From: "Nicolò Balzarotti" <anothersms@gmail.com>
To: Efraim Flashner <efraim@flashner.co.il>
Cc: Marius Bakke <mbakke@fastmail.com>,
38546@debbugs.gnu.org, zimoun <zimon.toutoune@gmail.com>
Subject: [bug#38546] [PATCH v5] Julia: Update to 1.3.1
Date: Mon, 06 Apr 2020 10:18:25 +0200 [thread overview]
Message-ID: <87lfn9hvse.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me> (raw)
In-Reply-To: <20200406060949.GB1518@E5400>
[-- Attachment #1: Type: text/plain, Size: 604 bytes --]
Efraim Flashner <efraim@flashner.co.il> writes:
Hi Efraim,
no, AFAIK.
The http-parser PR[1] received a comment 18 days ago, so maybe things are slowly
moving.
Julia issue[2] basically suggest to workaround the problem, while [3]
seems to have a patch for julia 1.4.0 ready.
In the meantime, I'm sending a quick patch that patches our http-parser
with the one applied system-wide by fedora[4].
How was the command to build all packages depending even indirectly from
another package (http-parser in this case)? I'll build everything and
hope tests will pass.
Thanks, Nicolò
[-- Attachment #2: 0001-gnu-Add-dsfmt.patch --]
[-- Type: text/x-patch, Size: 4225 bytes --]
From da44aeb1810a12d83aafee9db05acb9262e6e880 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=B2=20Balzarotti?= <nicolo@nixo.xyz>
Date: Thu, 2 Apr 2020 08:49:46 +0200
Subject: [PATCH 1/4] gnu: Add dsfmt.
* gnu/packages/maths.scm (dsfmt): New variable.
---
gnu/packages/maths.scm | 72 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5e56289682..be2b87a41d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -35,6 +35,7 @@
;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -375,6 +376,77 @@ semiconductors.")
(license license:gpl3+)
(home-page "https://www.gnu.org/software/dionysus/")))
+(define-public dsfmt
+ (package
+ (name "dsfmt")
+ (version "2.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
+ ;; julia needs those (and is the only program depending on dsfmt now)
+ (patches
+ (list
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://raw.githubusercontent.com/JuliaLang/julia/"
+ "v1.3.0/deps/patches/dSFMT.c.patch"))
+ (sha256 (base32
+ "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
+ (file-name "dSFMT.c.patch"))
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://raw.githubusercontent.com/JuliaLang/julia/"
+ "v1.3.0/deps/patches/dSFMT.h.patch"))
+ (sha256 (base32
+ "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
+ (file-name "dSFMT.h.patch"))))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ;no configure script
+ (replace 'build
+ ;; upstream Makefile does not build a shared library
+ (lambda _
+ (invoke
+ "gcc"
+ ;; flags copied from julia
+ ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
+ "-DNDEBUG" "-DDSFMT_MEXP=19937"
+ "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
+ "-O3" "-finline-functions" "-fomit-frame-pointer"
+ "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
+ "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
+ "-o" "libdSFMT.so")))
+ (replace 'install ;no "install" target
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((lib (string-append (assoc-ref outputs "out")
+ "/lib"))
+ (inc (string-append (assoc-ref outputs "out")
+ "/include")))
+ (install-file "libdSFMT.so" lib)
+ (install-file "dSFMT.h" inc)
+ #t))))))
+ (synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
+ (description
+ "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
+the expensive conversion of integer to double (floating point). dSFMT directly
+generates double precision floating point pseudorandom numbers which have the
+IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
+format. dSFMT is only available on the CPUs which use IEEE 754 format double
+precision floating point numbers.")
+ (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
+ (license license:bsd-3)))
+
(define-public gsl
(package
(name "gsl")
--
2.26.0
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-http-parser-add-patch-applied-by-libgit2.patch --]
[-- Type: text/x-patch, Size: 1750 bytes --]
From 544ea20e9f7105ee01c274895ab1c4687dc99090 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=B2=20Balzarotti?= <nicolo@nixo.xyz>
Date: Thu, 2 Apr 2020 11:50:27 +0200
Subject: [PATCH 2/4] gnu: http-parser: add patch applied by libgit2.
Fixes parsing of colon followed by empty port, allowed by RFC 3986
specifications. Fedora is applying it to system http-parser too.
