GNU bug report logs - #39839
[PATCH] gnu: suitesparse: Update to 5.7.1

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH] gnu: suitesparse: Update to 5.7.1
Date: Sat, 29 Feb 2020 16:46:47 +0100

* gnu/packages/math.scm (suitesparse): Update to 5.7.1
[source]: The latest releases of SuiteSparse have only been published on
GitHub. Fetch from git tag as GitHub releases page only contains
autogenerated tarballs that guix lint complains about.
[patches]: add patch for Mongoose's CMakeList.txt to find
SuiteSparse_config.
[arguments]: Add cmake flags used by new components GraphBLAS and
Mongoose.
[native-inputs]: add cmake and m4 needed to build GraphBLAS and Mongoose.
---
 gnu/packages/maths.scm                        | 26 ++++++++++++++-----
 .../patches/suitesparse-mongoose-cmake.patch  | 18 +++++++++++++
 2 files changed, 38 insertions(+), 6 deletions(-)
 create mode 100644 gnu/packages/patches/suitesparse-mongoose-cmake.patch

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index cab84a520b..cee626f179 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -34,6 +34,7 @@
 ;;; Copyright © 2019 Steve Sprang <scs <at> stevesprang.com>
 ;;; Copyright © 2019 Robert Smith <robertsmith <at> posteo.net>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
+;;; Copyright © 2020 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3405,16 +3406,18 @@ Fresnel integrals, and similar related functions as well.")
 (define-public suitesparse
   (package
     (name "suitesparse")
-    (version "4.5.5")
+    (version "5.7.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
-             version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DrTimothyAldenDavis/SuiteSparse.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
+         "174p3l78kv9gaa0i5hflyai2ydwnjzh34k9938sl4aa3li0543s8"))
+       (patches (search-patches "suitesparse-mongoose-cmake.patch"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled metis source
@@ -3429,6 +3432,14 @@ Fresnel integrals, and similar related functions as well.")
              "BLAS=-lblas"
              "TBB=-ltbb"
              "MY_METIS_LIB=-lmetis"
+             ;; Flags for cmake (only GraphBLAS and Mongoose)
+             (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
+                            (assoc-ref %outputs "out")
+                            " -DCMAKE_VERBOSE_MAKEFILE=ON"
+                            " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
+                            " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
+                            " -DCMAKE_SKIP_RPATH=TRUE"
+                            " -DCMAKE_BUILD_TYPE=Release")
              (string-append "INSTALL_LIB="
                             (assoc-ref %outputs "out") "/lib")
              (string-append "INSTALL_INCLUDE="
@@ -3441,6 +3452,9 @@ Fresnel integrals, and similar related functions as well.")
      `(("tbb" ,tbb)
        ("lapack" ,lapack)
        ("metis" ,metis)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("m4" ,m4)))
     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
     (synopsis "Suite of sparse matrix software")
     (description
diff --git a/gnu/packages/patches/suitesparse-mongoose-cmake.patch b/gnu/packages/patches/suitesparse-mongoose-cmake.patch
new file mode 100644
index 0000000000..e224d73a30
--- /dev/null
+++ b/gnu/packages/patches/suitesparse-mongoose-cmake.patch
@@ -0,0 +1,18 @@
+diff --git a/Mongoose/CMakeLists.txt b/Mongoose/CMakeLists.txt
+index 7e134ab..76fa9e2 100644
+--- a/Mongoose/CMakeLists.txt
++++ b/Mongoose/CMakeLists.txt
+@@ -148,10 +148,10 @@ set(CMAKE_CXX_STANDARD 11)
+ #set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+ # determine which SuiteSparse_config to use
+-if (EXISTS ${PROJECT_SOURCE_DIR}/../SuiteSparse_config)
+-    message(STATUS "External ../SuiteSparse_config" ${BoldBlue} " found" ${ColourReset} ".")
++if (EXISTS ${CMAKE_INSTALL_PREFIX})
++    message(STATUS "External SuiteSparse_config" ${BoldBlue} " found" ${ColourReset} ".")
+     set ( SUITESPARSE_CONFIG_DIR ${PROJECT_SOURCE_DIR}/../SuiteSparse_config )
+-    link_directories ( ${PROJECT_SOURCE_DIR}/../lib )
++    link_directories ( ${CMAKE_INSTALL_PREFIX}/lib )
+     message ( STATUS "Note: ../SuiteSparse_config must be compiled before compiling Mongoose" )
+     set ( SUITESPARSE_CONFIG_LIBRARY suitesparseconfig )
+ else ()
-- 
2.25.1

