From 05fb1e0017030f1c0cbc7e9a1adeccca57ef1d9d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 22 Sep 2018 08:19:09 +1000
Subject: 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(-)
 delete mode 100644 gnu/packages/patches/hmmer-remove-cpu-specificity.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4097ad5fcd..daf96ea4b6 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 9599e3096f..b619866ba3 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 ba98db4d0e..0000000000
--- 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
-- 
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