gnu: igraph: Update to 0.10.7.
* 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. Signed-off-by: Ludovic Courtès <ludo@gnu.org>master
David Elsing
Ludovic Courtès
parent
aa4959e602
commit
808f919063
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@ -1435,6 +1435,7 @@ dist_patch_DATA = \
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%D%/packages/patches/id3lib-CVE-2007-4460.patch \
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%D%/packages/patches/id3lib-UTF16-writing-bug.patch \
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%D%/packages/patches/idris-test-ffi008.patch \
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%D%/packages/patches/igraph-fix-varargs-integer-size.patch \
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%D%/packages/patches/igt-gpu-tools-Use-libproc2.patch \
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%D%/packages/patches/ilmbase-fix-tests.patch \
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%D%/packages/patches/imagemagick-CVE-2020-27829.patch \
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@ -10,6 +10,7 @@
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;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
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;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
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;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -40,13 +41,18 @@
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (gnu packages)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bioconductor)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages bison)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages c)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages datastructures)
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#:use-module (gnu packages docbook)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages gd)
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#:use-module (gnu packages graphics)
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#:use-module (gnu packages graphviz)
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@ -55,6 +61,7 @@
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages pretty-print)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-build)
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#:use-module (gnu packages python-compression)
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@ -93,49 +100,102 @@ distributions in empirical data. SIAM Review 51, 661-703 (2009)}).")
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(define-public igraph
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(package
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(name "igraph")
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(version "0.10.4")
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(version "0.10.7")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://github.com/igraph/igraph/releases/"
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"download/" version "/igraph-" version ".tar.gz"))
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/igraph/igraph")
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(commit version)))
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(file-name (git-file-name name version))
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(patches (search-patches "igraph-fix-varargs-integer-size.patch"))
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(modules '((guix build utils)
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(ice-9 ftw)
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(srfi srfi-26)))
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(snippet '(begin
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;; igraph insists on building its own copy of CxSparse
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;; (see: https://github.com/igraph/igraph/commit/\
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;; 334318b7dfe46501236272ca336580f4748114b0) and the build
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;; has no support to use a system provided 'pcg'.
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(define keep-libraries '("cs" "pcg"))
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(define keep (append '("." ".." "CMakeLists.txt")
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keep-libraries))
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(define keep? (cut member <> keep))
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(with-directory-excursion "vendor"
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(for-each delete-file-recursively
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(scandir "." (negate keep?))))
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(call-with-output-file "vendor/CMakeLists.txt"
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(cut format <> "~{add_subdirectory(~a)~%~}"
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keep-libraries))
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(delete-file-recursively "vendor")
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(delete-file-recursively "src/isomorphism/bliss")
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(substitute* '("src/CMakeLists.txt"
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"etc/cmake/benchmark_helpers.cmake")
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;; Remove extraneous bundling related variables.
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((".*_IS_VENDORED.*")
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""))))
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((".*_IS_VENDORED.*") "")
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((".*add_sub.*isomorphism/bliss.*") "")
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(("(.*TARGETS.*)bliss(.*)cxsparse_vendored(.*)pcg(.*)"
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_ part1 part2 part3 part4)
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(string-append part1 part2 part3 part4))
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(("cxsparse_vendored") "cxsparse")
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((" pcg ") " pcg_random "))
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(substitute* "CMakeLists.txt"
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(("add_sub.*vendor.*") ""))))
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(sha256
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(base32 "1z1ay3l1h64jc2igbl2ibvi20sswy56v2yk3ykhis7jzijsh0mxa"))))
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(base32
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"025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn"))))
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(build-system cmake-build-system)
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(arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")
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#:test-target "check"))
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(native-inputs (list pkg-config))
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(arguments
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(list
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#:configure-flags
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#~(list "-DBUILD_SHARED_LIBS=ON"
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;; Use the same integer width as suitesparse-cxsparse, which
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;; uses int64_t in SuiteSparse v6.0.0 and later.
