* [bug#41167] [PATCH 2/5] gnu: julia: Fix patch.
2020-05-10 8:15 ` [bug#41167] [PATCH 1/5] gnu: julia: Fix patch url nixo
@ 2020-05-10 8:15 ` nixo
2020-05-10 8:15 ` [bug#41167] [PATCH 3/5] gnu: Add libwhich nixo
` (2 subsequent siblings)
3 siblings, 0 replies; 9+ messages in thread
From: nixo @ 2020-05-10 8:15 UTC (permalink / raw)
To: 41167; +Cc: nixo
* gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch: replaced with
actual patch.
It was a patch creating the patch.
---
.../julia-SOURCE_DATE_EPOCH-mtime.patch | 54 +++++++++----------
1 file changed, 27 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
index 32dfd7b856..a6a4456303 100644
--- a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
+++ b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
@@ -1,28 +1,28 @@
---- /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 Nicolò 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
+From e4dc28db1d70819505fd1a68fd9d2bfc4fb61a7d Mon Sep 17 00:00:00 2001
+From: nixo <nicolo@nixo.xyz>
+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
+@@ -807,8 +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
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread* [bug#41167] [PATCH 4/5] gnu: julia: Update to 1.4.1.
2020-05-10 8:15 ` [bug#41167] [PATCH 1/5] gnu: julia: Fix patch url nixo
2020-05-10 8:15 ` [bug#41167] [PATCH 2/5] gnu: julia: Fix patch nixo
2020-05-10 8:15 ` [bug#41167] [PATCH 3/5] gnu: Add libwhich nixo
@ 2020-05-10 8:15 ` nixo
2020-05-10 8:15 ` [bug#41167] [PATCH 5/5] gnu: Add julia-compat nixo
3 siblings, 0 replies; 9+ messages in thread
From: nixo @ 2020-05-10 8:15 UTC (permalink / raw)
To: 41167; +Cc: nixo
* gnu/packages/julia.scm (julia): Update to 1.4.1.
* gnu/packages/julia.scm (julia-llvm): Update to 8.
---
gnu/packages/julia.scm | 191 +++++++++++++++++++----------------------
1 file changed, 86 insertions(+), 105 deletions(-)
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 2bef25277d..c636fa756b 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -53,7 +53,7 @@
(let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")
(revision "1"))
;; When upgrading Julia, also upgrade this. Get the commit from
- ;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
+ ;; https://github.com/JuliaLang/julia/blob/v1.4.1/deps/libuv.version
(package
(inherit libuv)
(name "libuv-julia")
@@ -103,7 +103,7 @@
"/deps/patches/" name ".patch"))
(define (julia-patch name sha)
- (let ((version "1.3.1"))
+ (let ((version "1.4.1"))
(origin (method url-fetch)
(uri (julia-patch-url version name))
(sha256 (base32 sha))
@@ -111,10 +111,10 @@
(define llvm-julia
(package
- (inherit llvm-6)
+ (inherit llvm-8)
(name "llvm-julia")
(source (origin
- (inherit (package-source llvm-6))
+ (inherit (package-source llvm-8))
;; 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.
@@ -124,42 +124,50 @@
((name hash)
(julia-patch name hash)))
(list
- '("llvm-6.0-D44650"
- "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
+ '("llvm-7.0-D44650"
+ "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
'("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"))))))
+ '("llvm8-D34078-vectorize-fdiv"
+ "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
+ '("llvm7-D50010-VNCoercion-ni"
+ "18scg6aa036xa1508s7q93w9dvc5gp69fz6yl6fkh4yffw4gymw6")
+ '("llvm-8.0-D50167-scev-umin"
+ "0g9w2x8yryjdkihnrf18x0yi5bi14c5p8wffda1w732dr5ckzk94")
+ '("llvm-D57118-powerpc"
+ "0vxz5s0s9b625v1rv8lg1566yhxh1i91ydzmvy5s7njvzc7p19aw")
+ '("llvm8-WASM-addrspaces"
+ "1176agj9hh7csdm2lnklb42zcdsb3q6lx9jiyp2shn4p2678y76q")
+ '("llvm-exegesis-mingw"
+ "0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
+ '("llvm-test-plugin-mingw"
+ "12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
+ '("llvm-8.0-D66401-mingw-reloc"
+ "15v3p5sznn979cfnd7gdn3nd701fd7xd5aks6lnj1mslvljlq3ls")
+ '("llvm7-revert-D44485"
+ "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
+ '("llvm-8.0-D63688-wasm-isLocal"
+ "0i9wi5n63ip3802z6m7aj3p07hkqjlmp4vg4wq3xkf9f6w9rksab")
+ '("llvm-8.0-D55758-tablegen-cond"
+ "1l08mg7qigravi7plsq3yzya80fljnp95n8faddr29wbr2qr0655")
+ '("llvm-8.0-D59389-refactor-wmma"
+ "0rgrwk4xlwpk7yai2j7xadcfws93rmk2hhh44fysa88imvrbp478")
+ '("llvm-8.0-D59393-mma-ptx63-fix"
+ "094jcsxbcx9fljj623mgmc0rjpk12s2rs0di0ck0hakzhr8mbv5n")
+ '("llvm-8.0-D66657-codegen-degenerate"
+ "1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
+ '("llvm-8.0-D71495-vectorize-freduce"
+ "1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
+ '("llvm-8.0-D75072-SCEV-add-type"
+ "0amlyyndsc90ml2k6prdahf24q0j23nfmlbqf8gcqcxpl5sqq3i6")
+ '("llvm-8.0-D65174-limit-merge-stores"
