* [bug#66889] [PATCH 0/2] Unbundle igraph dependencies.
@ 2023-11-01 22:53 David Elsing
2023-11-01 22:57 ` [bug#66889] [PATCH 1/2] gnu: Add pcg-c David Elsing
` (2 more replies)
0 siblings, 3 replies; 4+ messages in thread
From: David Elsing @ 2023-11-01 22:53 UTC (permalink / raw)
To: 66889; +Cc: David Elsing
These patches unbundle everything from igraph and update it to 0.10.7.
As newer SuiteSparse versions always use an integer width of 64, I set
the same in igraph. Would it be better to create a package variant of
suitesparse-cxsparse for igraph with an integer width depending on the
architecture? Upstream doesn't recommend unbundling CXSparse for that
reason.
David Elsing (2):
gnu: Add pcg-c.
gnu: igraph: Update to 0.10.7.
gnu/local.mk | 1 +
gnu/packages/c.scm | 55 +++++++++
gnu/packages/graph.scm | 114 +++++++++++++-----
.../igraph-fix-varargs-integer-size.patch | 39 ++++++
4 files changed, 182 insertions(+), 27 deletions(-)
create mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch
--
2.41.0
^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#66889] [PATCH 1/2] gnu: Add pcg-c.
2023-11-01 22:53 [bug#66889] [PATCH 0/2] Unbundle igraph dependencies David Elsing
@ 2023-11-01 22:57 ` David Elsing
2023-11-01 22:57 ` [bug#66889] [PATCH 2/2] gnu: igraph: Update to 0.10.7 David Elsing
2023-12-02 10:58 ` bug#66889: [PATCH 0/2] Unbundle igraph dependencies Ludovic Courtès
2 siblings, 0 replies; 4+ messages in thread
From: David Elsing @ 2023-11-01 22:57 UTC (permalink / raw)
To: 66889; +Cc: David Elsing
* gnu/packages/c.scm (pcg-c): New variable.
---
gnu/packages/c.scm | 55 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index ea58c68262..0c218b9656 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -20,6 +20,7 @@
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2023 zamfofex <zamfofex@twdb.moe>
;;; Copyright © 2023 Foundation Devices, Inc. <hello@foundationdevices.com>
+;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1585,3 +1586,57 @@ (define-public ispc
program instances execute in parallel on the hardware.")
(home-page "https://github.com/ispc/ispc")
(license license:bsd-3)))
+
+(define-public pcg-c
+ (let ((commit "83252d9c23df9c82ecb42210afed61a7b42402d7")
+ (revision "1"))
+ (package
+ (name "pcg-c")
+ (version (git-version "0.0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/imneme/pcg-c")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0768h0vw75a3smk39qsz1504v04a43s5w1ili1ijbixxv8gm42nf"))
+ (modules '((guix build utils)))
+ ;; Autogenerated files with some tests from test-high. If
+ ;; 128-bit integers are not supported, the build fails, but
+ ;; this is checked when building the tests.
+ (snippet #~(delete-file-recursively "sample"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:test-target "test"
+ #:make-flags
+ #~(list
+ "CC=gcc"
+ (string-append "PREFIX=" #$output))
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'disable-sample
+ (lambda _
+ (substitute* "Makefile"
+ ((".*cd sample.*") ""))))
+ (add-after 'unpack 'set-shared-library
+ (lambda _
+ (substitute* '("Makefile" "src/Makefile")
+ (("\\.a") "\\.so")
+ ((".*ar .*") "\t$(CC) $(CFLAGS) -o $@ $(LDFLAGS) -shared $^")
+ ((".*ranlib.*") "")
+ ((".*CFLAGS \\+=.*O3.*" orig)
+ (string-append orig "CFLAGS += -fPIC\n")))))
+ (add-before 'install 'make-dirs
+ (lambda _
+ (mkdir-p (string-append #$output "/lib"))
+ (mkdir-p (string-append #$output "/include")))))))
+ (home-page "https://www.pcg-random.org")
+ (synopsis "C implementation of the PCG random generators")
+ (description "The Permuted Congruential Generator (PCG) extends the
+Linear Congruential Generator (LCG) with a permutation function to increase
+output randomness while retaining speed, simplicity, and conciseness.")
+ (license (list license:expat license:asl2.0))))) ; dual licensed
--
2.41.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#66889] [PATCH 2/2] gnu: igraph: Update to 0.10.7.