Message #8 received at 39839 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 39839 <at> debbugs.gnu.org
Subject: Re: [bug#39839] [PATCH] gnu: suitesparse: Update to 5.7.1
Date: Wed, 4 Mar 2020 15:07:25 -0500

On Sat, Feb 29, 2020 at 04:46:47PM +0100, Felix Gruber wrote:
> * gnu/packages/math.scm (suitesparse): Update to 5.7.1
> [source]: The latest releases of SuiteSparse have only been published on
> GitHub. Fetch from git tag as GitHub releases page only contains
> autogenerated tarballs that guix lint complains about.
> [patches]: add patch for Mongoose's CMakeList.txt to find
> SuiteSparse_config.
> [arguments]: Add cmake flags used by new components GraphBLAS and
> Mongoose.
> [native-inputs]: add cmake and m4 needed to build GraphBLAS and Mongoose.

Thanks! Remember to also register the patch file in 'gnu/local.mk',
mention that in the commit message, and also mention the new patch file.

Check this commit for an example:

https://git.savannah.gnu.org/cgit/guix.git/commit/?id=ca5e404f9a1ff81a38a32578c9c3a6c866482a9a

> -       (method url-fetch)
> -       (uri (string-append
> -             "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
> -             version ".tar.gz"))
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/DrTimothyAldenDavis/SuiteSparse.git")
> +             (commit (string-append "v" version))))

Okay.

> @@ -3429,6 +3432,14 @@ Fresnel integrals, and similar related functions as well.")
>               "BLAS=-lblas"
>               "TBB=-ltbb"
>               "MY_METIS_LIB=-lmetis"
> +             ;; Flags for cmake (only GraphBLAS and Mongoose)

Can you clarify "only GraphBLAS and Mongoose" here? Like, are these
flags so that we can build those components?

> diff --git a/gnu/packages/patches/suitesparse-mongoose-cmake.patch b/gnu/packages/patches/suitesparse-mongoose-cmake.patch

Can you add a comment at the beginning of this file explaining what
problem it solves?

Can you send a revised patch?

Message #11 received at 39839 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: Leo Famulari <leo <at> famulari.name>
Cc: Felix Gruber <felgru <at> posteo.net>, 39839 <at> debbugs.gnu.org
Subject: [PATCH v2] gnu: suitesparse: Update to 5.7.1
Date: Wed,  4 Mar 2020 22:41:08 +0100

* gnu/packages/math.scm (suitesparse): Update to 5.7.1
[source]: The latest releases of SuiteSparse have only been published on
GitHub. Fetch from git tag as GitHub releases page only contains
autogenerated tarballs that guix lint complains about.
[patches]: apply patch for Mongoose's CMakeList.txt to find
SuiteSparse_config.
[arguments]: Add cmake flags used by new components GraphBLAS and
Mongoose.
[native-inputs]: add cmake and m4 needed to build GraphBLAS and Mongoose.
* gnu/packages/patches/suitesparse-mongoose-cmake.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add new patch.
---
This revised version of the patch adds suitesparse-mongoose-cmake.patch
to gnu/local.mk and documents its purpose.
It also clarifies that the new CMake options are required to build the
Mongoose and GraphBLAS components.

