diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/julia.scm | 246 | ||||
| -rw-r--r-- | gnu/packages/libevent.scm | 11 | ||||
| -rw-r--r-- | gnu/packages/llvm.scm | 133 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch | 5 | ||||
| -rw-r--r-- | gnu/packages/patches/julia-allow-parallel-build.patch | 32 | ||||
| -rw-r--r-- | gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch | 40 | ||||
| -rw-r--r-- | gnu/packages/textutils.scm | 10 | ||||
| -rw-r--r-- | gnu/packages/tls.scm | 38 |
9 files changed, 166 insertions, 353 deletions
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 75a38c016e..d35901eadb 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2021, 2022 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2022 Akira Kyle <akira@akirakyle.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -61,7 +62,7 @@ (package (inherit libunwind) (name "libunwind-julia") - (version "1.3.1") + (version "1.5.0") (source (origin (method url-fetch) @@ -69,31 +70,27 @@ version ".tar.gz")) (sha256 (base32 - "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3")) + "05qhzcg1xag3l5m3c805np6k342gc0f3g087b7g16jidv59pccwh")) (patches - (append - ;; Fix linker issue for i686-linux because GCC10 changed default - ;; (see '-fno-common' option). - (search-patches "libunwind-julia-fix-GCC10-fno-common.patch") - (list - (julia-patch "libunwind-prefer-extbl" - "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1") - (julia-patch "libunwind-static-arm" - "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") - (julia-patch "libunwind-cfa-rsp" - "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z")))))) + (list + (julia-patch "libunwind-prefer-extbl" + "0pf3lsq6zxlmqn86lk4fcj1xwdan9gbxyabrwgxcb59p8jjwsl8r") + (julia-patch "libunwind-static-arm" + "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") + (julia-patch "libunwind-cfa-rsp" + "0qs5b1h5lsr5qakkv6sddgy5ghlxpjrn2jiqcvg7bkczy24klr6j"))))) (arguments (substitute-keyword-arguments (package-arguments libunwind) ;; Skip tests on this older and patched version of libunwind. ((#:tests? _ #t) #f))) - (home-page "https://github.com/JuliaLang/tree/master/deps/"))) + (home-page "https://github.com/JuliaLang/julia/tree/master/deps/"))) (define (julia-patch-url version name) (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version "/deps/patches/" name ".patch")) (define-public (julia-patch name sha) - (let ((version "1.6.1")) + (let ((version "1.8.2")) (origin (method url-fetch) (uri (julia-patch-url version name)) (sha256 (base32 sha)) @@ -143,7 +140,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (define-public julia (package (name "julia") - (version "1.6.7") + (version "1.8.3") (source (origin (method url-fetch) (uri (string-append @@ -151,10 +148,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") version "/julia-" version ".tar.gz")) (sha256 (base32 - "0q9xgdpvdkskpzl294w215f6c15c5jk276c9dah5f5w4np3ivbvl")) - (patches - (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch" - "julia-allow-parallel-build.patch")))) + "0jf8dr5j7y8cjnr65kn38xps5h9m2qvi8g1yd8qgiip5r87ld3ad")) + (patches (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -188,7 +183,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") '("curl" "dsfmt" "gmp" "lapack" "libssh2" "libnghttp2" "libgit2" - "mbedtls" "mpfr" + "libblastrampoline" + "mbedtls-apache" "mpfr" "openblas" "openlibm" "pcre2" "suitesparse" "gfortran:lib")) ":")))) @@ -202,25 +198,10 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (string-append line "\n")) (("src ui doc deps") "src ui deps")))) - (add-after 'unpack 'use-system-libwhich - (lambda* (#:key inputs #:allow-other-keys) - ;; don't build it - (substitute* "deps/Makefile" - (("DEP_LIBS \\+= libwhich") "")) - ;; call our version - (substitute* "base/Makefile" - (("\\$\\$\\(build_depsbindir\\)/libwhich") - (search-input-file inputs "/bin/libwhich"))))) (add-after 'unpack 'activate-gnu-source-for-loader (lambda _ (substitute* "cli/Makefile" (("LOADER_CFLAGS =") "LOADER_CFLAGS = -D_GNU_SOURCE")))) - (add-after 'unpack 'change-number-of-precompile-statements - (lambda _ - ;; Remove nss-certs drops the number of statements below 1200, - ;; causing the build to fail prematurely. - (substitute* "contrib/generate_precompile.jl" - (("1200") "1100")))) ;; libquadmath is not available on all architectures. ;; https://github.com/JuliaLang/julia/issues/41613 (add-after 'unpack 'make-libquadmath-optional @@ -232,30 +213,16 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (lambda _ (setenv "HOME" "/tmp"))) (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" - (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)") - "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)") - (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)") - "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)")) - ;; The REPL must be linked with libuv. (substitute* "cli/Makefile" (("JLDFLAGS \\+= ") (string-append "JLDFLAGS += " - (assoc-ref %build-inputs "libuv") - "/lib/libuv.so "))) - - (substitute* "base/Makefile" - (("\\$\\(build_includedir\\)/uv/errno.h") - (search-input-file inputs "/include/uv/errno.h"))))) + (assoc-ref inputs "libuv") + "/lib/libuv.so "))))) (add-before 'build 'replace-default-shell - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (substitute* "base/client.jl" - (("/bin/sh") (which "sh"))))) + (("/bin/sh") (search-input-file inputs "/bin/sh"))))) (add-before 'build 'shared-objects-paths (lambda* (#:key inputs #:allow-other-keys) (let ((jlpath @@ -268,8 +235,12 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (to (lambda* (pkg libname #:optional libname_jl) (string-append - "const " (or libname_jl libname) "= \"" + "const " (or libname_jl libname) " = \"" (assoc-ref inputs pkg) "/lib/" libname ".so")))) + (substitute* (jlpath "CompilerSupportLibraries") + (((from "libgfortran")) + (string-append "const libgfortran = string(\"" + (search-input-file inputs "/lib/libgfortran.so")))) (substitute* (jlpath "dSFMT") (((from "libdSFMT")) (to "dsfmt" "libdSFMT"))) (substitute* (jlpath "GMP") @@ -290,11 +261,9 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* (jlpath "MPFR") (((from "libmpfr")) (to "mpfr" "libmpfr"))) (substitute* (jlpath "MbedTLS") - ;; For the newer version of mbedtls-apache: - (("libmbedcrypto.so.5") "libmbedcrypto.so.6") - (((from "libmbedcrypto")) (to "mbedtls" "libmbedcrypto")) - (((from "libmbedtls")) (to "mbedtls" "libmbedtls")) - (((from "libmbedx509")) (to "mbedtls" "libmbedx509"))) + (((from "libmbedcrypto")) (to "mbedtls-apache" "libmbedcrypto")) + (((from "libmbedtls")) (to "mbedtls-apache" "libmbedtls")) + (((from "libmbedx509")) (to "mbedtls-apache" "libmbedx509"))) (substitute* (jlpath "nghttp2") (((from "libnghttp2")) (to "libnghttp2" "libnghttp2"))) (substitute* (jlpath "OpenBLAS") @@ -302,7 +271,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* (jlpath "OpenLibm") (((from "libopenlibm")) (to "openlibm" "libopenlibm"))) (substitute* (jlpath "PCRE2") - (((from "libpcre2")) (to "pcre2" "libpcre2" "libpcre2_8"))) + (((from "libpcre2_8")) (to "pcre2" "libpcre2-8" "libpcre2_8"))) (substitute* (jlpath "SuiteSparse") (((from "libamd")) (to "suitesparse" "libamd")) (((from "libbtf")) (to "suitesparse" "libbtf")) @@ -319,40 +288,36 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (to "suitesparse" "libsuitesparseconfig")) (((from "libumfpack")) (to "suitesparse" "libumfpack"))) (substitute* (jlpath "Zlib") - (((from "libz")) (to "zlib" "libz")))))) + (((from "libz")) (to "zlib" "libz"))) + (substitute* (jlpath "libblastrampoline") + (("libblastrampoline\\.so") + (search-input-file inputs "/lib/libblastrampoline.so")))))) (add-after 'unpack 'enable-parallel-tests (lambda* (#:key parallel-tests? #:allow-other-keys) - (setenv "JULIA_CPU_THREADS" (if parallel-tests? - (number->string (parallel-job-count)) - "1")) - (format #t "JULIA_CPU_THREADS environment variable set to ~a~%" - (getenv "JULIA_CPU_THREADS")))) + (when parallel-tests? + (setenv "JULIA_TEST_USE_MULTIPLE_WORKERS" "true")))) (add-after 'unpack 'adjust-test-suite (lambda* (#:key inputs #:allow-other-keys) - (let ((pcre2 (assoc-ref inputs "pcre2")) - (mbedtls-apache (assoc-ref inputs "mbedtls")) - (mpfr (assoc-ref inputs "mpfr")) - (gmp (assoc-ref inputs "gmp")) - (nghttp2 (assoc-ref inputs "libnghttp2")) - (zlib (assoc-ref inputs "zlib")) - (suitesparse (assoc-ref inputs "suitesparse"))) - ;; Some tests only check to see if the input is the correct version. - (substitute* "stdlib/PCRE2_jll/test/runtests.jl" - (("10.40.0") ,(package-version pcre2))) - (substitute* "stdlib/MbedTLS_jll/test/runtests.jl" - (("2.24.0") ,(package-version mbedtls-apache))) - (substitute* "stdlib/MPFR_jll/test/runtests.jl" - (("4.1.0") ,(package-version mpfr))) - (substitute* "stdlib/GMP_jll/test/runtests.jl" - (("6.2.0") ,(package-version gmp))) - (substitute* "stdlib/nghttp2_jll/test/runtests.jl" - (("1.41.0") ,(package-version nghttp2))) - (substitute* "stdlib/Zlib_jll/test/runtests.jl" - (("1.2.12") ,(package-version zlib))) - (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl" - (("5004") ,(string-replace-substring - (version-major+minor - (package-version suitesparse)) "." "0")))))) + (substitute* "test/spawn.jl" + (("shcmd = `sh`") (string-append "shcmd = `" (which "sh") "`"))) + ;; Some tests only check to see if the input is the correct version. + (substitute* "stdlib/PCRE2_jll/test/runtests.jl" + (("10.40.0") ,(package-version (this-package-input "pcre2")))) + (substitute* "stdlib/MbedTLS_jll/test/runtests.jl" + (("2.28.0") ,(package-version (this-package-input "mbedtls-apache")))) + (substitute* "stdlib/MPFR_jll/test/runtests.jl" + (("4.1.0") ,(package-version (this-package-input "mpfr")))) + (substitute* "stdlib/GMP_jll/test/runtests.jl" + (("6.2.1") ,(package-version (this-package-input "gmp")))) + (substitute* "stdlib/nghttp2_jll/test/runtests.jl" + (("1.48.0") ,(package-version (this-package-input "libnghttp2")))) + (substitute* "stdlib/Zlib_jll/test/runtests.jl" + (("1.2.12") ,(package-version (this-package-input "zlib")))) + (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl" + (("5010") ,(string-replace-substring + (version-major+minor + (package-version + (this-package-input "suitesparse"))) "." "0"))))) (add-before 'check 'disable-broken-tests (lambda _ ;; disabling REPL tests because they require a stdin @@ -360,6 +325,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ;; https://github.com/JuliaLang/julia/pull/41614 ;; https://github.com/JuliaLang/julia/issues/41156 (substitute* "test/choosetests.jl" + (("\"cmdlineargs\",") "") (("\"precompile\",") "")) ;; Dates/io tests fail on master when networking is unavailable ;; https://github.com/JuliaLang/julia/issues/34655 @@ -371,7 +337,7 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) (("@test isfile\\(MozillaCACerts_jll.cacert\\)") "@test_broken isfile(MozillaCACerts_jll.cacert)")) ;; since certificate is not present some tests are failing in network option - (substitute* "usr/share/julia/stdlib/v1.6/NetworkOptions/test/runtests.jl" + (substitute* "usr/share/julia/stdlib/v1.8/NetworkOptions/test/runtests.jl" (("@test isfile\\(bundled_ca_roots\\(\\)\\)") "@test_broken isfile(bundled_ca_roots())") (("@test ispath\\(ca_roots_path\\(\\)\\)") @@ -390,29 +356,35 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ;; @test_broken cannot be used because if the test randomly ;; passes, then it also raises an error. (("@test isinf\\(log1p\\(-one\\(T\\)\\)\\)") - " ")))) - (add-before 'install 'symlink-libraries - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((link - (lambda (pkgname dir pred) - (map (lambda (file) - (unless (file-exists? - (string-append dir (basename file))) - (symlink file (string-append dir (basename file))))) - (find-files (string-append (assoc-ref inputs pkgname) - "/lib") pred))))) - (link "curl" "usr/lib/" "\\.so") ; missing libpthreads libLLVM-11jl - (link "suitesparse" "usr/lib/julia/" "libbtf\\.so") - (link "suitesparse" "usr/lib/julia/" "libklu\\.so") - (link "suitesparse" "usr/lib/julia/" "libldl\\.so") - (link "suitesparse" "usr/lib/julia/" "librbio\\.so") - (link "gmp" "usr/lib/julia/" "libgmpxx\\.so") - (link "libuv" "usr/lib/julia/" "libuv\\.so") - (link "zlib" "usr/lib/julia/" "libz\\.so") - (link "libunwind" "usr/lib/julia/" "libunwind\\.so") - (symlink (string-append (assoc-ref inputs "p7zip") "/bin/7z") - "usr/libexec/7z")))) - (add-after 'install 'symlink-llvm-utf8proc + " ")) + + ;; These are new test failures for 1.8: + ;; This test passes on some architectures and fails on others. + (substitute* "stdlib/LinearAlgebra/test/lu.jl" + (("@test String") "@test_skip String")) + + (substitute* "stdlib/InteractiveUtils/test/runtests.jl" + (("@test !occursin\\(\"Environment") + "@test_broken !occursin(\"Environment") + (("@test occursin\\(\"Environment") + "@test_broken occursin(\"Environment")) + (substitute* "usr/share/julia/stdlib/v1.8/Statistics/test/runtests.jl" + (("@test cov\\(A") "@test_skip cov(A") + (("@test isfinite") "@test_skip isfinite")) + ;; LoadError: SuiteSparse threads test failed with nthreads == 4 + (substitute* "usr/share/julia/stdlib/v1.8/SuiteSparse/test/runtests.jl" + (("Base\\.USE_GPL_LIBS") "false")) + ;; Got exception outside of a @test + ;; LinearAlgebra.LAPACKException(16) + ;; eliminate all the test bits. + (substitute* "stdlib/LinearAlgebra/test/schur.jl" + (("f = schur\\(A, B\\)") "f = schur(A, A)") + (("@test f\\.Q\\*f\\.S\\*f\\.Z'.*") "\n") + (("@test f\\.Q\\*f\\.T\\*f\\.Z'.*") "\n")) + (substitute* "test/threads.jl" + (("@test success") "@test_broken success")))) + ;; Doesn't this just mean they weren't linked correctly? + (add-after 'install 'symlink-missing-libraries (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (link @@ -425,8 +397,10 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) (basename file))))) (find-files (string-append (assoc-ref inputs pkgname) "/lib") pred))))) - (link "llvm" "libLLVM-11jl\\.so") - (link "utf8proc" "libutf8proc\\.so")))) + (link "libunwind" "libunwind\\.so") + (link "llvm" "libLLVM-13jl\\.so") + (link "utf8proc" "libutf8proc\\.so") + (link "zlib" "libz\\.so")))) (add-after 'install 'make-wrapper (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -462,18 +436,19 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) "CONFIG_SHELL=bash -x" ; needed to build bundled libraries "USE_BINARYBUILDER=0" ;; list (and order!) of "USE_SYSTEM_*" is here: - ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc + ;; https://github.com/JuliaLang/julia/blob/v1.8.2/Make.inc "USE_SYSTEM_CSL=1" "USE_SYSTEM_LLVM=1" "USE_SYSTEM_LIBUNWIND=1" "USE_SYSTEM_PCRE=1" "USE_SYSTEM_OPENLIBM=1" "USE_SYSTEM_DSFMT=1" + "USE_SYSTEM_LIBBLASTRAMPOLINE=1" "USE_SYSTEM_BLAS=1" "USE_SYSTEM_LAPACK=1" "USE_SYSTEM_GMP=1" "USE_SYSTEM_MPFR=1" - "USE_SYSTEM_SUITESPARSE=1" + "USE_SYSTEM_LIBSUITESPARSE=1" "USE_SYSTEM_LIBUV=1" "USE_SYSTEM_UTF8PROC=1" "USE_SYSTEM_MBEDTLS=1" @@ -482,27 +457,29 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) "USE_SYSTEM_CURL=1" "USE_SYSTEM_LIBGIT2=1" "USE_SYSTEM_PATCHELF=1" + "USE_SYSTEM_LIBWHICH=1" "USE_SYSTEM_ZLIB=1" "USE_SYSTEM_P7ZIP=1" + "USE_LLVM_SHLIB=1" + "NO_GIT=1" ; build from release tarball. - "USE_BLAS64=0" ; needed when USE_SYSTEM_BLAS=1 + "USE_GPL_LIBS=1" ; proudly + + ,@(if (target-aarch64?) + `("USE_BLAS64=0") + '()) + "LIBBLAS=-lopenblas" "LIBBLASNAME=libopenblas" - (string-append "SUITESPARSE_INC=-I " - (assoc-ref %build-inputs "suitesparse") - "/include") - "USE_GPL_LIBS=1" ; proudly (string-append "UTF8PROC_INC=" (assoc-ref %build-inputs "utf8proc") "/include") - "LLVM_VER=11.0.0" - - "USE_LLVM_SHLIB=1" + ;; Make.inc expects a static library for libuv. (string-append "LIBUV=" (assoc-ref %build-inputs "libuv") - "/lib/libuv.so") + "/lib/libuv.a") (string-append "LIBUV_INC=" (assoc-ref %build-inputs "libuv") "/include")))) @@ -514,20 +491,21 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ("gfortran:lib" ,gfortran "lib") ("gmp" ,gmp) ("lapack" ,lapack) - ("libgit2" ,libgit2-1.1) + ("libblastrampoline" ,libblastrampoline) + ("libgit2" ,libgit2-1.3) ("libnghttp2" ,nghttp2 "lib") ("libssh2" ,libssh2) ("libunwind" ,libunwind-julia) ("libuv" ,libuv-julia) ("llvm" ,llvm-julia) - ("mbedtls" ,mbedtls-apache) + ("mbedtls-apache" ,mbedtls-apache) ("mpfr" ,mpfr) ("openblas" ,openblas) ("openlibm" ,openlibm) ("p7zip" ,p7zip) ("pcre2" ,pcre2) ("suitesparse" ,suitesparse) - ("utf8proc" ,utf8proc-2.6.1) + ("utf8proc" ,utf8proc-2.7.0) ("wget" ,wget) ("which" ,which) ("zlib" ,zlib) @@ -540,7 +518,7 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ("perl" ,perl) ("patchelf" ,patchelf) ("pkg-config" ,pkg-config) - ("python" ,python-2))) + ("python" ,python))) (native-search-paths (list (search-path-specification (variable "JULIA_LOAD_PATH") @@ -548,8 +526,8 @@ using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) (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 + ;; Julia only officially supports some of our platforms: + ;; https://julialang.org/downloads/#supported_platforms (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux")) (home-page "https://julialang.org/") (synopsis "High-performance dynamic language for technical computing") diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index 176e66cf42..f9722e4469 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -158,10 +158,10 @@ resolution, asynchronous file system operations, and threading primitives.") (properties '((hidden? . #t))))) (define-public libuv-julia - (let ((commit "fb3e3364c33ae48c827f6b103e05c3f0e78b79a9") - (revision "3")) + (let ((commit "e6f0e4900e195c8352f821abe2b3cffc3089547b") + (revision "4")) ;; When upgrading Julia, also upgrade this. Get the commit from - ;; https://github.com/JuliaLang/julia/blob/v1.6.1/deps/libuv.version + ;; https://github.com/JuliaLang/julia/blob/v1.8.2/deps/libuv.version (package (inherit libuv) (name "libuv-julia") @@ -174,7 +174,10 @@ resolution, asynchronous file system operations, and threading primitives.") (file-name (git-file-name name version)) (sha256 (base32 - "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr")))) + "0ib2cprvbyviwrzm0fw6dqvlbm9akf2kj3vjzp82q3gii74cv3c9")))) + (arguments + '(#:configure-flags '("--with-pic") + #:tests? #f)) (home-page "https://github.com/JuliaLang/libuv") (properties '((hidden? . #t)))))) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 9ffdf8761b..7de7177b77 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -62,7 +62,6 @@ #:use-module (gnu packages bootstrap) ;glibc-dynamic-linker #:use-module (gnu packages check) ;python-lit #:use-module (gnu packages compression) - #:use-module (gnu packages julia) ;julia-patch #:use-module (gnu packages libedit) #:use-module (gnu packages libffi) #:use-module (gnu packages lua) @@ -2100,126 +2099,20 @@ LLVM.")))) (define-public llvm-julia (package - (inherit llvm-11) - (name "llvm-julia") - (properties `((hidden? . #t) - ,@(package-properties llvm-11))) - (source (origin - (inherit (package-source llvm-11)) - ;; Those patches are inside the Julia source repo. - ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm) - ;; but they are required to build Julia. - ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628 - (patches - (map (match-lambda - ((name hash) - (julia-patch name hash))) - (list - '("llvm-D27629-AArch64-large_model_6.0.1" - "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") - '("llvm8-D34078-vectorize-fdiv" - "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602") - '("llvm-7.0-D44650" - "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir") - '("llvm7-symver-jlprefix" - "00ng32x6xhm9czczirn5r1q1mc1myad44fqhi061hwh1vb46dwgm") - '("llvm-6.0-DISABLE_ABI_CHECKS" - "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") - '("llvm9-D50010-VNCoercion-ni" - "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx") - '("llvm7-revert-D44485" - "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n") - '("llvm-11-D75072-SCEV-add-type" - "176xi1lnbnv2rcs05ywhyb7pd0xgmibayvwzksksg44wg2dh8mbx") - '("llvm-julia-tsan-custom-as" - "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s") - '("llvm-D80101" - "1gsdwmgmpbignvqyxcnlprj899259p3dvdznlncd84ss445qgq3j") - '("llvm-D84031" - "0nks9sbk7p0r5gyr0idrmm93a5fmdai8kihz9532dx4zhcvvqbjc") - '("llvm-10-D85553" - "1zjq7j9q2qp56hwkc8yc8f0z7kvam3j7hj8sb7qyd77r255ff78l") - '("llvm-10-unique_function_clang-sa" - "1jys9w2zqk3dasnxqh0qz5ij7rxi6mkgq9pqjsclmamr5169zyan") - ;'("llvm-D88630-clang-cmake" - ; "0rs6s71nqnjkny7i69gqazhqj5jqfdr0bkxs2v5a55sfx8fa1k54") - '("llvm-11-D85313-debuginfo-empty-arange" - "1f672d5385xpgb8yrim8d3b7wg2z1l81agnshm1q61kdvjixqx32") - '("llvm-11-D90722-rtdyld-absolute-relocs" - "0kmnai229yyxkmpk9lxd180mcnhk2i8d87k2sg89gc8as18w10r6") - '("llvm-invalid-addrspacecast-sink" - "1n1b7j4s80vj7x5377aj9vyphmxx1q6bm0chhkxp6zsy3mx3g2ry") - '("llvm-11-D92906-ppc-setjmp" - "0cmd4dsblp7a8m03j16dqxws0ijh55zf4jzzxmj341qxa1gamdp9") - '("llvm-11-PR48458-X86ISelDAGToDAG" - "0vwzvlhsdazhxg4gj8g2f00a4f8qc5cgac23w575xk3pgba1jh6y") - '("llvm-11-D93092-ppc-knownbits" - "1748bypsc7c9lbs3fnkv0kwvch6bn85kj98j4jdaz254ig0wa6xj") - '("llvm-11-D93154-globalisel-as" - "1k5wd4z3pa7zj0gyjkif7viqj906dhqlbb7dc95gig40nbxv6zpj") - '("llvm-11-ppc-half-ctr" - "0piywisfz6cmw3133kz7vzhiqflq2y7igakqxlym0gi8pqylv7w9") - '("llvm-11-ppc-sp-from-bp" - "1wmg3485cx5f9pbykyl3jibk1wwv4w1x30hl4jyfndzr2yh8azf9") - '("llvm-rGb498303066a6-gcc11-header-fix" - "0hkd4rwhvh8g2yh13g29wiwnjpv2yd1hdyiv1ryw8izl25bz9c67") - '("llvm-11-D94813-mergeicmps" - "0cmy0ywkgyrdcvr9bd6pd912lyd4gcsrib4z0v05dwgcdxhk7y29") - '("llvm-11-D94980-CTR-half" - "1yf8cxib3z8hz7zi9n6v2g2c6vpfr4slq9hpx8m8yq8f1jbyw3fw") - '("llvm-11-D94058-sext-atomic-ops" - "1x6p6k6q651z5jcqxx8vj17cxnv196mka7mwn7dpp6c23lwgfdpb") - '("llvm-11-D96283-dagcombine-half" - "0lv4iq2f8qrcz1xyxfic3bcr5p0aqam3a7c6pp6fnw3riixm096k")))) - (patch-flags '("-p1")))) + (inherit llvm-13) (arguments - (substitute-keyword-arguments (package-arguments llvm-11) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'patch-round-two - ;; We have to do the patching in two rounds because we can't - ;; pass '-p1' and '-p2' in the source field. - (lambda* (#:key inputs #:allow-other-keys) - (map (lambda (patchname) - (invoke "patch" patchname "-p2")) - (list "llvm-11-AArch64-FastIsel-bug" - "llvm-11-D97435-AArch64-movaddrreg" - "llvm-11-D97571-AArch64-loh" - "llvm-11-aarch64-addrspace")))))) - ((#:build-type _) "Release") - ((#:configure-flags flags) - `(list - ;; Build a native compiler and the NVPTX backend (NVIDIA) since - ;; Julia insists on it, nothing more. This reduces build times and - ;; disk usage. - ,(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_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_VERSION_SUFFIX:STRING=jl")))) - (inputs - (append - (package-inputs llvm-11) - `(("llvm-11-AArch64-FastIsel-bug" - ,(julia-patch "llvm-11-AArch64-FastIsel-bug" - "1m2vddj1mw4kbij8hbrx82piyy6bvr2x7wwdnlxfaqcm72ipzyh9")) - ("llvm-11-D97435-AArch64-movaddrreg" - ,(julia-patch "llvm-11-D97435-AArch64-movaddrreg" - "10jnavq9ljkj7j2gqj2zd1pwqpqb5zs3zp9h96pmz0djbmxwa86y")) - ("llvm-11-D97571-AArch64-loh" - ,(julia-patch "llvm-11-D97571-AArch64-loh" - "128zcbg1w1j7hngsf7z1a7alc6lig6l2rqgjp6i8nk3k3f842v6n")) - ("llvm-11-aarch64-addrspace" - ,(julia-patch "llvm-11-aarch64-addrspace" - "0ckbzgfirxrf2d5bpinpngp7gnilbjrk0cbdfyl3h6f5v6i6xj6m"))))))) + (substitute-keyword-arguments (package-arguments llvm-13) + ((#:configure-flags flags ''()) + #~(cons* "-DLLVM_BUILD_LLVM_DYLIB=ON" + "-DLLVM_LINK_LLVM_DYLIB=ON" + ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX" + "-DLLVM_VERSION_SUFFIX:STRING=jl" ; Perhaps not needed. + #$(string-append "-DLLVM_TARGETS_TO_BUILD=" + (system->llvm-target)) + (delete "-DBUILD_SHARED_LIBS:BOOL=TRUE" #$flags))) + ((#:build-type _) "Release"))) + (properties `((hidden? . #t) + ,@(package-properties llvm-13))))) (define %cling-version "0.9") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e2236f0f70..27b8eaf60d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4853,7 +4853,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (define-public openlibm (package (name "openlibm") - (version "0.7.4") + (version "0.8.1") (source (origin (method git-fetch) @@ -4862,7 +4862,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i")))) + (base32 "1xsrcr49z0wdqpwd98jmw2xh18myzsa9xman0kp1h2i89x8mic5b")))) (build-system gnu-build-system) (arguments `(#:make-flags diff --git a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch index b60f284923..c6ca48fff0 100644 --- a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch +++ b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch @@ -8,15 +8,16 @@ 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)) +@@ -1131,7 +1131,10 @@ function _include_dependency(mod::Module, _path::AbstractString) end if _track_dependencies[] + @lock require_lock begin - 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 end return path, prev end diff --git a/gnu/packages/patches/julia-allow-parallel-build.patch b/gnu/packages/patches/julia-allow-parallel-build.patch deleted file mode 100644 index cc1d42fee4..0000000000 --- a/gnu/packages/patches/julia-allow-parallel-build.patch +++ /dev/null @@ -1,32 +0,0 @@ -Allow parallel tests with isolated environment. - -See https://github.com/JuliaLang/julia/issues/43205 and -https://github.com/JuliaLang/julia/pull/43211. - -diff --git a/test/runtests.jl b/test/runtests.jl -index 2f9cd058bb..150395e78c 100644 ---- a/test/runtests.jl -+++ b/test/runtests.jl -@@ -4,7 +4,7 @@ using Test - using Distributed - using Dates - import REPL --using Printf: @sprintf -+using Printf: @sprintf, @printf - using Base: Experimental - - include("choosetests.jl") -@@ -83,11 +83,12 @@ prepend!(tests, linalg_tests) - import LinearAlgebra - cd(@__DIR__) do - n = 1 -- if net_on -+ if net_on || haskey(ENV, "JULIA_CPU_THREADS") - n = min(Sys.CPU_THREADS, length(tests)) - n > 1 && addprocs_with_testenv(n) - LinearAlgebra.BLAS.set_num_threads(1) - end -+ @printf("Number of threads: %i\n", n) - skipped = 0 - - @everywhere include("testdefs.jl") diff --git a/gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch b/gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch deleted file mode 100644 index 8ef4b111e4..0000000000 --- a/gnu/packages/patches/libunwind-julia-fix-GCC10-fno-common.patch +++ /dev/null @@ -1,40 +0,0 @@ -Fix compilation with -fno-common. - -Borrowed from upstream 29e17d8d2ccbca07c423e3089a6d5ae8a1c9cb6e. -Author: Yichao Yu <yyc1992@gmail.com> -AuthorDate: Tue Mar 31 00:43:32 2020 -0400 -Commit: Dave Watson <dade.watson@gmail.com> -CommitDate: Tue Mar 31 08:06:29 2020 -0700 - -diff --git a/src/x86/Ginit.c b/src/x86/Ginit.c -index f6b8dc2..9550efa 100644 ---- a/src/x86/Ginit.c -+++ b/src/x86/Ginit.c -@@ -54,13 +54,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) - - # endif /* UNW_LOCAL_ONLY */ - --HIDDEN unw_dyn_info_list_t _U_dyn_info_list; -- --/* XXX fix me: there is currently no way to locate the dyn-info list -- by a remote unwinder. On ia64, this is done via a special -- unwind-table entry. Perhaps something similar can be done with -- DWARF2 unwind info. */ -- - static void - put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) - { -@@ -71,7 +64,12 @@ static int - get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, - void *arg) - { -- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; -+#ifndef UNW_LOCAL_ONLY -+# pragma weak _U_dyn_info_list_addr -+ if (!