---
gnu/packages/web.scm | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index a553dc2150..6c73720689 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5788,6 +5788,20 @@ into your tests. It automatically starts up a HTTP server in a separate thread
(uri (git-reference (url home-page)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
+ (patches
+ ;; When parsing URLs, treat an empty port (eg
+ ;; `http://hostname:/`) as if it were unspecified. This patch is
+ ;; applied to fedora http-parser and to libgit2 bundled version.
+ (list
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://src.fedoraproject.org/rpms/http-parser/raw/"
+ "e89b4c4e2874c19079a5a1a2d2ccc61b551aa289/"
+ "f/0001-url-treat-empty-port-as-default.patch"))
+ (sha256
+ (base32
+ "0pbxf2nq9pcn299k2b2ls8ldghaqln9glnp79gi57mamx4iy0f6g")))))
(sha256
(base32
"189zi61vczqgmqjd2myjcjbbi5icrk7ccs0kn6nj8hxqiv5j3811"))))
--
2.26.0
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: 0003-gnu-libgit2-Use-system-http-parser.patch --]
[-- Type: text/x-patch, Size: 2402 bytes --]
From 2bd301c0e04a182295c4cce973e5b7553c4aa5b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=B2=20Balzarotti?= <nicolo@nixo.xyz>
Date: Thu, 2 Apr 2020 11:54:15 +0200
Subject: [PATCH 3/4] gnu: libgit2: Use system http-parser.
---
gnu/packages/version-control.scm | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 8af54c6e35..00fb96f474 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -612,16 +612,13 @@ on @command{git}, and use any regular Git hosting service.")
(base32
"0qxzv49ip378g1n7hrbifb9c6pys2kj1hnxcafmbb94gj3pgd9kg"))
(patches (search-patches "libgit2-mtime-0.patch"))
-
- ;; Remove bundled software. Keep "http-parser" because it
- ;; contains patches that are not available in the system version.
(snippet '(begin
(with-directory-excursion "deps"
(for-each (lambda (dir)
(delete-file-recursively dir))
(lset-difference equal?
(scandir ".")
- '("." ".." "http-parser"))))
+ '("." ".."))))
#t))
(modules '((guix build utils)
(srfi srfi-1)
@@ -630,7 +627,8 @@ on @command{git}, and use any regular Git hosting service.")
(outputs '("out" "debug"))
(arguments
`(#:configure-flags '("-DUSE_NTLMCLIENT=OFF" ;TODO: package this
- "-DREGEX_BACKEND=pcre2")
+ "-DREGEX_BACKEND=pcre2"
+ "-DUSE_HTTP_PARSER=system")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-pcre2-reference
@@ -657,7 +655,8 @@ on @command{git}, and use any regular Git hosting service.")
(replace 'check
(lambda _ (invoke "./libgit2_clar" "-v" "-Q"))))))
(inputs
- `(("libssh2" ,libssh2)))
+ `(("libssh2" ,libssh2)
+ ("http-parser" ,http-parser)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python" ,python)))
--
2.26.0
[-- Attachment #5: 0004-gnu-julia-Upgrade-to-1.3.1.patch --]
[-- Type: text/x-patch, Size: 26850 bytes --]
From f01ecb8c6f19180e790cf412b69149ebb6382996 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=B2=20Balzarotti?= <nicolo@nixo.xyz>
Date: Thu, 2 Apr 2020 11:55:20 +0200
Subject: [PATCH 4/4] gnu: julia: Upgrade to 1.3.1.
---
gnu/local.mk | 2 +
gnu/packages/julia.scm | 348 +++++++++---------
.../julia-SOURCE_DATE_EPOCH-mtime.patch | 22 ++
3 files changed, 188 insertions(+), 184 deletions(-)
create mode 100644 gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
diff --git a/gnu/local.mk b/gnu/local.mk
index 6c85e6e806..2b8c99ef57 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -28,6 +28,7 @@