 gnu/local.mk                                  |  1 +
 gnu/packages/maths.scm                        | 26 +++++++++++++-----
 .../patches/suitesparse-mongoose-cmake.patch  | 27 +++++++++++++++++++
 3 files changed, 48 insertions(+), 6 deletions(-)
 create mode 100644 gnu/packages/patches/suitesparse-mongoose-cmake.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 857345cfad..928428e95d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1411,6 +1411,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
   %D%/packages/patches/spice-fix-test-armhf.patch		\
   %D%/packages/patches/steghide-fixes.patch			\
+  %D%/packages/patches/suitesparse-mongoose-cmake.patch		\
   %D%/packages/patches/superlu-dist-awpm-grid.patch		\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
   %D%/packages/patches/supertux-unbundle-squirrel.patch		\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index cab84a520b..a990ffc45e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -34,6 +34,7 @@
 ;;; Copyright © 2019 Steve Sprang <scs <at> stevesprang.com>
 ;;; Copyright © 2019 Robert Smith <robertsmith <at> posteo.net>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
+;;; Copyright © 2020 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3405,16 +3406,18 @@ Fresnel integrals, and similar related functions as well.")
 (define-public suitesparse
   (package
     (name "suitesparse")
-    (version "4.5.5")
+    (version "5.7.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
-             version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DrTimothyAldenDavis/SuiteSparse.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
+         "174p3l78kv9gaa0i5hflyai2ydwnjzh34k9938sl4aa3li0543s8"))
+       (patches (search-patches "suitesparse-mongoose-cmake.patch"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled metis source
@@ -3429,6 +3432,14 @@ Fresnel integrals, and similar related functions as well.")
              "BLAS=-lblas"
              "TBB=-ltbb"
              "MY_METIS_LIB=-lmetis"
+             ;; Flags for cmake (required to build GraphBLAS and Mongoose)
+             (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
+                            (assoc-ref %outputs "out")
+                            " -DCMAKE_VERBOSE_MAKEFILE=ON"
+                            " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
+                            " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
+                            " -DCMAKE_SKIP_RPATH=TRUE"
+                            " -DCMAKE_BUILD_TYPE=Release")
              (string-append "INSTALL_LIB="
                             (assoc-ref %outputs "out") "/lib")
              (string-append "INSTALL_INCLUDE="
@@ -3441,6 +3452,9 @@ Fresnel integrals, and similar related functions as well.")
      `(("tbb" ,tbb)
        ("lapack" ,lapack)
        ("metis" ,metis)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("m4" ,m4)))
     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
     (synopsis "Suite of sparse matrix software")
     (description
diff --git a/gnu/packages/patches/suitesparse-mongoose-cmake.patch b/gnu/packages/patches/suitesparse-mongoose-cmake.patch
new file mode 100644
index 0000000000..e5062f9aaa
--- /dev/null
+++ b/gnu/packages/patches/suitesparse-mongoose-cmake.patch
@@ -0,0 +1,27 @@
+Fix required by suitesparse to build Mongoose
+
+The CMakeLists.txt of Mongoose assumes that SuiteSparse_config has been
+installed into the suitesparse source directory, which is not the case
+for us, as we are building suitesparse out-of-tree.
+
+SuiteSparse_config can instead be found in the ${CMAKE_INSTALL_PREFIX}
+directory.
+
+diff --git a/Mongoose/CMakeLists.txt b/Mongoose/CMakeLists.txt
+index 7e134ab..76fa9e2 100644
+--- a/Mongoose/CMakeLists.txt
++++ b/Mongoose/CMakeLists.txt
+@@ -148,10 +148,10 @@ set(CMAKE_CXX_STANDARD 11)
+ #set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+ # determine which SuiteSparse_config to use
+-if (EXISTS ${PROJECT_SOURCE_DIR}/../SuiteSparse_config)
+-    message(STATUS "External ../SuiteSparse_config" ${BoldBlue} " found" ${ColourReset} ".")
++if (EXISTS ${CMAKE_INSTALL_PREFIX})
++    message(STATUS "External SuiteSparse_config" ${BoldBlue} " found" ${ColourReset} ".")
+     set ( SUITESPARSE_CONFIG_DIR ${PROJECT_SOURCE_DIR}/../SuiteSparse_config )
+-    link_directories ( ${PROJECT_SOURCE_DIR}/../lib )
++    link_directories ( ${CMAKE_INSTALL_PREFIX}/lib )
+     message ( STATUS "Note: ../SuiteSparse_config must be compiled before compiling Mongoose" )
+     set ( SUITESPARSE_CONFIG_LIBRARY suitesparseconfig )
+ else ()
-- 
2.25.1

Message #16 received at 39839-done <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 39839-done <at> debbugs.gnu.org
Subject: Re: [PATCH v2] gnu: suitesparse: Update to 5.7.1
Date: Wed, 4 Mar 2020 18:08:41 -0500

On Wed, Mar 04, 2020 at 10:41:08PM +0100, Felix Gruber wrote:
> * gnu/packages/math.scm (suitesparse): Update to 5.7.1
> [source]: The latest releases of SuiteSparse have only been published on
> GitHub. Fetch from git tag as GitHub releases page only contains
> autogenerated tarballs that guix lint complains about.
> [patches]: apply patch for Mongoose's CMakeList.txt to find
> SuiteSparse_config.
> [arguments]: Add cmake flags used by new components GraphBLAS and
> Mongoose.
> [native-inputs]: add cmake and m4 needed to build GraphBLAS and Mongoose.
> * gnu/packages/patches/suitesparse-mongoose-cmake.patch: New file.
> * gnu/local.mk (dist_patch_DATA): Add new patch.

Thanks! Pushed as aac148a87b9a79b9992b8b1a9d76c217175d4a88

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