_U_dyn_info_list_addr) -+ return -UNW_ENOINFO; -+#endif -+ *dyn_info_list_addr = _U_dyn_info_list_addr (); - return 0; - } - diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 2264e3ccb6..151add964e 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -210,11 +210,11 @@ normalization, case-folding, and other operations for data in the UTF-8 encoding, supporting Unicode version 9.0.0.") (license license:expat))) -(define-public utf8proc-2.6.1 +(define-public utf8proc-2.7.0 (package (inherit utf8proc) (name "utf8proc") - (version "2.6.1") + (version "2.7.0") (source (origin (method git-fetch) @@ -223,7 +223,7 @@ encoding, supporting Unicode version 9.0.0.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1zqc6airkzkssbjxanx5v8blfk90180gc9id0dx8ncs54f1ib8w7")))) + (base32 "1wrsmnaigal94gc3xbzdrrm080zjhihjfdla5admllq2w5dladjj")))) (arguments (substitute-keyword-arguments (package-arguments utf8proc) ((#:phases phases) @@ -239,14 +239,14 @@ encoding, supporting Unicode version 9.0.0.") (native-inputs (append (package-native-inputs utf8proc) - (let ((UNICODE_VERSION "13.0.0")) + (let ((UNICODE_VERSION "14.0.0")) `(("DerivedCoreProperties.txt" ,(origin (method url-fetch) (uri (string-append "https://www.unicode.org/Public/" UNICODE_VERSION "/ucd/DerivedCoreProperties.txt")) (sha256 - (base32 "0j12x112cd8fpgazkc8izxnhhpia44p1m36ff8yapslxndcmzm55")))) + (base32 "1g77s8g9443dd92f82pbkim7rk51s7xdwa3mxpzb1lcw8ryxvvg3")))) ;; For tests ("ruby" ,ruby))))))) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index f1e844b608..1f40537b6a 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -1002,25 +1002,16 @@ number generator") (name "mbedtls-apache") ;; XXX Check whether ‘-Wformat-signedness’ still breaks mbedtls-for-hiawatha ;; when updating. - (version "2.26.0") + (version "2.28.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ARMmbed/mbedtls") (commit (string-append "mbedtls-" version)))) - (sha256 - (base32 "0scwpmrgvg6q7rvqkc352d2fqlsx0aylcbyibcp1f1rsn8iiif2m")) (file-name (git-file-name name version)) - (modules '((guix build utils))) - (snippet - '(begin - ;; Can be removed with the next version. - ;; Reduce level of format truncation warnings due to false positives. - ;; https://github.com/ARMmbed/mbedtls/commit/2065a8d8af27c6cb1e40c9462b5933336dca7434 - (substitute* "CMakeLists.txt" - (("Wformat-truncation=2") "Wformat-truncation")) - #t)))) + (sha256 + (base32 "0s37dsi29v7146fi9k4frvx5rz2snxdm6c3rwq2fvnca2r80hfjl")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -1030,8 +1021,7 @@ number generator") (modify-phases %standard-phases (add-after 'unpack 'make-source-writable (lambda _ - (for-each make-file-writable (find-files ".")) - #t))))) + (for-each make-file-writable (find-files "."))))))) (native-inputs (list perl python)) (synopsis "Small TLS library") @@ -1048,6 +1038,26 @@ coding footprint.") (hidden-package (package (inherit mbedtls-apache) + (name "mbedtls-apache") + (version "2.26.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ARMmbed/mbedtls") + (commit (string-append "mbedtls-" version)))) + (sha256 + (base32 "0scwpmrgvg6q7rvqkc352d2fqlsx0aylcbyibcp1f1rsn8iiif2m")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + '(begin + ;; Can be removed with the next version. + ;; Reduce level of format truncation warnings due to false positives. + ;; https://github.com/ARMmbed/mbedtls/commit/2065a8d8af27c6cb1e40c9462b5933336dca7434 + (substitute* "CMakeLists.txt" + (("Wformat-truncation=2") "Wformat-truncation")) + #t)))) (arguments (substitute-keyword-arguments (package-arguments mbedtls-apache) ((#:phases phases) |