# Copyright © 2019 Amin Bandali <bandali@gnu.org>
# Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
# Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
+# Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz
#
# This file is part of GNU Guix.
#
@@ -1053,6 +1054,7 @@ dist_patch_DATA = \
%D%/packages/patches/java-xerces-bootclasspath.patch \
%D%/packages/patches/java-xerces-build_dont_unzip.patch \
%D%/packages/patches/java-xerces-xjavac_taskdef.patch \
+ %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \
%D%/packages/patches/jbig2dec-ignore-testtest.patch \
%D%/packages/patches/jfsutils-add-sysmacros.patch \
%D%/packages/patches/jfsutils-include-systypes.patch \
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 65a5e42beb..74d214930e 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -28,6 +29,7 @@
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages curl)
#:use-module (gnu packages elf)
#:use-module (gnu packages gcc)
#:use-module (gnu packages llvm)
@@ -43,18 +45,18 @@
#:use-module (gnu packages textutils)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
+ #:use-module (gnu packages ssh)
#:use-module (gnu packages wget)
#:use-module (ice-9 match))
(define libuv-julia
- (let ((commit "26dbe5672c33fc885462c509fe2a9b36f35866fd")
- (revision "6"))
- ;; When upgrading Julia, also upgrade this.
- ;; Get the commit from https://github.com/JuliaLang/julia/blob/v1.1.1/deps/libuv.version
+ (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1"))
+ ;; When upgrading Julia, also upgrade this. Get the commit from
+ ;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
(package
(inherit libuv)
(name "libuv-julia")
- (version (string-append "1.9.0-" revision "." (string-take commit 8)))
+ (version (string-append "2.0.0" "." (string-take commit 8)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -63,7 +65,7 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n"))))
+ "0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments libuv)
@@ -72,14 +74,37 @@
(delete 'autogen)))))
(home-page "https://github.com/JuliaLang/libuv"))))
-(define (llvm-patch-url version name)
+(define libunwind-julia
+ ;; The Julia projects requires their patched version.
+ ;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
+ (package
+ (inherit libunwind)
+ (name "libunwind-julia")
+ (version "1.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://savannah/libunwind/libunwind-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
+ (patches
+ (list
+ (julia-patch "libunwind-prefer-extbl"
+ "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
+ (julia-patch "libunwind-static-arm"
+ "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
+ (home-page "https://github.com/JuliaLang/tree/master/deps/")))
+
+(define (julia-patch-url version name)
(string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
- "/deps/patches/" name))
+ "/deps/patches/" name ".patch"))
-(define (llvm-patch name sha)
- (let ((version "1.1.1"))
+(define (julia-patch name sha)
+ (let ((version "1.3.1"))
(origin (method url-fetch)
- (uri (llvm-patch-url version name))
+ (uri (julia-patch-url version name))
(sha256 (base32 sha))
(file-name name))))
@@ -98,41 +123,44 @@
;; but they are required to build Julia.
;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
(patches
- (list
- (llvm-patch "llvm-6.0-D44650.patch"
- "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
- (llvm-patch "llvm-6.0-DISABLE_ABI_CHECKS.patch"
- "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
- (llvm-patch "llvm-6.0-NVPTX-addrspaces.patch"
- "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
- (llvm-patch "llvm-6.0.0_D27296-libssp.patch"
- "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
- (llvm-patch "llvm-D27629-AArch64-large_model_6.0.1.patch"
- "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
- (llvm-patch "llvm-D34078-vectorize-fdiv.patch"
- "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
- (llvm-patch "llvm-D42262-jumpthreading-not-i1.patch"
- "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
- (llvm-patch "llvm-D44892-Perf-integration.patch"
- "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
- (llvm-patch "llvm-D46460.patch"
- "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
- (llvm-patch "llvm-D49832-SCEVPred.patch"
- "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