+ "1ls5114fhgip9rbqabqc16mi367ra0k75ngc1vyqqhq1ghm9x7y9"))))))
(arguments
- (substitute-keyword-arguments (package-arguments llvm-6)
+ (substitute-keyword-arguments (package-arguments llvm-8)
((#:configure-flags flags)
`(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
"-DCMAKE_BUILD_TYPE=Release"
@@ -191,6 +199,7 @@
(url "https://github.com/vtjnash/libwhich.git")
;; fixes linux-vdso.so related tests
(commit "87cffe10080c98e7b5786c5166e420bf1ada1d41")))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1bpa0fcqpa3ai3hm8mz0p13bf76fsq53wsfcx5qw302zh22108xr"))))
@@ -222,7 +231,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(define-public julia
(package
(name "julia")
- (version "1.3.1")
+ (version "1.4.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -230,7 +239,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
version "/julia-" version ".tar.gz"))
(sha256
(base32
- "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
+ "030aza3qj5zcinxbrbqgi7p64q6klwq2bhwccraarx7l0hg9lw3i"))
(patches
(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(build-system gnu-build-system)
@@ -253,15 +262,6 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(delete 'configure)
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
- (mkdir "deps/srccache")
- ;; no USE_SYSTEM_{OBJCONV/LIBWHICH} option
- (copy-file (assoc-ref inputs "objconv")
- "deps/srccache/objconv.zip")
- (copy-file (assoc-ref inputs "libwhich")
- (string-append "deps/srccache/libwhich-"
- "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
- ".tar.gz"))
-
;; needed by libwhich
(setenv "LD_LIBRARY_PATH"
(string-join (map (lambda (pkg)
@@ -286,21 +286,19 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
(("src ui doc deps")
"src ui deps"))
#t))
+ (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")
+ (string-append (assoc-ref inputs "libwhich") "/bin/libwhich")))
+ #t))
(add-before 'check 'set-home
;; 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"
- "\"")))
- #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
@@ -343,10 +341,14 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
;; 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\"]),
+ "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",\"precompile\",
+ \"client\",\"stacktraces\"]),
testnames)"))
+ ;; precompile test is broken, fixed in
+ ;; fed29f893544d1dc8f86444c65d632c68168d0f3
+ (substitute* "test/precompile.jl"
+ (("@test !isdefined\\(Base.Nothing.name.mt")
+ "# @test !isdefined(Base.Nothing.name.mt"))
;; 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
@@ -356,24 +358,31 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
;; https://github.com/JuliaLang/julia/issues/32377
(substitute* "stdlib/REPL/test/replcompletions.jl"
(("@test count") "@test_broken count"))
+ ;; Dates has a similar bug:
+ ;; https://github.com/JuliaLang/julia/issues/34655
+ (substitute* "stdlib/Dates/test/io.jl"
+ (("\"Dates.Time") "\"Time"))
+ ;; Upstream bug I found when packaging
+ ;; https://github.com/JuliaLang/julia/issues/35785
+ (substitute* "test/file.jl"
+ (("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d"))
#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))))
+ (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"))
- (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "prefix=" (assoc-ref %outputs "out"))
;; Passing the MARCH flag is necessary to build binary substitutes for
;; the supported architectures.
@@ -421,17 +430,12 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_PCRE=1"
"USE_SYSTEM_OPENLIBM=1"
-
+ "USE_SYSTEM_MBEDTLS=1"
+ "USE_SYSTEM_LIBSSH2=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=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)
@@ -462,30 +466,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
("suitesparse" ,suitesparse)
;; Find dependencies versions here:
;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
- ("objconv"
- ,(origin
- (method url-fetch)
- ;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
- (uri "https://www.agner.org/optimize/objconv.zip")
- (file-name "objconv-2018-10-07.zip")
- (sha256
- (base32
- "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
- ("libwhich"
- ,(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
- "https://api.github.com/repos/vtjnash/libwhich/tarball/"
- commit))
- (file-name (string-append "libwhich-" (string-take commit 7)
- ".tar.gz"))
- (sha256
- (base32
- "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
+ ("libwhich" ,libwhich)
("dsfmt" ,dsfmt)))
(native-inputs
`(("openssl" ,openssl)
--
2.26.2
^ permalink raw reply related [flat|nested] 9+ messages in thread