From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:48279) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ispCq-00073J-AX for guix-patches@gnu.org; Sat, 18 Jan 2020 09:36:13 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ispCl-0001SR-8F for guix-patches@gnu.org; Sat, 18 Jan 2020 09:36:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34766) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1ispCk-0001SC-Mf for guix-patches@gnu.org; Sat, 18 Jan 2020 09:36:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ispCk-0002Eq-J9 for guix-patches@gnu.org; Sat, 18 Jan 2020 09:36:02 -0500 Subject: [bug#38546] Julia patches v3 References: <87v9qpvbyr.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me> In-Reply-To: <87v9qpvbyr.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me> Resent-Message-ID: From: anothersms@gmail.com (=?UTF-8?Q?Nicol=C3=B2?= Balzarotti) Date: Sat, 18 Jan 2020 15:35:06 +0100 Message-ID: <87r1zwu92d.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 38546@debbugs.gnu.org --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Sorry again, I fixed some unrelated changes that slipped in Thanks, Nicol=C3=B2 --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0001-gnu-julia-Update-to-1.3.1.patch Content-Transfer-Encoding: quoted-printable >From ae58a1dd7b24989e281b07d9a90e1bb6de5199e2 Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 15:14:32 +0100 Subject: [PATCH 01/11] gnu: julia: Update to 1.3.1. * gnu/packages/julia.scm (julia): Update to 1.3.1. --- gnu/packages/julia.scm | 281 +++++++++++++++++------------------------ 1 file changed, 115 insertions(+), 166 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 65a5e42beb..3455dc6239 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright =C2=A9 2015, 2016, 2017 Ricardo Wurmus ;;; Copyright =C2=A9 2016 Efraim Flashner +;;; Copyright =C2=A9 2020 Nicol=C3=B2 Balzarotti ;;; ;;; 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 +45,30 @@ #: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)) =20 +(define (julia-patch-url version name) + (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" ver= sion + "/deps/patches/" name ".patch")) + +(define (julia-patch name sha) + (let ((version "1.3.1")) + (origin (method url-fetch) + (uri (julia-patch-url version name)) + (sha256 (base32 sha)) + (file-name name)))) + (define libuv-julia - (let ((commit "26dbe5672c33fc885462c509fe2a9b36f35866fd") - (revision "6")) + (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")) ;; When upgrading Julia, also upgrade this. - ;; Get the commit from https://github.com/JuliaLang/julia/blob/v1.1.1/= deps/libuv.version + ;; 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 +77,7 @@ (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n"))= )) + "0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))= )) (build-system gnu-build-system) (arguments (substitute-keyword-arguments (package-arguments libuv) @@ -72,16 +86,27 @@ (delete 'autogen))))) (home-page "https://github.com/JuliaLang/libuv")))) =20 -(define (llvm-patch-url version name) - (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" ver= sion - "/deps/patches/" name)) - -(define (llvm-patch name sha) - (let ((version "1.1.1")) - (origin (method url-fetch) - (uri (llvm-patch-url version name)) - (sha256 (base32 sha)) - (file-name name)))) +(define libunwind-julia + ;; julia requires a patched version + (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" + "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hh= xfgnh2m1") + (julia-patch "libunwind-static-arm" + "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic87= 0zh3lhgq"))))) + (build-system gnu-build-system) + (home-page "https://github.com/JuliaLang/libuv"))) =20 (define llvm-julia (package @@ -99,39 +124,39 @@ ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi= ?bug=3D919628 (patches (list - (llvm-patch "llvm-6.0-D44650.patch" + (julia-patch "llvm-6.0-D44650" "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb") - (llvm-patch "llvm-6.0-DISABLE_ABI_CHECKS.patch" + (julia-patch "llvm-6.0-DISABLE_ABI_CHECKS" "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") - (llvm-patch "llvm-6.0-NVPTX-addrspaces.patch" + (julia-patch "llvm-6.0-NVPTX-addrspaces" "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc") - (llvm-patch "llvm-6.0.0_D27296-libssp.patch" + (julia-patch "llvm-6.0.0_D27296-libssp" "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh") - (llvm-patch "llvm-D27629-AArch64-large_model_6.0.1.patch" + (julia-patch "llvm-D27629-AArch64-large_model_6.0.1" "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") - (llvm-patch "llvm-D34078-vectorize-fdiv.patch" + (julia-patch "llvm-D34078-vectorize-fdiv" "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay") - (llvm-patch "llvm-D42262-jumpthreading-not-i1.patch" + (julia-patch "llvm-D42262-jumpthreading-not-i1" "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq") - (llvm-patch "llvm-D44892-Perf-integration.patch" + (julia-patch "llvm-D44892-Perf-integration" "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05") - (llvm-patch "llvm-D46460.patch" + (julia-patch "llvm-D46460" "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb") - (llvm-patch "llvm-D49832-SCEVPred.patch" + (julia-patch "llvm-D49832-SCEVPred" "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn") - (llvm-patch "llvm-D50010-VNCoercion-ni.patch" + (julia-patch "llvm-D50010-VNCoercion-ni" "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp") - (llvm-patch "llvm-D50167-scev-umin.patch" + (julia-patch "llvm-D50167-scev-umin" "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v") - (llvm-patch "llvm-OProfile-line-num.patch" + (julia-patch "llvm-OProfile-line-num" "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7") - (llvm-patch "llvm-PPC-addrspaces.patch" + (julia-patch "llvm-PPC-addrspaces" "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p") - (llvm-patch "llvm-rL323946-LSRTy.patch" + (julia-patch "llvm-rL323946-LSRTy" "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns") - (llvm-patch "llvm-rL326967-aligned-load.patch" + (julia-patch "llvm-rL326967-aligned-load" "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4") - (llvm-patch "llvm-rL327898.patch" + (julia-patch "llvm-rL327898" "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))) (arguments (substitute-keyword-arguments (package-arguments llvm-6) @@ -158,7 +183,7 @@ (define-public julia (package (name "julia") - (version "1.1.1") + (version "1.3.1") (source (origin (method url-fetch) (uri (string-append @@ -166,7 +191,7 @@ version "/julia-" version ".tar.gz")) (sha256 (base32 - "0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f")))) + "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -188,30 +213,24 @@ (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-" "81e9723c0273d78493dc8c8ed570f68d9c= e7e89e" ".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 +252,12 @@ ;; using the output of "/sbin/ldconfig -p". Since ldconfig is n= ot ;; 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 Sys= tem. - (("popen\\(.*ldconfig.*\\);") - "NULL;\n") - - ;; Populate 'sonameMap'. - (("jl_read_sonames.*;") - (string-join - (map (match-lambda - ((input libname soname) - (string-append - "sonameMap[\"" libname "\"] =3D " - "\"" (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.s= o") - ("fftwf" "libfftw3f" "libfftw3f_threads.= so")))))) (substitute* "base/math.jl" (("const libm =3D Base.libm_name") (string-append "const libm =3D \"" (assoc-ref inputs "openlibm") "/lib/libopenlibm.so" - "\"")) - (("const openspecfun =3D \"libopenspecfun\"") - (string-append "const openspecfun =3D \"" - (assoc-ref inputs "openspecfun") - "/lib/libopenspecfun.so" - "\""))) - #t)) + "\""))))) (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 +265,10 @@ ;; collection of build targets and a list of libraries to link ;; against. (substitute* "src/flisp/Makefile" - (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(L= IBFILES_release\\)") - "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)") - (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) = \\$\\(LIBFILES_debug\\)") - "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)")) + (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OB= JS\\) \\$\\(LIBFILES_release\\)") + "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)") + (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DO= BJS\\) \\$\\(LIBFILES_debug\\)") + "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_= debug)")) =20 ;; The REPL must be linked with libuv. (substitute* "ui/Makefile" @@ -296,43 +283,34 @@ "/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 'check 'disable-broken-tests + (add-before 'check 'fix-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\",") "")) + (substitute* "test/choosetests.jl" + (("tests =3D 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 =3D filter(e->!in(e,[\"backtrace\",\"exceptions\",\= "client\", + \"stacktraces\",\"stress\",\"pre= compile\"]), + 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\"=3D>\"/tmp\", \"JULIA_PROJE= CT\"")) + ;; 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))) #:make-flags (list (string-append "prefix=3D" (assoc-ref %outputs "out")) - (string-append "PREFIX=3D" (assoc-ref %outputs "out")) =20 ;; Passing the MARCH flag is necessary to build binary substitutes= for ;; the supported architectures. @@ -345,26 +323,21 @@ ;; platforms, e.g. when running "guix package --search=3D" (_ "MARCH=3DUNSUPPORTED")) =20 - "CONFIG_SHELL=3Dbash" ;needed to build bundled libraries - "USE_SYSTEM_DSFMT=3D0" ;not packaged for Guix and upstream has = no - ;build system for a shared library. + "CONFIG_SHELL=3Dbash" ;needed to build bundled librari= es + ;; list of "USE_SYSTEM_*" is here: + ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc + "USE_SYSTEM_DSFMT=3D1" + "USE_SYSTEM_P7ZIP=3D1" "USE_SYSTEM_LAPACK=3D1" "USE_SYSTEM_BLAS=3D1" "USE_BLAS64=3D0" ;needed when USE_SYSTEM_BLAS=3D1 "LIBBLAS=3D-lopenblas" "LIBBLASNAME=3Dlibopenblas" =20 - "USE_SYSTEM_FFTW=3D1" - "LIBFFTWNAME=3Dlibfftw3" - "LIBFFTWFNAME=3Dlibfftw3f" - - ;; TODO: Suitesparse does not install shared libraries, so we cann= ot - ;; use the suitesparse package. - ;; "USE_SYSTEM_SUITESPARSE=3D1" - ;; (string-append "SUITESPARSE_INC=3D-I " - ;; (assoc-ref %build-inputs "suitesparse") - ;; "/include") - + "USE_SYSTEM_SUITESPARSE=3D1" + (string-append "SUITESPARSE_INC=3D-I " + (assoc-ref %build-inputs "suitesparse") + "/include") "USE_GPL_LIBS=3D1" ;proudly "USE_SYSTEM_UTF8PROC=3D1" (string-append "UTF8PROC_INC=3D" @@ -385,16 +358,19 @@ "USE_SYSTEM_PATCHELF=3D1" "USE_SYSTEM_PCRE=3D1" "USE_SYSTEM_OPENLIBM=3D1" - + "USE_SYSTEM_LIBM=3D0" + "USE_SYSTEM_LIBSSH2=3D1" + "USE_SYSTEM_CURL=3D1" "USE_SYSTEM_GMP=3D1" "USE_SYSTEM_MPFR=3D1" + "USE_SYSTEM_MBEDTLS=3D1" "USE_SYSTEM_ARPACK=3D1" "USE_SYSTEM_LIBGIT2=3D1" - "USE_SYSTEM_ZLIB=3D1" - "USE_SYSTEM_OPENSPECFUN=3D1"))) + "USE_SYSTEM_ZLIB=3D1"))) (inputs `(("llvm" ,llvm-julia) =20 + ("p7zip" ,p7zip) ;; The bundled version is 3.3.0 so stick to that version. With oth= er ;; versions, we get test failures in 'linalg/arnoldi' as described = in ;; . @@ -403,12 +379,12 @@ ("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 +394,12 @@ ("which" ,which) ("zlib" ,zlib) ("gmp" ,gmp) - ("virtualenv" ,python2-virtualenv) + ("suitesparse" ,suitesparse) ;; FIXME: The following inputs are downloaded from upstream to allo= w us ;; to use the lightweight Julia release tarball. Ideally, these in= puts ;; would eventually be replaced with proper Guix packages. - - ;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" t= o copy static lib - ;; Find dependency versions here: - ;; https://raw.githubusercontent.com/JuliaLang/julia/77a2c1e245c858= 12dc1c7687540beedecc52758f/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/Ve= rsions.make ("objconv" ,(origin (method url-fetch) @@ -467,15 +424,7 @@ (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")))))) + ("dsfmt" ,dsfmt))) (native-inputs `(("openssl" ,openssl) ("perl" ,perl) --=20 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0002-gnu-julia-use-SOURCE_DATE_EPOCH-for-precompilation-t.patch >From f849311d8b97688966d5e6d93d856c7c50d9eab2 Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 13:58:37 +0100 Subject: [PATCH 02/11] gnu: julia: use SOURCE_DATE_EPOCH for precompilation timestamp * gnu/packages/patches/julia-fake-mtime-with-SOURCE_DATE_EPOCH.patch: new file --- gnu/local.mk | 1 + gnu/packages/julia.scm | 4 ++- ...ia-fake-mtime-with-SOURCE_DATE_EPOCH.patch | 29 +++++++++++++++++++ 3 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/julia-fake-mtime-with-SOURCE_DATE_EPOCH.patch diff --git a/gnu/local.mk b/gnu/local.mk index 00ff3b8d61..fe8634b44d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1010,6 +1010,7 @@ 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/kdbusaddons-kinit-file-name.patch \ %D%/packages/patches/libvirt-create-machine-cgroup.patch \ diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 3455dc6239..156dc722f9 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -191,7 +191,9 @@ version "/julia-" version ".tar.gz")) (sha256 (base32 - "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x")))) + "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x")) + (patches + (search-patches "julia-fake-mtime-with-SOURCE_DATE_EPOCH.patch")))) (build-system gnu-build-system) (arguments `(#:test-target "test" diff --git a/gnu/packages/patches/julia-fake-mtime-with-SOURCE_DATE_EPOCH.patch b/gnu/packages/patches/julia-fake-mtime-with-SOURCE_DATE_EPOCH.patch new file mode 100644 index 0000000000..467e6d68d1 --- /dev/null +++ b/gnu/packages/patches/julia-fake-mtime-with-SOURCE_DATE_EPOCH.patch @@ -0,0 +1,29 @@ +From e4dc28db1d70819505fd1a68fd9d2bfc4fb61a7d Mon Sep 17 00:00:00 2001 +From: nixo +Date: Fri, 17 Jan 2020 11:28:30 +0100 +Subject: [PATCH] base: loading: support fake mtime with SOURCE_DATE_EPCOCH + +Do this when loading libraries +--- + base/loading.jl | 5 ++++- + 1 file changed, 4 insertions(+), 1 deletion(-) + +diff --git a/base/loading.jl b/base/loading.jl +index 7f11a2d4fc..1b4686d1dc 100644 +--- a/base/loading.jl ++++ b/base/loading.jl +@@ -807,7 +807,10 @@ function _include_dependency(mod::Module, _path::AbstractString) + 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 +-- +2.24.1 + -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0003-gnu-julia-Adjust-indentation.patch >From 5d453dbdc1939a4a334730bab55d20c48a8afcf0 Mon Sep 17 00:00:00 2001 From: nixo Date: Fri, 10 Jan 2020 10:25:49 +0100 Subject: [PATCH 03/11] gnu: julia: Adjust indentation. * gnu/packages/julia.scm (julia): Correct indentation, untabify --- gnu/packages/julia.scm | 216 ++++++++++++++++++++--------------------- 1 file changed, 108 insertions(+), 108 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 156dc722f9..40924b0ced 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -51,14 +51,14 @@ (define (julia-patch-url version name) (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version - "/deps/patches/" name ".patch")) + "/deps/patches/" name ".patch")) (define (julia-patch