- (llvm-patch "llvm-D50010-VNCoercion-ni.patch"
- "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
- (llvm-patch "llvm-D50167-scev-umin.patch"
- "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
- (llvm-patch "llvm-OProfile-line-num.patch"
- "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
- (llvm-patch "llvm-PPC-addrspaces.patch"
- "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
- (llvm-patch "llvm-rL323946-LSRTy.patch"
- "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
- (llvm-patch "llvm-rL326967-aligned-load.patch"
- "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
- (llvm-patch "llvm-rL327898.patch"
- "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq")))))
+ (map (match-lambda
+ ((name hash)
+ (julia-patch name hash)))
+ (list
+ '("llvm-6.0-D44650"
+ "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
+ '("llvm-6.0-DISABLE_ABI_CHECKS"
+ "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
+ '("llvm-6.0-NVPTX-addrspaces"
+ "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
+ '("llvm-6.0.0_D27296-libssp"
+ "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
+ '("llvm-D27629-AArch64-large_model_6.0.1"
+ "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
+ '("llvm-D34078-vectorize-fdiv"
+ "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
+ '("llvm-D42262-jumpthreading-not-i1"
+ "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
+ '("llvm-D44892-Perf-integration"
+ "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
+ '("llvm-D46460"
+ "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
+ '("llvm-D49832-SCEVPred"
+ "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
+ '("llvm-D50010-VNCoercion-ni"
+ "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
+ '("llvm-D50167-scev-umin"
+ "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
+ '("llvm-OProfile-line-num"
+ "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
+ '("llvm-PPC-addrspaces"
+ "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
+ '("llvm-rL323946-LSRTy"
+ "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
+ '("llvm-rL326967-aligned-load"
+ "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
+ '("llvm-rL327898"
+ "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))))
(arguments
(substitute-keyword-arguments (package-arguments llvm-6)
((#:configure-flags flags)
@@ -158,7 +186,7 @@
(define-public julia
(package
(name "julia")
- (version "1.1.1")
+ (version "1.3.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -166,7 +194,9 @@
version "/julia-" version ".tar.gz"))
(sha256
(base32
- "0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f"))))
+ "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
+ (patches
+ (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@@ -188,30 +218,25 @@
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "deps/srccache")
- (copy-file (assoc-ref inputs "dsfmt")
- "deps/srccache/dsfmt-2.2.3.tar.gz")
+ ;; no USE_SYSTEM_{OBJCONV/LIBWHICH}
(copy-file (assoc-ref inputs "objconv")
"deps/srccache/objconv.zip")
- (copy-file (assoc-ref inputs "suitesparse")
- "deps/srccache/SuiteSparse-4.4.5.tar.gz")
- (copy-file (string-append (assoc-ref inputs "virtualenv")
- "/bin/virtualenv")
- "julia-env")
(copy-file (assoc-ref inputs "libwhich")
(string-append "deps/srccache/libwhich-"
"81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
".tar.gz"))
- (copy-file (assoc-ref inputs "rmath")
- "deps/srccache/Rmath-julia-0.1.tar.gz")
;; needed by libwhich
(setenv "LD_LIBRARY_PATH"
(string-join (map (lambda (pkg)
(string-append (assoc-ref inputs pkg)
"/lib"))
- '("arpack-ng" "fftw" "gmp" "lapack"
- "libgit2" "mpfr" "openblas" "openlibm"
- "openspecfun" "pcre2"))
+ '("arpack-ng" "curl" "dsfmt"
+ "gmp" "lapack"
+ "libssh2" "libgit2"
+ "mbedtls" "mpfr"
+ "openblas" "openlibm" "pcre2"
+ "suitesparse"))
":"))
#t))
;; FIXME: Building the documentation requires Julia packages that
@@ -233,44 +258,12 @@
;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
(lambda* (#:key inputs #:allow-other-keys)
- (use-modules (ice-9 match))
- (substitute* "src/runtime_ccall.cpp"
- ;; Patch out invocations of '/sbin/ldconfig' to avoid getting
- ;; error messages about missing '/sbin/ldconfig' on Guix System.
- (("popen\\(.*ldconfig.*\\);")
- "NULL;\n")
-
- ;; Populate 'sonameMap'.
