GKlib made in SuiteSparse
-(CHOLMOD) for the version 7.2.0
+(CHOLMOD) for the version 7.10.2
 (https://github.com/DrTimothyAldenDavis/SuiteSparse/commit/8a7641cdb4809533c681417e94f98058c07c5da2).
 The disabling of signal handling when MATLAB_MEX_FILE is defined is omitted.
 
@@ -10,7 +10,7 @@ diff -ur a/CMakeLists.txt b/CMakeLists.txt
  
  option(BUILD_SHARED_LIBS "Build shared libraries (.dll/.so) instead of static ones (.lib/.a)" OFF)
  
-+find_package ( SuiteSparse_config 7.1.0 REQUIRED )
++find_package ( SuiteSparse_config 7.10.2 REQUIRED )
 +
  get_filename_component(abs "." ABSOLUTE)
  set(GKLIB_PATH ${abs})
@@ -25,7 +25,7 @@ diff -ur a/GKlib.h b/GKlib.h
 +/* -------------------------------------------------------------------------- */
 +/* Added for incorporation into SuiteSparse.
 +   Tim Davis, Oct 31, 2022, Texas A&M University. */
-+#include "SuiteSparse_config.h"
++#include "suitesparse/SuiteSparse_config.h"
 +#define malloc  SuiteSparse_config_malloc
 +#define calloc  SuiteSparse_config_calloc
 +#define realloc SuiteSparse_config_realloc
-- 
2.49.0

Last modified: Fri, 18 Apr 2025 15:30:02 UTC

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Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.