2023-11-01 22:53 [bug#66889] [PATCH 0/2] Unbundle igraph dependencies David Elsing
2023-11-01 22:57 ` [bug#66889] [PATCH 1/2] gnu: Add pcg-c David Elsing
@ 2023-11-01 22:57 ` David Elsing
2023-12-02 10:58 ` bug#66889: [PATCH 0/2] Unbundle igraph dependencies Ludovic Courtès
2 siblings, 0 replies; 4+ messages in thread
From: David Elsing @ 2023-11-01 22:57 UTC (permalink / raw)
To: 66889; +Cc: David Elsing
* gnu/packages/graph.scm (igraph): Update to 0.10.7.
[source]: Use git-fetch. Apply patch.
<snippet>: Remove the entire "vendor" and "src/isomorphism/bliss" directories.
Patch CMakeLists.txt to not build and use vendored dependencies.
[arguments]: Add -DIGRAPH_INTEGER_SIZE=64 to #:configure-flags. Add phases to
use unbundled libraries and build documentation.
[native-inputs]: Add bison, docbook-xml-4.3, docbook-xsl, flex, pcg-c, python,
source-highlight and xmlto.
[inputs]: Remove gmp and libxml2. Add bliss and suitesparse-cxsparse.
* gnu/packages/patches/igraph-fix-varargs-integer-size.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
gnu/local.mk | 1 +
gnu/packages/graph.scm | 114 +++++++++++++-----
.../igraph-fix-varargs-integer-size.patch | 39 ++++++
3 files changed, 127 insertions(+), 27 deletions(-)
create mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 8d817379a7..b51d9d15e8 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1428,6 +1428,7 @@ 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/igt-gpu-tools-Use-libproc2.patch \
%D%/packages/patches/ilmbase-fix-tests.patch \
%D%/packages/patches/imagemagick-CVE-2020-27829.patch \
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 45a591b9f3..a40b580417 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -10,6 +10,7 @@
;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -40,13 +41,18 @@ (define-module (gnu packages graph)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
+ #:use-module (gnu packages bison)
#:use-module (gnu packages boost)
+ #:use-module (gnu packages c)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages datastructures)
+ #:use-module (gnu packages docbook)
+ #:use-module (gnu packages flex)
#:use-module (gnu packages gd)
#:use-module (gnu packages graphics)
#:use-module (gnu packages graphviz)
@@ -55,6 +61,7 @@ (define-module (gnu packages graph)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages pretty-print)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-compression)
@@ -93,49 +100,102 @@ (define-public plfit
(define-public igraph
(package
(name "igraph")
- (version "0.10.4")
+ (version "0.10.7")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/igraph/igraph/releases/"
- "download/" version "/igraph-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (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)))
(snippet '(begin
- ;; igraph insists on building its own copy of CxSparse
- ;; (see: https://github.com/igraph/igraph/commit/\
- ;; 334318b7dfe46501236272ca336580f4748114b0) and the build
- ;; has no support to use a system provided 'pcg'.
- (define keep-libraries '("cs" "pcg"))
- (define keep (append '("." ".." "CMakeLists.txt")
- keep-libraries))
- (define keep? (cut member <> keep))
- (with-directory-excursion "vendor"
- (for-each delete-file-recursively
- (scandir "." (negate keep?))))
- (call-with-output-file "vendor/CMakeLists.txt"
- (cut format <> "~{add_subdirectory(~a)~%~}"
- keep-libraries))
+
+ (delete-file-recursively "vendor")
+ (delete-file-recursively "src/isomorphism/bliss")
(substitute* '("src/CMakeLists.txt"
"etc/cmake/benchmark_helpers.cmake")
;; Remove extraneous bundling related variables.
- ((".*_IS_VENDORED.*")
- ""))))
+ ((".*_IS_VENDORED.*") "")
+ ((".*add_sub.*isomorphism/bliss.*") "")
+ (("(.*TARGETS.*)bliss(.*)cxsparse_vendored(.*)pcg(.*)"
+ _ part1 part2 part3 part4)
+ (string-append part1 part2 part3 part4))
+ (("cxsparse_vendored") "cxsparse")
+ ((" pcg ") " pcg_random "))
+ (substitute* "CMakeLists.txt"
+ (("add_sub.*vendor.*") ""))))
(sha256
- (base32 "1z1ay3l1h64jc2igbl2ibvi20sswy56v2yk3ykhis7jzijsh0mxa"))))
+ (base32
+ "025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn"))))
(build-system cmake-build-system)
- (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")
- #:test-target "check"))
- (native-inputs (list pkg-config))
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "-DBUILD_SHARED_LIBS=ON"
+ ;; Use the same integer width as suitesparse-cxsparse, which
+ ;; uses int64_t in SuiteSparse v6.0.0 and later.