- (("jl_read_sonames.*;")
- (string-join
- (map (match-lambda
- ((input libname soname)
- (string-append
- "sonameMap[\"" libname "\"] = "
- "\"" (assoc-ref inputs input) "/lib/" soname "\";")))
- '(("libc" "libc" "libc.so.6")
- ("pcre2" "libpcre2-8" "libpcre2-8.so")
- ("mpfr" "libmpfr" "libmpfr.so")
- ("openblas" "libblas" "libopenblas.so")
- ("arpack-ng" "libarpack" "libarpack.so")
- ("lapack" "liblapack" "liblapack.so")
- ("libgit2" "libgit2" "libgit2.so")
- ("gmp" "libgmp" "libgmp.so")
- ("openspecfun" "libopenspecfun" "libopenspecfun.so")
- ("fftw" "libfftw3" "libfftw3_threads.so")
- ("fftwf" "libfftw3f" "libfftw3f_threads.so"))))))
- (substitute* "base/math.jl"
- (("const libm = Base.libm_name")
- (string-append "const libm = \""
- (assoc-ref inputs "openlibm")
- "/lib/libopenlibm.so"
- "\""))
- (("const openspecfun = \"libopenspecfun\"")
- (string-append "const openspecfun = \""
- (assoc-ref inputs "openspecfun")
- "/lib/libopenspecfun.so"
- "\"")))
- #t))
+ (substitute* "base/math.jl"
+ (("const libm = Base.libm_name")
+ (string-append "const libm = \""
+ (assoc-ref inputs "openlibm")
+ "/lib/libopenlibm.so"
+ "\"")))))
(add-before 'build 'fix-include-and-link-paths
(lambda* (#:key inputs #:allow-other-keys)
;; LIBUTF8PROC is a linker flag, not a build target. It is
@@ -278,10 +271,10 @@
;; collection of build targets and a list of libraries to link
;; against.
(substitute* "src/flisp/Makefile"
- (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
- "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
- (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
- "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
+ (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
+ "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
+ (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
+ "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
;; The REPL must be linked with libuv.
(substitute* "ui/Makefile"
@@ -296,39 +289,50 @@
"/include/uv/errno.h")))
#t))
(add-before 'build 'replace-default-shell
- (lambda _
- (substitute* "base/client.jl"
- (("/bin/sh") (which "sh")))
- #t))
- (add-after 'unpack 'hardcode-paths
(lambda _
- (substitute* "stdlib/InteractiveUtils/src/InteractiveUtils.jl"
- (("`which") (string-append "`" (which "which")))
- (("`wget") (string-append "`" (which "wget"))))
+ (substitute* "base/client.jl"
+ (("/bin/sh") (which "sh")))
+ #t))
+ (add-before 'build 'fix-precompile
+ (lambda _
+ (substitute* "base/loading.jl"
+ (("something(Base.active_project(), \"\")") "\"\""))
#t))
(add-before 'check 'disable-broken-tests
(lambda _
- (define (touch file-name)
- (call-with-output-file file-name (const #t)))
- ;; FIXME: All git tests works except this one. But *THIS* "fix"
- ;; is not working, so right now I'm disabling all libgit2.jl tests
- ;; (substitute* "stdlib/LibGit2/test/libgit2.jl"
- ;; (("!LibGit2.use_http_path(cfg, github_cred)") "true")
- ;; (("LibGit2.use_http_path(cfg, mygit_cred)") "true"))
- (map (lambda (test)
- (delete-file test)
- (touch test))
- '("stdlib/Sockets/test/runtests.jl"
- "stdlib/Distributed/test/runtests.jl"
- ;; FIXME: see above
- "stdlib/LibGit2/test/libgit2.jl"))
- (substitute* "test/choosetests.jl"
- ;; These tests fail, probably because some of the input
- ;; binaries have been stripped and thus backtraces don't look
- ;; as expected.
- (("\"backtrace\",") "")
- (("\"cmdlineargs\",") ""))
- #t)))
+ (substitute* "test/choosetests.jl"
+ (("tests = testnames")
+ ;; Those failings are not deterministic. They depends on the
+ ;; running order. I think it depends on the number of
+ ;; runners, disabling it for now
+ ;; https://github.com/JuliaLang/julia/issues/34330
+ "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",
+ \"stress\",\"precompile\",
+ \"client\",\"stacktraces\"]),
+ testnames)"))
+ ;; When HOME is not set, julia calls uv_os_homedir, which in
+ ;; turns call getpwuid_r. Add the HOME env variable to the
+ ;; external julia call to fix this
+ (substitute* "test/cmdlineargs.jl"
+ (("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
+ ;; Marking the test as broken as it's a known bug:
+ ;; https://github.com/JuliaLang/julia/issues/32377
+ (substitute* "stdlib/REPL/test/replcompletions.jl"
+ (("@test count") "@test_broken count"))
+ #t))
+ (add-after 'install 'make-wrapper
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (program "julia"))
+ (with-directory-excursion bin
+ (wrap-program program
+ `("JULIA_LOAD_PATH" ":" prefix
+ ("" "$JULIA_LOAD_PATH")))
+ (wrap-program program
+ `("JULIA_DEPOT_PATH" ":" prefix
+ ("" "$JULIA_DEPOT_PATH"))))
+ #t))))
#:make-flags
(list
(string-append "prefix=" (assoc-ref %outputs "out"))
@@ -346,25 +350,20 @@
(_ "MARCH=UNSUPPORTED"))
"CONFIG_SHELL=bash" ;needed to build bundled libraries
- "USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no
- ;build system for a shared library.