name sha) (let ((version "1.3.1")) (origin (method url-fetch) - (uri (julia-patch-url version name)) - (sha256 (base32 sha)) - (file-name name)))) + (uri (julia-patch-url version name)) + (sha256 (base32 sha)) + (file-name name)))) (define libuv-julia (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")) @@ -101,7 +101,7 @@ "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3")) (patches (list - (julia-patch "libunwind-prefer-extbl" + (julia-patch "libunwind-prefer-extbl" "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1") (julia-patch "libunwind-static-arm" "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq"))))) @@ -124,45 +124,45 @@ ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628 (patches (list - (julia-patch "llvm-6.0-D44650" - "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb") - (julia-patch "llvm-6.0-DISABLE_ABI_CHECKS" - "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") - (julia-patch "llvm-6.0-NVPTX-addrspaces" - "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc") - (julia-patch "llvm-6.0.0_D27296-libssp" - "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh") - (julia-patch "llvm-D27629-AArch64-large_model_6.0.1" - "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") - (julia-patch "llvm-D34078-vectorize-fdiv" - "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay") - (julia-patch "llvm-D42262-jumpthreading-not-i1" - "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq") - (julia-patch "llvm-D44892-Perf-integration" - "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05") - (julia-patch "llvm-D46460" - "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb") - (julia-patch "llvm-D49832-SCEVPred" - "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn") - (julia-patch "llvm-D50010-VNCoercion-ni" - "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp") - (julia-patch "llvm-D50167-scev-umin" - "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v") - (julia-patch "llvm-OProfile-line-num" - "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7") - (julia-patch "llvm-PPC-addrspaces" - "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p") - (julia-patch "llvm-rL323946-LSRTy" - "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns") - (julia-patch "llvm-rL326967-aligned-load" - "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4") - (julia-patch "llvm-rL327898" - "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))) + (julia-patch "llvm-6.0-D44650" + "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb") + (julia-patch "llvm-6.0-DISABLE_ABI_CHECKS" + "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") + (julia-patch "llvm-6.0-NVPTX-addrspaces" + "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc") + (julia-patch "llvm-6.0.0_D27296-libssp" + "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh") + (julia-patch "llvm-D27629-AArch64-large_model_6.0.1" + "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") + (julia-patch "llvm-D34078-vectorize-fdiv" + "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay") + (julia-patch "llvm-D42262-jumpthreading-not-i1" + "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq") + (julia-patch "llvm-D44892-Perf-integration" + "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05") + (julia-patch "llvm-D46460" + "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb") + (julia-patch "llvm-D49832-SCEVPred" + "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn") + (julia-patch "llvm-D50010-VNCoercion-ni" + "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp") + (julia-patch "llvm-D50167-scev-umin" + "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v") + (julia-patch "llvm-OProfile-line-num" + "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7") + (julia-patch "llvm-PPC-addrspaces" + "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p") + (julia-patch "llvm-rL323946-LSRTy" + "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns") + (julia-patch "llvm-rL326967-aligned-load" + "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4") + (julia-patch "llvm-rL327898" + "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))) (arguments (substitute-keyword-arguments (package-arguments llvm-6) ((#:configure-flags flags) `(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so - "-DCMAKE_BUILD_TYPE=Release" + "-DCMAKE_BUILD_TYPE=Release" ;; Build a native compiler and the NVPTX backend (NVIDIA) since ;; Julia insists on it, nothing more. This reduces build times and @@ -170,15 +170,15 @@ ,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target)) "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX" - "-DLLVM_INSTALL_UTILS=ON" - "-DLLVM_BUILD_TESTS=ON" - "-DLLVM_ENABLE_FFI=ON" - "-DLLVM_ENABLE_RTTI=ON" + "-DLLVM_INSTALL_UTILS=ON" + "-DLLVM_BUILD_TESTS=ON" + "-DLLVM_ENABLE_FFI=ON" + "-DLLVM_ENABLE_RTTI=ON" ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}" ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" - ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" - "-DLLVM_ENABLE_DUMP=ON" - "-DLLVM_LINK_LLVM_DYLIB=ON")))))) + ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" + "-DLLVM_ENABLE_DUMP=ON" + "-DLLVM_LINK_LLVM_DYLIB=ON")))))) (define-public julia (package @@ -222,9 +222,9 @@ (string-append "deps/srccache/libwhich-" "81e9723c0273d78493dc8c8ed570f68d9ce7e89e" ".tar.gz")) - ;; needed by libwhich - (setenv "LD_LIBRARY_PATH" - (string-join (map (lambda (pkg) + ;; needed by libwhich + (setenv "LD_LIBRARY_PATH" + (string-join (map (lambda (pkg) (string-append (assoc-ref inputs pkg) "/lib")) '("arpack-ng" "curl" "dsfmt" @@ -234,7 +234,7 @@ "openblas" "openlibm" "pcre2" "suitesparse")) ":")) - #t)) + #t)) ;; FIXME: Building the documentation requires Julia packages that ;; would be downloaded from the Internet. We should build them in a ;; separate build phase. @@ -250,40 +250,40 @@ ;; Some tests require a home directory to be set. (lambda _ (setenv "HOME" "/tmp") #t)) (add-after 'unpack 'hardcode-soname-map - ;; ./src/runtime_ccall.cpp creates a map from library names to paths - ;; 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) - (substitute* "base/math.jl" - (("const libm = Base.libm_name") - (string-append "const libm = \"" - (assoc-ref inputs "openlibm") - "/lib/libopenlibm.so" - "\""))))) + ;; ./src/runtime_ccall.cpp creates a map from library names to paths + ;; 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) + (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 - ;; included in the LIBFILES_* variable which is used as a - ;; collection of build targets and a list of libraries to link - ;; against. - (substitute* "src/flisp/Makefile" + (lambda* (#:key inputs #:allow-other-keys) + ;; LIBUTF8PROC is a linker flag, not a build target. It is + ;; included in the LIBFILES_* variable which is used as a + ;; collection of build targets and a list of libraries to link + ;; against. + (substitute* "src/flisp/Makefile" (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)") "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)") (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)") "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)")) - ;; The REPL must be linked with libuv. - (substitute* "ui/Makefile" - (("JLDFLAGS \\+= ") - (string-append "JLDFLAGS += " - (assoc-ref %build-inputs "libuv") - "/lib/libuv.so "))) + ;; The REPL must be linked with libuv. + (substitute* "ui/Makefile" + (("JLDFLAGS \\+= ") + (string-append "JLDFLAGS += " + (assoc-ref %build-inputs "libuv") + "/lib/libuv.so "))) - (substitute* "base/Makefile" - (("\\$\\(build_includedir\\)/uv/errno.h") - (string-append (assoc-ref inputs "libuv") - "/include/uv/errno.h"))) - #t)) + (substitute* "base/Makefile" + (("\\$\\(build_includedir\\)/uv/errno.h") + (string-append (assoc-ref inputs "libuv") + "/include/uv/errno.h"))) + #t)) (add-before 'build 'replace-default-shell (lambda _ (substitute* "base/client.jl" @@ -309,7 +309,7 @@ ;; https://github.com/JuliaLang/julia/issues/32377 (substitute* "stdlib/REPL/test/replcompletions.jl" (("@test count") "@test_broken count")) - #t))) + #t))) #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")) @@ -332,7 +332,7 @@ "USE_SYSTEM_P7ZIP=1" "USE_SYSTEM_LAPACK=1" "USE_SYSTEM_BLAS=1" - "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1 + "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1 "LIBBLAS=-lopenblas" "LIBBLASNAME=libopenblas" @@ -340,35 +340,35 @@ (string-append "SUITESPARSE_INC=-I " (assoc-ref %build-inputs "suitesparse") "/include") - "USE_GPL_LIBS=1" ;proudly + "USE_GPL_LIBS=1" ;proudly "USE_SYSTEM_UTF8PROC=1" (string-append "UTF8PROC_INC=" (assoc-ref %build-inputs "utf8proc") "/include") "USE_SYSTEM_LLVM=1" - "LLVM_VER=6.0.1" + "LLVM_VER=6.0.1" - "USE_LLVM_SHLIB=1" - "USE_SYSTEM_LIBUNWIND=1" - "USE_SYSTEM_LIBUV=1" - (string-append "LIBUV=" - (assoc-ref %build-inputs "libuv") - "/lib/libuv.so") - (string-append "LIBUV_INC=" - (assoc-ref %build-inputs "libuv") - "/include") - "USE_SYSTEM_PATCHELF=1" - "USE_SYSTEM_PCRE=1" - "USE_SYSTEM_OPENLIBM=1" + "USE_LLVM_SHLIB=1" + "USE_SYSTEM_LIBUNWIND=1" + "USE_SYSTEM_LIBUV=1" + (string-append "LIBUV=" + (assoc-ref %build-inputs "libuv") + "/lib/libuv.so") + (string-append "LIBUV_INC=" + (assoc-ref %build-inputs "libuv") + "/include") + "USE_SYSTEM_PATCHELF=1" + "USE_SYSTEM_PCRE=1" + "USE_SYSTEM_OPENLIBM=1" "USE_SYSTEM_LIBM=0" "USE_SYSTEM_LIBSSH2=1" "USE_SYSTEM_CURL=1" - "USE_SYSTEM_GMP=1" - "USE_SYSTEM_MPFR=1" - "USE_SYSTEM_MBEDTLS=1" - "USE_SYSTEM_ARPACK=1" - "USE_SYSTEM_LIBGIT2=1" - "USE_SYSTEM_ZLIB=1"))) + "USE_SYSTEM_GMP=1" + "USE_SYSTEM_MPFR=1" + "USE_SYSTEM_MBEDTLS=1" + "USE_SYSTEM_ARPACK=1" + "USE_SYSTEM_LIBGIT2=1" + "USE_SYSTEM_ZLIB=1"))) (inputs `(("llvm" ,llvm-julia) @@ -378,9 +378,9 @@ ;; . ("arpack-ng" ,arpack-ng-3.3.0) - ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like + ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like ("lapack" ,lapack) - ("openblas" ,openblas) ;Julia does not build with Atlas + ("openblas" ,openblas) ;Julia does not build with Atlas ("libunwind" ,libunwind-julia) ("openlibm" ,openlibm) ("mbedtls" ,mbedtls-apache) @@ -412,20 +412,20 @@ (base32 "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs")))) ("libwhich" - ,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e")) + ,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e")) (origin ;; Note: We use a /tarball URL, but that's because Julia's build ;; system checks the hash of that tarball; thus we can't use ;; 'git-fetch'. - (method url-fetch) - (uri (string-append + (method url-fetch) + (uri (string-append "https://api.github.com/repos/vtjnash/libwhich/tarball/" commit)) (file-name (string-append "libwhich-" (string-take commit 7) ".tar.gz")) - (sha256 - (base32 - "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b"))))) + (sha256 + (base32 + "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b"))))) ("dsfmt" ,dsfmt))) (native-inputs `(("openssl" ,openssl) -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0004-gnu-julia-use-wrapper-to-set-JULIA_LOAD_PATH-and-JUL.patch >From a14f7c993da9ead8b497de94c112f0a3ec93ef6c Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:23:44 +0100 Subject: [PATCH 04/11] gnu: julia: use wrapper to set JULIA_LOAD_PATH and JULIA_DEPOT_PATH --- gnu/packages/julia.scm | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 40924b0ced..39c7d6d34f 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -309,7 +309,20 @@ ;; https://github.com/JuliaLang/julia/issues/32377 (substitute* "stdlib/REPL/test/replcompletions.jl" (("@test count") "@test_broken count")) - #t))) + #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")) @@ -436,7 +449,10 @@ (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")) -- 2.24.1 --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0005-gnu-build-julia-build-system-fix-package-precompilat.patch Content-Transfer-Encoding: quoted-printable >From fe7101742199677293cdbbd34be8992c95f7bd8c Mon Sep 17 00:00:00 2001 From: nixo Date: Fri, 17 Jan 2020 19:40:55 +0100 Subject: [PATCH 05/11] gnu: build: julia-build-system: fix package precompilation --- guix/build/julia-build-system.scm | 51 +++++++++++++------------------ 1 file changed, 22 insertions(+), 29 deletions(-) diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-sys= tem.scm index ff6fcf5fe3..dbd4af623d 100644 --- a/guix/build/julia-build-system.scm +++ b/guix/build/julia-build-system.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright =C2=A9 2019 Nicol=C3=B2 Balzarotti +;;; Copyright =C2=A9 2019, 2020 Nicol=C3=B2 Balzarotti ;;; ;;; This file is part of GNU Guix. ;;; @@ -37,53 +37,46 @@ ;; subpath where we store the package content (define %package-path "/share/julia/packages/") =20 -(define (generate-load-path inputs outputs) - (string-append - (string-join (map (match-lambda - ((_ . path) - (string-append path %package-path))) - ;; Restrict to inputs beginning with "julia-". - (filter (match-lambda - ((name . _) - (string-prefix? "julia-" name))) - inputs)) - ":") - (string-append ":" (assoc-ref outputs "out") %package-path) - ;; stdlib is always required to find Julia's standard libraries. - ;; usually there are other two paths in this variable: - ;; "@" and "@v#.#" - ":@stdlib")) - (define* (install #:key source inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (package-dir (string-append out %package-path - (string-append - (strip-store-file-name source))))) - (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs)) + (strip-store-file-name source)))) (mkdir-p package-dir) - (copy-recursively source package-dir)) + (copy-recursively (getcwd) package-dir)) #t) =20 -;; TODO: Precompilation is working, but I don't know how to tell -;; julia to use use it. If (on rantime) we set HOME to -;; store path, julia tries to write files there (failing) (define* (precompile #:key source inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (builddir (string-append out "/share/julia/")) (package (strip-store-file-name source))) (mkdir-p builddir) + ;; With a patch, SOURCE_DATE_EPOCH is honored + (setenv "SOURCE_DATE_EPOCH" "1") (setenv "JULIA_DEPOT_PATH" builddir) - (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs)) - ;; Actual precompilation - (invoke-julia (string-append "using " package))) + ;; add new package dir to the load path + (setenv "JULIA_LOAD_PATH" + (string-append builddir "packages/" ":" + (or (getenv "JULIA_LOAD_PATH") + ""))) + ;; Actual precompilation. + (invoke-julia + ;; when using julia as a user, julia writes precompile cache to the f= irst + ;; entry of the DEPOT_PATH list (by default, the home dir). We want = to + ;; write it to the store, so let's push the store path as the first + ;; element of DEPOT_PATH. Once the cache file exists, this hack is n= ot + ;; needed anymore (like in the check phase). If the user install new + ;; pacakges, those will be installed and precompiled in the home dir + (string-append "pushfirst!(DEPOT_PATH, pop!