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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-11-07 20:24:18 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-11-07 20:26:46 +0100 |
| commit | 152bebd9e0c7fc0863d6b82af014e61a8cb6a488 (patch) | |
| tree | 16ed100c552b041adb1b426343b1199dd91eab2c | |
| parent | b113f39019913ad8eda4d72624ce9769920d22cb (diff) | |
| download | gnu-guix-152bebd9e0c7fc0863d6b82af014e61a8cb6a488.tar gnu-guix-152bebd9e0c7fc0863d6b82af014e61a8cb6a488.tar.gz | |
gnu: gemma: Update to 0.98.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 19 | ||||
| -rw-r--r-- | gnu/packages/patches/gemma-intel-compat.patch | 44 |
3 files changed, 15 insertions, 49 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index bfe93159dc..9a8330aa41 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -722,7 +722,6 @@ dist_patch_DATA = \ %D%/packages/patches/gd-fix-tests-on-i686.patch \ %D%/packages/patches/gd-freetype-test-failure.patch \ %D%/packages/patches/gdm-CVE-2018-14424.patch \ - %D%/packages/patches/gemma-intel-compat.patch \ %D%/packages/patches/geoclue-config.patch \ %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \ %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3cd0e03587..5337b7bf02 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2829,7 +2829,7 @@ comment or quality sections.") (define-public gemma (package (name "gemma") - (version "0.96") + (version "0.98") (source (origin (method git-fetch) (uri (git-reference @@ -2838,11 +2838,13 @@ comment or quality sections.") (file-name (git-file-name name version)) (sha256 (base32 - "0sa4mllp7890v5pss0mm02ik8yixl7az3vprcw3kp7qmr9gwrdai")) - (patches (search-patches "gemma-intel-compat.patch")))) + "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg")))) (inputs - `(("gsl" ,gsl) + `(("eigen" ,eigen) + ("gfortran" ,gfortran "lib") + ("gsl" ,gsl) ("lapack" ,lapack) + ("openblas" ,openblas) ("zlib" ,zlib))) (build-system gnu-build-system) (arguments @@ -2857,6 +2859,15 @@ comment or quality sections.") #:phases (modify-phases %standard-phases (delete 'configure) + (add-after 'unpack 'find-eigen + (lambda* (#:key inputs #:allow-other-keys) + ;; Ensure that Eigen headers can be found + (setenv "CPLUS_INCLUDE_PATH" + (string-append (getenv "CPLUS_INCLUDE_PATH") + ":" + (assoc-ref inputs "eigen") + "/include/eigen3")) + #t)) (add-before 'build 'bin-mkdir (lambda _ (mkdir-p "bin") diff --git a/gnu/packages/patches/gemma-intel-compat.patch b/gnu/packages/patches/gemma-intel-compat.patch deleted file mode 100644 index f12ec56d9b..0000000000 --- a/gnu/packages/patches/gemma-intel-compat.patch +++ /dev/null @@ -1,44 +0,0 @@ -From da1ed24209121f7b0f03f360b1029d7125a38e70 Mon Sep 17 00:00:00 2001 -From: Efraim Flashner <efraim@flashner.co.il> -Date: Tue, 4 Jul 2017 12:44:53 +0300 -Subject: [PATCH] Add NO_INTEL_COMPAT flag to Makefile. - -see also: https://github.com/xiangzhou/GEMMA/pull/47 - ---- - Makefile | 12 ++++++++---- - 1 file changed, 8 insertions(+), 4 deletions(-) - -diff --git a/Makefile b/Makefile -index 5bb8748..712b1ad 100644 ---- a/Makefile -+++ b/Makefile -@@ -11,6 +11,7 @@ - SYS = LNX - # Leave blank after "=" to disable; put "= 1" to enable - WITH_LAPACK = 1 -+NO_INTEL_COMPAT = - FORCE_32BIT = - FORCE_DYNAMIC = - DIST_NAME = gemma-0.96 -@@ -64,10 +65,13 @@ endif - HDR += $(SRC_DIR)/lapack.h - endif - --ifdef FORCE_32BIT -- CPPFLAGS += -m32 --else -- CPPFLAGS += -m64 -+ifdef NO_INTEL_COMPAT -+ else -+ ifdef FORCE_32BIT -+ CPPFLAGS += -m32 -+ else -+ CPPFLAGS += -m64 -+ endif - endif - - ifdef FORCE_DYNAMIC --- -2.13.2 - |