+ ;; list of "USE_SYSTEM_*" is here:
+ ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
+ "USE_SYSTEM_DSFMT=1"
+ "USE_SYSTEM_P7ZIP=1"
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
"LIBBLAS=-lopenblas"
"LIBBLASNAME=libopenblas"
- "USE_SYSTEM_FFTW=1"
- "LIBFFTWNAME=libfftw3"
- "LIBFFTWFNAME=libfftw3f"
-
- ;; TODO: Suitesparse does not install shared libraries, so we cannot
- ;; use the suitesparse package.
- ;; "USE_SYSTEM_SUITESPARSE=1"
- ;; (string-append "SUITESPARSE_INC=-I "
- ;; (assoc-ref %build-inputs "suitesparse")
- ;; "/include")
-
+ "USE_SYSTEM_SUITESPARSE=1"
+ (string-append "SUITESPARSE_INC=-I "
+ (assoc-ref %build-inputs "suitesparse")
+ "/include")
"USE_GPL_LIBS=1" ;proudly
"USE_SYSTEM_UTF8PROC=1"
(string-append "UTF8PROC_INC="
@@ -390,11 +389,16 @@
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=1"
- "USE_SYSTEM_ZLIB=1"
- "USE_SYSTEM_OPENSPECFUN=1")))
+ (string-append "LIBUV="
+ (assoc-ref %build-inputs "libuv")
+ "/lib/libuv.so")
+ (string-append "LIBUV_INC="
+ (assoc-ref %build-inputs "libuv")
+ "/include")
+ "USE_SYSTEM_ZLIB=1")))
(inputs
`(("llvm" ,llvm-julia)
-
+ ("p7zip" ,p7zip)
;; The bundled version is 3.3.0 so stick to that version. With other
;; versions, we get test failures in 'linalg/arnoldi' as described in
;; <https://bugs.gnu.org/30282>.
@@ -403,12 +407,12 @@
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
("lapack" ,lapack)
("openblas" ,openblas) ;Julia does not build with Atlas
- ("libunwind" ,libunwind)
+ ("libunwind" ,libunwind-julia)
("openlibm" ,openlibm)
- ("openspecfun" ,openspecfun)
+ ("mbedtls" ,mbedtls-apache)
+ ("curl" ,curl)
("libgit2" ,libgit2)
- ("fftw" ,fftw)
- ("fftwf" ,fftwf)
+ ("libssh2" ,libssh2)
("fortran" ,gfortran)
("libuv" ,libuv-julia)
("pcre2" ,pcre2)
@@ -418,31 +422,12 @@
("which" ,which)
("zlib" ,zlib)
("gmp" ,gmp)
- ("virtualenv" ,python2-virtualenv)
+ ("suitesparse" ,suitesparse)
;; FIXME: The following inputs are downloaded from upstream to allow us
;; to use the lightweight Julia release tarball. Ideally, these inputs
;; would eventually be replaced with proper Guix packages.
-
- ;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
- ;; Find dependency versions here:
- ;; https://raw.githubusercontent.com/JuliaLang/julia/77a2c1e245c85812dc1c7687540beedecc52758f/deps/Versions.make
- ("rmath"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaLang/Rmath-julia")
- (commit "v0.1")))
- (file-name "rmath-julia-0.1-checkout")
- (sha256
- (base32
- "1zkpy0cg5zivq40zbhbdgj9128fqzs2j94wkwih8nc6xaj3gp9p6"))))
- ("suitesparse"
- ,(origin
- (method url-fetch)
- (uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
- (sha256
- (base32
- "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
+ ;; Find dependencies versions here:
+ ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
("objconv"
,(origin
(method url-fetch)
@@ -466,16 +451,8 @@
".tar.gz"))
(sha256
(base32
- "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
- ("dsfmt"
- ,(origin
- (method url-fetch)
- (uri (string-append
- "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
- "SFMT/dSFMT-src-2.2.3.tar.gz"))
- (sha256
- (base32
- "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
+ "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
+ ("dsfmt" ,dsfmt)))
(native-inputs
`(("openssl" ,openssl)
("perl" ,perl)
@@ -485,7 +462,10 @@
(native-search-paths
(list (search-path-specification
(variable "JULIA_LOAD_PATH")
- (files (list "share/julia/packages/")))))
+ (files (list "share/julia/packages/")))
+ (search-path-specification
+ (variable "JULIA_DEPOT_PATH")
+ (files (list "share/julia/")))))
;; Julia is not officially released for ARM and MIPS.