+ "-DIGRAPH_INTEGER_SIZE=64")
+ #:test-target "check"
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'version-file
+ (lambda _
+ (let ((port (open-file "IGRAPH_VERSION" "w")))
+ (display #$version port)
+ (close port))))
+ (add-after 'unpack 'patch-suitesparse
+ (lambda _
+ (substitute* '("src/core/sparsemat.c"
+ "include/igraph_sparsemat.h")
+ (("<cs/cs\\.h>") "<cs.h>")
+ (("cs_igraph") "cs_dl")
+ (("__BEGIN_DECLS.*" all)
+ (string-append all "\n#define CS_LONG\n")))))
+ (add-after 'unpack 'patch-pcg
+ (lambda _
+ (substitute* '("src/random/rng_pcg32.c"
+ "src/random/rng_pcg64.c")
+ (("#include \"pcg/(.*)\"" _ name)
+ (string-append "#include <" name ">")))))
+ (add-after 'unpack 'patch-bliss
+ (lambda _
+ (substitute* "src/isomorphism/bliss.cc"
+ (("#include \"bliss.*")
+ (string-append
+ "#include <bliss/graph.hh>\n"
+ "#include <bliss/digraph.hh>\n")))))
+ (add-after 'build 'build-doc
+ (lambda _
+ (invoke "cmake" "--build" "." "--target" "html")))
+ (add-after 'install 'install-doc
+ (lambda _
+ (copy-recursively
+ "doc/html"
+ (string-append #$output "/share/doc/"
+ #$name "-" #$version "/html")))))))
+ (native-inputs
+ (list bison
+ docbook-xml-4.3
+ docbook-xsl
+ flex
+ pcg-c
+ pkg-config
+ ;; For the HTML documentation.
+ python
+ source-highlight
+ xmlto))
(inputs
(list arpack-ng
- gmp
+ bliss
glpk
- libxml2
lapack
openblas
- plfit))
+ plfit
+ suitesparse-cxsparse))
;; 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
new file mode 100644
index 0000000000..2d7ffd7e68
--- /dev/null
+++ b/gnu/packages/patches/igraph-fix-varargs-integer-size.patch
@@ -0,0 +1,39 @@
+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");
--
2.41.0
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#66889: [PATCH 0/2] Unbundle igraph dependencies.
2023-11-01 22:53 [bug#66889] [PATCH 0/2] Unbundle igraph dependencies David Elsing
2023-11-01 22:57 ` [bug#66889] [PATCH 1/2] gnu: Add pcg-c David Elsing
2023-11-01 22:57 ` [bug#66889] [PATCH 2/2] gnu: igraph: Update to 0.10.7 David Elsing
@ 2023-12-02 10:58 ` Ludovic Courtès
2 siblings, 0 replies; 4+ messages in thread
From: Ludovic Courtès @ 2023-12-02 10:58 UTC (permalink / raw)
To: David Elsing; +Cc: 66889-done
Hi David,
David Elsing <david.elsing@posteo.net> skribis:
> These patches unbundle everything from igraph and update it to 0.10.7.
> As newer SuiteSparse versions always use an integer width of 64, I set
> the same in igraph. Would it be better to create a package variant of
> suitesparse-cxsparse for igraph with an integer width depending on the
> architecture? Upstream doesn't recommend unbundling CXSparse for that
> reason.
I don’t know what would be better, but what you did here LGTM.
> David Elsing (2):
> gnu: Add pcg-c.
> gnu: igraph: Update to 0.10.7.
Finally applied, thanks!
Ludo’.
^ permalink raw reply [flat|nested] 4+ messages in thread
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2023-11-01 22:53 [bug#66889] [PATCH 0/2] Unbundle igraph dependencies David Elsing
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2023-11-01 22:57 ` [bug#66889] [PATCH 2/2] gnu: igraph: Update to 0.10.7 David Elsing
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