(DEPOT_PATH)); using " pac= kage))) #t) =20 (define* (check #:key source inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (package (strip-store-file-name source)) (builddir (string-append out "/share/julia/"))) + ;; With a patch, SOURCE_DATE_EPOCH is honored + (setenv "SOURCE_DATE_EPOCH" "1") (setenv "JULIA_DEPOT_PATH" builddir) - (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs)) + (setenv "JULIA_LOAD_PATH" (string-append builddir "packages/")) (invoke-julia (string-append "using Pkg;Pkg.test(\"" package "\")"))) #t) =20 --=20 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0006-gnu-Add-julia-compat.patch >From 607383a2523efd85f8ec454c31fee8fb68b38249 Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:05:00 +0100 Subject: [PATCH 06/11] gnu: Add julia-compat. * gnu/packages/julia-xyz.scm: New file * gnu/packages/julia-xyz.scm (julia-compat): New variable --- gnu/local.mk | 1 + gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 gnu/packages/julia-xyz.scm diff --git a/gnu/local.mk b/gnu/local.mk index fe8634b44d..e07229ee20 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -277,6 +277,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/jrnl.scm \ %D%/packages/jose.scm \ %D%/packages/julia.scm \ + %D%/packages/julia-xyz.scm \ %D%/packages/jupyter.scm \ %D%/packages/kawa.scm \ %D%/packages/kde.scm \ diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm new file mode 100644 index 0000000000..7d9faa63e9 --- /dev/null +++ b/gnu/packages/julia-xyz.scm @@ -0,0 +1,27 @@ +(define-module (gnu packages julia-xyz) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix git-download) + #:use-module (guix build-system julia)) + +(define-public julia-compat + (package + (name "julia-compat") + (version "3.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLang/Compat.jl") + (commit (string-append "v" version)))) + (file-name "Compat") + (sha256 + (base32 "0d21h3l2ry2mmlhpg7b9cxifayzwcv7r13h5wydcbd5pjf6k4qd4")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaLang/Compat.jl") + (synopsis "Compatibility across Julia versions") + (description "The Compat package is designed to ease interoperability +between older and newer versions of the Julia language. The Compat package +provides a macro that lets you use the latest syntax in a backwards-compatible +way.") + (license license:expat))) -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0007-gnu-Add-julia-inifile.patch >From c503ef2c5421939ed28a7f6a676c9c70f812d3fb Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:06:11 +0100 Subject: [PATCH 07/11] gnu: Add julia-inifile. * gnu/packages/julia-xyz.scm (julia-inifile): New variable. --- gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 7d9faa63e9..6b8053e5f8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -25,3 +25,23 @@ between older and newer versions of the Julia language. The Compat package provides a macro that lets you use the latest syntax in a backwards-compatible way.") (license license:expat))) + +(define-public julia-inifile + (package + (name "julia-inifile") + (version "0.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/IniFile.jl") + (commit "8ba59958495fa276d6489d2c3903e765d75e0bc0"))) + (file-name "IniFile") + (sha256 + (base32 "11h6f99jpbg729lplw841m68jprka7q3n8yw390bndlmcdsjabpd")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaIO/IniFile.jl") + (synopsis "Reading Windows-style INI files") + (description "This is a julia package that defines an IniFile type that +allows to interface with @file{.ini} files") + (license license:expat))) -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0008-gnu-Add-julia-sha.patch >From a2ff2e6f01b022972205d4efd47cf06e9ec1899b Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:07:13 +0100 Subject: [PATCH 08/11] gnu: Add julia-sha. * gnu/packages/julia-xyz.scm (julia-sha): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 6b8053e5f8..92ffde58e7 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -45,3 +45,26 @@ way.") (description "This is a julia package that defines an IniFile type that allows to interface with @file{.ini} files") (license license:expat))) + +(define-public julia-sha + (package + (name "julia-sha") + (version "0.5.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/staticfloat/SHA.jl") + (commit (string-append "v" version)))) + (file-name "SHA") + (sha256 + (base32 "10a09kg9z0m8rvwmlgsna6p342kyvizx2axdqc6pzyhraddr8jrp")))) + (propagated-inputs `(("julia-compat" ,julia-compat))) + (build-system julia-build-system) + (home-page "https://github.com/staticfloat/SHA.jl") + (synopsis + "Performant, 100% native-julia SHA1, SHA2, and SHA3 implementation") + (description "Julia package implementing SHA algorithms. Each exported +function takes in either an @code{Array{UInt8}}, a @code{ByteString} or an +@code{IO} object.") + (license license:expat))) -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0009-gnu-Add-julia-binaryprovider.patch >From 189ca6851f5f57ce09e65c81e9b8f50ba0008a80 Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:07:36 +0100 Subject: [PATCH 09/11] gnu: Add julia-binaryprovider. * gnu/packages/julia-xyz.scm (julia-binaryprovider): New variable. --- gnu/packages/julia-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 92ffde58e7..0f8e04b4d1 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -68,3 +68,36 @@ allows to interface with @file{.ini} files") function takes in either an @code{Array{UInt8}}, a @code{ByteString} or an @code{IO} object.") (license license:expat))) + +(define-public julia-binaryprovider + (package + (name "julia-binaryprovider") + (version "0.5.