;; See https://github.com/JuliaLang/julia/issues/10639
(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
diff --git a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
new file mode 100644
index 0000000000..b60f284923
--- /dev/null
+++ b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
@@ -0,0 +1,22 @@
+Fix one of upstream non-determinism, tracked here:
+
+https://github.com/JuliaLang/julia/issues/34115
+https://github.com/JuliaLang/julia/issues/25900
+
+
+Patch by Nicoló Balzarotti <nicolo@nixo.xyz>.
+
+--- a/base/loading.jl
++++ b/base/loading.jl
+@@ -807,7 +807,10 @@
+ path = normpath(joinpath(dirname(prev), _path))
+ end
+ if _track_dependencies[]
+- push!(_require_dependencies, (mod, path, mtime(path)))
++ push!(_require_dependencies,
++ (mod, path,
++ haskey(ENV, "SOURCE_DATE_EPOCH") ?
++ parse(Float64, ENV["SOURCE_DATE_EPOCH"]) : mtime(path)))
+ end
+ return path, prev
+ end
--
2.26.0
[-- Attachment #6: Type: text/plain, Size: 1636 bytes --]
[1] https://github.com/nodejs/http-parser/pull/483
[2] https://github.com/JuliaLang/julia/issues/33111
[3] https://github.com/JuliaLang/julia/pull/35232
[4] https://src.fedoraproject.org/rpms/http-parser/c/e89b4c4e2874c19079a5a1a2d2ccc61b551aa289?branch=master
> On Thu, Mar 19, 2020 at 01:28:09PM +0100, Marius Bakke wrote:
>> Nicolò Balzarotti <anothersms@gmail.com> writes:
>>
>> > Hi,
>> >
>> > I looked at it. THe patch is literally a one-line change[1] they make
>> > to support RFC 3986. According to [2], the patch has been ported to
>> > fedora http-parser. Our version is different form the one bundled in
>> > libgit2, but deleting the corresponding line (see snippet) libgit2 tests
>> > are now passing. However, this http-parser test is failing:
>> >
>> > *** http_parser_parse_url("http://hostname:/") "proxy empty port" test failed, unexpected rv 0 ***
>> >
>> > I opened an issue upstream here [3] so that if they fix it we can
>> > continue unbundling it without having to patch it ourselves.
>> >
>> > Hope they decide to upstream it
>> >
>> > I'll send updates if there are news on the issue,
>>
>> Awesome, thank you very much for looking into it. I have no objections
>> to taking the patches from the upstream PR [0] if that helps updating
>> Julia. :-)
>>
>> 0: https://github.com/nodejs/http-parser/pull/483
>
> Any news from upstream?
