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01/01: gnu: hmmer: Update to 3.2.1.
From: |
Ben Woodcroft |
Subject: |
01/01: gnu: hmmer: Update to 3.2.1. |
Date: |
Fri, 21 Sep 2018 19:47:23 -0400 (EDT) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit 05fb1e0017030f1c0cbc7e9a1adeccca57ef1d9d
Author: Ben Woodcroft <address@hidden>
Date: Sat Sep 22 08:19:09 2018 +1000
gnu: hmmer: Update to 3.2.1.
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
gnu/local.mk | 1 -
gnu/packages/bioinformatics.scm | 19 +++++++------------
.../patches/hmmer-remove-cpu-specificity.patch | 22 ----------------------
3 files changed, 7 insertions(+), 35 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 4097ad5..daf96ea 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -805,7 +805,6 @@ dist_patch_DATA =
\
%D%/packages/patches/hdf-eos5-remove-gctp.patch \
%D%/packages/patches/hdf-eos5-fix-szip.patch \
%D%/packages/patches/hdf-eos5-fortrantests.patch \
- %D%/packages/patches/hmmer-remove-cpu-specificity.patch \
%D%/packages/patches/higan-remove-march-native-flag.patch \
%D%/packages/patches/hubbub-sort-entities.patch \
%D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9599e30..b619866 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2936,18 +2936,15 @@ indexing scheme is called a @dfn{Hierarchical Graph FM
index} (HGFM).")
(define-public hmmer
(package
(name "hmmer")
- (version "3.1b2")
+ (version "3.2.1")
(source
(origin
(method url-fetch)
(uri (string-append
- "http://eddylab.org/software/hmmer"
- (version-major version) "/"
- version "/hmmer-" version ".tar.gz"))
+ "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz"))
(sha256
(base32
- "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
- (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
+ "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(home-page "http://hmmer.org/")
@@ -2957,12 +2954,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM
index} (HGFM).")
sequences, and for making protein sequence alignments. It implements methods
using probabilistic models called profile hidden Markov models (profile
HMMs).")
- (license (list license:gpl3+
- ;; The bundled library 'easel' is distributed
- ;; under The Janelia Farm Software License.
- (license:non-copyleft
- "file://easel/LICENSE"
- "See easel/LICENSE in the distribution.")))))
+ ;; hmmer uses non-portable SSE intrinsics so building fails on other
+ ;; platforms.
+ (supported-systems '("x86_64-linux" "i686-linux"))
+ (license license:bsd-3)))
(define-public htseq
(package
diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
deleted file mode 100644
index ba98db4..0000000
--- a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-This patch removes compilation flags which make the build for the machine
-where compilation takes place, rendering the build not reproducible.
-
-diff --git a/configure b/configure
-index 8b6aaef..49a6afc 100755
---- a/configure
-+++ b/configure
-@@ -6125,14 +6125,6 @@ fi # guess arch
-
- if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then
- for arch in $ax_gcc_arch; do
-- if test "x$acx_maxopt_portable" = xyes; then # if we require portable code
-- flags="-mtune=$arch"
-- # -mcpu=$arch and m$arch generate nonportable code on every arch except
-- # x86. And some other arches (e.g. Alpha) don't accept -mtune. Grrr.
-- case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac
-- else
-- flags="-march=$arch -mcpu=$arch -m$arch"
-- fi
- for flag in $flags; do
- as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts
$flag" >&5