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/BinaryProvider.jl") + (commit (string-append "v" version)))) + (file-name "BinaryProvider") + (sha256 + (base32 "174jmg4w8ncgfhdvfnm0p4cnlayw31j4s9sksqlwz1sipywqvww7")))) + (propagated-inputs `(("julia-sha" ,julia-sha))) + ;; We don't really need BinaryProvider (as guix provides the binaries) but + ;; since it's a dependency of other packages we want to precompile it. + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-engine-probe + (lambda _ + (substitute* "src/BinaryProvider.jl" + ;; Precompilation tries to download things from the internet, + ;; disable the download part + (("probe_platform_engines") "# probe_platform_engines")) + #t))))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaPackaging/BinaryProvider.jl") + (synopsis "Reliable Binary provider for Julia") + (description "@code{BinaryProvider.jl} simplifies the installation of +binaries required by julia packages.") + (license license:expat))) -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0010-gnu-Add-julia-mbedtls.patch >From 87b37b3f041709a1926f441a9643b723ca2ef8a1 Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:11:14 +0100 Subject: [PATCH 10/11] gnu: Add julia-mbedtls. * gnu/packages/julia-xyz.scm (julia-mbedtls): New variable. --- gnu/packages/julia-xyz.scm | 49 +++++++++++++++++++++++++++++++++++++- 1 file changed, 48 insertions(+), 1 deletion(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 0f8e04b4d1..3e9f532697 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2,7 +2,8 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix git-download) - #:use-module (guix build-system julia)) + #:use-module (guix build-system julia) + #:use-module (gnu packages tls)) (define-public julia-compat (package @@ -101,3 +102,49 @@ function takes in either an @code{Array{UInt8}}, a @code{ByteString} or an (description "@code{BinaryProvider.jl} simplifies the installation of binaries required by julia packages.") (license license:expat))) + +(define-public julia-mbedtls + (package + (name "julia-mbedtls") + (version "0.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLang/MbedTLS.jl") + (commit (string-append "v" version)))) + (file-name "MbedTLS") + (sha256 + (base32 "1a8snw9gi21lm6r3kh6ly7ngi99s9k5shqkfiizj3g9li20q23h2")))) + (propagated-inputs + `(("julia-binaryprovider" ,julia-binaryprovider) + ("mbedtls-apache" ,mbedtls-apache))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'precompile 'build-deps + (lambda* (#:key outputs source inputs #:allow-other-keys) + (let ((f (open-file + (string-append + (assoc-ref outputs "out") + "/share/julia/packages/" + (string-append + (strip-store-file-name source) "/deps/deps.jl")) + "w"))) + (display (string-append "const libmbedcrypto = \"" + (assoc-ref inputs "mbedtls-apache") + "/lib/libmbedcrypto.so\"\n") f) + (display (string-append "const libmbedtls = \"" + (assoc-ref inputs "mbedtls-apache") + "/lib/libmbedtls.so\"\n") f) + (display (string-append "const libmbedx509 = \"" + (assoc-ref inputs "mbedtls-apache") + "/lib/libmbedx509.so\"\n") f) + (close-port f)) + #t))))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaLang/MbedTLS.jl") + (synopsis "Apache's mbed TLS library wrapper") + (description "@code{MbedTLS.jl} provides a wrapper around the mbed TLS and +cryptography C libary for Julia.") + (license license:expat))) -- 2.24.1 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0011-gnu-Add-julia-http.patch >From 488857fdd17d1cb8d479dd18b367b33cb449cd22 Mon Sep 17 00:00:00 2001 From: nixo Date: Sat, 18 Jan 2020 14:11:45 +0100 Subject: [PATCH 11/11] gnu: Add julia-http. * gnu/packages/julia-xyz.scm (julia-http): New variable. --- gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3e9f532697..ff1bb483f9 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -148,3 +148,27 @@ binaries required by julia packages.") (description "@code{MbedTLS.jl} provides a wrapper around the mbed TLS and cryptography C libary for Julia.") (license license:expat))) + +(define-public julia-http + (package + (name "julia-http") + (version "0.8.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaWeb/HTTP.jl") + (commit (string-append "v" version)))) + (file-name "HTTP") + (sha256 + (base32 "0928fvncfp07i5hvqxjyj8i27xmxxllas1m5idqq2i8h7jshzq3y")))) + (propagated-inputs + `(("julia-inifile" ,julia-inifile) + ("julia-mbedtls" ,julia-mbedtls) + ("julia-compat" ,julia-compat))) + (build-system julia-build-system) + (home-page "https://juliaweb.github.io/HTTP.jl/") + (synopsis "HTTP support for Julia") + (description "@code{HTTP.jl} is a Julia library for HTTP Messages, +implementing both a client and a server.") + (license license:expat))) -- 2.24.1 --=-=-=--