>
>
> --
> Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
> GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
> Confidentiality cannot be guaranteed on emails sent or received unencrypted
next prev parent reply other threads:[~2020-04-06 8:19 UTC|newest]
Thread overview: 54+ messages / expand[flat|nested] mbox.gz Atom feed top
[not found] <87pnfgvqgt.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me>
2019-12-09 13:36 ` [bug#38546] [PATCH 0/3] Julia: fix package build and add julia-xyz nixo
2019-10-10 15:49 ` [bug#38546] [PATCH 2/3] gnu: julia-build-system: Enable tests Nicolò Balzarotti
2019-12-15 21:45 ` Ludovic Courtès
2019-10-10 15:49 ` [bug#38546] [PATCH 3/3] gnu: julia-xyz: Add julia-compat Nicolò Balzarotti
2019-12-15 21:46 ` Ludovic Courtès
2019-10-10 15:49 ` [bug#38546] [PATCH 1/3] gnu: julia: Set to JULIA_LOAD_PATH and JULIA_DEPOT_PATH variables Nicolò Balzarotti
2019-12-15 21:43 ` Ludovic Courtès
2019-12-12 8:43 ` [bug#38546] [PATCH 01/11] gnu: julia: Update to 1.3.1 nixo
2019-12-15 21:40 ` [bug#38546] [PATCH 0/3] Julia: fix package build and add julia-xyz Ludovic Courtès
2020-01-10 9:25 ` [bug#38546] [PATCH 03/11] gnu: julia: Adjust indentation nixo
2020-01-17 18:40 ` [bug#38546] [PATCH 05/11] gnu: build: julia-build-system: fix package nixo
2020-01-18 12:58 ` [bug#38546] [PATCH 02/11] gnu: julia: use SOURCE_DATE_EPOCH for precompilation timestamp nixo
2020-01-18 13:05 ` [bug#38546] [PATCH 06/11] gnu: Add julia-compat nixo
2020-01-18 13:06 ` [bug#38546] [PATCH 07/11] gnu: Add julia-inifile nixo
2020-01-18 13:07 ` [bug#38546] [PATCH 08/11] gnu: Add julia-sha nixo
2020-01-18 13:07 ` [bug#38546] [PATCH 09/11] gnu: Add julia-binaryprovider nixo
2020-01-18 13:11 ` [bug#38546] [PATCH 10/11] gnu: Add julia-mbedtls nixo
2020-01-18 13:11 ` [bug#38546] [PATCH 11/11] gnu: Add julia-http nixo
2020-01-18 13:23 ` [bug#38546] [PATCH 04/11] use wrapper to set JULIA_LOAD_PATH and JULIA_DEPOT_PATH nixo
2020-01-18 13:32 ` [bug#38546] [Nicolò Balzarotti] [PATCH 00/11] Update julia to 1.3.1, fix precompilation, add HTTP.jl Nicolò Balzarotti
2020-01-18 13:36 ` [bug#38546] [nixo] [PATCH 01/11] gnu: julia: Update to 1.3.1 Nicolò Balzarotti
2020-01-18 13:42 ` [bug#38546] [Nicolò Balzarotti] [PATCH 00/10] Update julia to 1.3.1, fix precompilation, add HTTP.jl Nicolò Balzarotti
2020-01-18 13:59 ` [bug#38546] [00/11] Update Julia, Fix " Nicolò Balzarotti
2020-01-20 18:49 ` zimoun
2020-01-21 13:45 ` Nicolò Balzarotti
2020-01-22 9:22 ` zimoun
2020-01-22 9:59 ` Nicolò Balzarotti
2020-01-24 17:26 ` zimoun
2020-02-04 18:03 ` zimoun
2020-02-07 12:06 ` zimoun
2020-02-11 14:51 ` zimoun
2020-02-11 15:10 ` Nicolò Balzarotti
2020-02-11 15:19 ` zimoun
2020-02-11 15:24 ` Nicolò Balzarotti
2020-01-18 14:35 ` [bug#38546] Julia patches v3 Nicolò Balzarotti
2020-02-11 17:58 ` [bug#38546] [PATCH v4] Update Julia 1.3.1: almost done zimoun
2020-02-24 12:50 ` zimoun
2020-02-24 20:59 ` Nicolò Balzarotti
2020-02-25 16:12 ` zimoun
2020-02-25 18:08 ` Nicolò Balzarotti
2020-02-26 12:32 ` [bug#38546] [PATCH v5] Julia: Update to 1.3.1 Nicolò Balzarotti
2020-03-16 10:06 ` Efraim Flashner
2020-03-17 7:51 ` Nicolò Balzarotti
2020-03-17 8:12 ` Efraim Flashner
2020-03-17 12:21 ` Marius Bakke
2020-03-17 13:37 ` Nicolò Balzarotti
2020-03-19 12:28 ` Marius Bakke
2020-04-06 6:09 ` Efraim Flashner
2020-04-06 8:18 ` Nicolò Balzarotti [this message]
2020-04-06 8:37 ` Efraim Flashner
2020-04-06 23:18 ` Nicolò Balzarotti
2020-04-07 5:41 ` Efraim Flashner
2020-04-07 6:05 ` Efraim Flashner
2020-04-07 14:35 ` bug#38546: " Efraim Flashner
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