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"-DIGRAPH_INTEGER_SIZE=64")
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#:test-target "check"
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'version-file
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(lambda _
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(let ((port (open-file "IGRAPH_VERSION" "w")))
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(display #$version port)
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(close port))))
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(add-after 'unpack 'patch-suitesparse
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(lambda _
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(substitute* '("src/core/sparsemat.c"
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"include/igraph_sparsemat.h")
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(("<cs/cs\\.h>") "<cs.h>")
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(("cs_igraph") "cs_dl")
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(("__BEGIN_DECLS.*" all)
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(string-append all "\n#define CS_LONG\n")))))
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(add-after 'unpack 'patch-pcg
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(lambda _
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(substitute* '("src/random/rng_pcg32.c"
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"src/random/rng_pcg64.c")
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(("#include \"pcg/(.*)\"" _ name)
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(string-append "#include <" name ">")))))
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(add-after 'unpack 'patch-bliss
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(lambda _
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(substitute* "src/isomorphism/bliss.cc"
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(("#include \"bliss.*")
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(string-append
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"#include <bliss/graph.hh>\n"
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"#include <bliss/digraph.hh>\n")))))
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(add-after 'build 'build-doc
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(lambda _
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(invoke "cmake" "--build" "." "--target" "html")))
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(add-after 'install 'install-doc
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(lambda _
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(copy-recursively
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"doc/html"
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(string-append #$output "/share/doc/"
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#$name "-" #$version "/html")))))))
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(native-inputs
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(list bison
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docbook-xml-4.3
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docbook-xsl
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flex
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pcg-c
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pkg-config
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;; For the HTML documentation.
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python
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source-highlight
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xmlto))
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(inputs
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(list arpack-ng
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gmp
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bliss
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glpk
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libxml2
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lapack
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openblas
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plfit))
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plfit
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suitesparse-cxsparse))
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;; libxml2 is in the 'Requires.private' of igraph.pc.
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(propagated-inputs (list libxml2))
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(home-page "https://igraph.org")
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@ -0,0 +1,39 @@
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If the size of int is different from IGRAPH_INTEGER_SIZE, the integer size
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passed to these vararg arguments is different from the assumed one,
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leading to undefined behavior.
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Submitted upstream: https://github.com/igraph/igraph/pull/2423
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diff -ur a/examples/simple/igraph_union.c b/examples/simple/igraph_union.c
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--- a/examples/simple/igraph_union.c
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+++ b/examples/simple/igraph_union.c
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@@ -103,7 +103,7 @@
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igraph_vector_ptr_init(&glist, 10);
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for (i = 0; i < igraph_vector_ptr_size(&glist); i++) {
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VECTOR(glist)[i] = calloc(1, sizeof(igraph_t));
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- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1);
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+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1);
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igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_DIRECTED);
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igraph_vector_int_destroy(&v);
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}
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@@ -123,7 +123,7 @@
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igraph_vector_ptr_init(&glist, 10);
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for (i = 0; i < igraph_vector_ptr_size(&glist); i++) {
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VECTOR(glist)[i] = calloc(1, sizeof(igraph_t));
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- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1);
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+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1);
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igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_UNDIRECTED);
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igraph_vector_int_destroy(&v);
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}
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diff -ur a/src/core/matrix.pmt b/src/core/matrix.pmt
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--- a/src/core/matrix.pmt
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+++ b/src/core/matrix.pmt
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@@ -1863,7 +1863,7 @@
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#ifdef FPRINTFUNC_ALIGNED
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FPRINTFUNC_ALIGNED(file, VECTOR(column_width)[j], MATRIX(*m, i, j));
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#else
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- fprintf(file, format, VECTOR(column_width)[j], MATRIX(*m, i, j));
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+ fprintf(file, format, (int) VECTOR(column_width)[j], MATRIX(*m, i, j));
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#endif
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}
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fprintf(file, "\n");
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