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author | Efraim Flashner | 2021-11-16 14:41:48 +0200 |
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committer | Efraim Flashner | 2021-11-16 14:42:07 +0200 |
commit | af6f5ea38d4871f22096adfe862b0f52563f47fa (patch) | |
tree | 857e59b0972e677218ae4966e233351e28dae083 | |
parent | 814c2bf2f4b9db13b2aef7e7e8b8aebc469bbc6d (diff) | |
download | guix-bioinformatics-af6f5ea38d4871f22096adfe862b0f52563f47fa.tar.gz |
gn: Adjust to changes in julia-build-system
-rw-r--r-- | VERSION | 2 | ||||
-rw-r--r-- | gn/packages/julia.scm | 20 |
2 files changed, 12 insertions, 10 deletions
@@ -1 +1 @@ -9c3b2cf0b3328a08d026dbbf4fea4c26eafc67ef +3af351a7de41b8d50f27f3623c46392f571b9a4e diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm index 7795a7c..276a21a 100644 --- a/gn/packages/julia.scm +++ b/gn/packages/julia.scm @@ -40,6 +40,7 @@ `(#:tests? #f ; no test suite #:phases (modify-phases %standard-phases + (delete 'link-depot) ; Not really needed on this package. (add-after 'unpack 'patch-source (lambda* (#:key inputs #:allow-other-keys) (chmod "runpluto.sh" #o555) ; it starts as #o444 @@ -222,7 +223,7 @@ distributed computing.") #:phases (modify-phases %standard-phases ;(delete 'precompile) - (add-after 'unpack 'hardcode-conda-path + (add-after 'link-depot 'hardcode-conda-path (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Conda.jl" (("bin_dir\\(ROOTENV\\), \"conda\"") (string-append "\"" (assoc-ref inputs "conda") "/bin/\", \"conda\""))) @@ -424,12 +425,12 @@ optimization of functions.") `(#:tests? #f ; Test suite fails to load HTTP.jl. #:phases (modify-phases %standard-phases - (add-after 'unpack 'dont-check-for-upgrades + (add-after 'link-depot 'dont-check-for-upgrades (lambda _ (substitute* "frontend/components/Welcome.js" (("local_index !== -1") "false")) #t)) - (add-after 'unpack 'skip-network-tests + (add-after 'link-depot 'skip-network-tests (lambda _ (substitute* "test/runtests.jl" ;; Attempts to update the package registry. @@ -498,7 +499,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'adjust-test-suite + (add-after 'link-depot 'adjust-test-suite (lambda _ (substitute* "test/misc.jl" (("test logmvbeta\\(1") "test_nowarn logmvbeta(1")) @@ -537,6 +538,7 @@ and numerical functions for statistical computing.") `(#:phases (modify-phases %standard-phases (delete 'precompile) ; No Project.toml. + (delete 'link-depot) ; Not really needed on this package. (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? @@ -579,7 +581,7 @@ functions.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'link-to-librmath-directly + (add-after 'link-depot 'link-to-librmath-directly (lambda* (#:key inputs #:allow-other-keys) (let* ((rmath (assoc-ref inputs "rmath")) (librmath (string-append rmath "/lib/libRmath-julia.so"))) @@ -618,7 +620,7 @@ R's d-p-q-r functions for probability distributions. It is a wrapper around '(#:tests? #f ; no runtests #:phases (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path + (add-after 'link-depot 'override-binary-path (lambda* (#:key inputs #:allow-other-keys) (map (lambda (wrapper) @@ -656,7 +658,7 @@ R's d-p-q-r functions for probability distributions. It is a wrapper around (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-optim-tests + (add-after 'link-depot 'skip-optim-tests (lambda _ (substitute* "test/examples.jl" ;; Prevent a cycle with Optim.jl. @@ -792,7 +794,7 @@ polynomials.") `(#:tests? #f ; Tests attempt to download timezone information #:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-tzdata + (add-after 'link-depot 'patch-tzdata (lambda* (#:key inputs #:allow-other-keys) ;(substitute* "src/tzdata/TZData.jl" ; (("(COMPILED_DIR = ).*" _ key) @@ -910,7 +912,7 @@ that still support Julia versions older than 1.6.") `(#:tests? #f ; no runtests.jl #:phases (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path + (add-after 'link-depot 'override-binary-path (lambda* (#:key inputs #:allow-other-keys) (map (lambda (wrapper) |