[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
01/04: gnu: metabat: Update to 2.11.3.
From: |
Ben Woodcroft |
Subject: |
01/04: gnu: metabat: Update to 2.11.3. |
Date: |
Wed, 30 Aug 2017 22:44:08 -0400 (EDT) |
benwoodcroft pushed a commit to branch master
in repository guix.
commit 690a904ad766dfecf78749d121af528a7a49fa77
Author: Ben Woodcroft <address@hidden>
Date: Thu Aug 31 09:31:54 2017 +0800
gnu: metabat: Update to 2.11.3.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch. Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
gnu/local.mk | 1 -
gnu/packages/bioinformatics.scm | 16 ++++++-------
gnu/packages/patches/metabat-fix-boost-issue.patch | 27 ----------------------
3 files changed, 8 insertions(+), 36 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 708b50e..1becca3 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -841,7 +841,6 @@ dist_patch_DATA =
\
%D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch \
%D%/packages/patches/metabat-remove-compilation-date.patch \
%D%/packages/patches/metabat-fix-compilation.patch \
- %D%/packages/patches/metabat-fix-boost-issue.patch \
%D%/packages/patches/mhash-keygen-test-segfault.patch \
%D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch \
%D%/packages/patches/mpc123-initialize-ao.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d0df0ee..e372953 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3475,19 +3475,19 @@ form of assemblies or reads.")
(define-public metabat
(package
(name "metabat")
- (version "2.11.2")
+ (version "2.11.3")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://bitbucket.org/berkeleylab/metabat.git")
+ (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0rws9r1ziv6way8cf49jg8bzj7x2131kfqkhj8byf0z5hnrq3bwv"))
+ "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
(patches (search-patches "metabat-remove-compilation-date.patch"
- "metabat-fix-compilation.patch"
- "metabat-fix-boost-issue.patch"))))
+ "metabat-fix-compilation.patch"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/patches/metabat-fix-boost-issue.patch
b/gnu/packages/patches/metabat-fix-boost-issue.patch
deleted file mode 100644
index 3382d84..0000000
--- a/gnu/packages/patches/metabat-fix-boost-issue.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-This patch fixes the issue described at
-https://bitbucket.org/berkeleylab/metabat/issues/28/compilation-fail-with-boost-164
-
-diff --git a/src/metabat.h b/src/metabat.h
-index 32ae94c..2292c04 100644
---- a/src/metabat.h
-+++ b/src/metabat.h
-@@ -35,6 +35,7 @@ KSEQ_INIT(gzFile, gzread)
-
- #include <boost/program_options.hpp>
- #include <boost/algorithm/string.hpp>
-+#include <boost/serialization/array_wrapper.hpp>
- #include <boost/numeric/ublas/matrix.hpp>
- #include <boost/math/distributions.hpp>
- #include <boost/serialization/serialization.hpp>
-diff --git a/src/metabat2.h b/src/metabat2.h
-index 60a9998..19fa815 100644
---- a/src/metabat2.h
-+++ b/src/metabat2.h
-@@ -41,6 +41,7 @@ KSEQ_INIT(gzFile, gzread)
-
- #include <boost/program_options.hpp>
- #include <boost/algorithm/string.hpp>
-+#include <boost/serialization/array_wrapper.hpp>
- #include <boost/numeric/ublas/matrix.hpp>
- #include <boost/numeric/ublas/matrix_sparse.hpp>
- #include <boost/numeric/ublas/matrix_proxy.hpp>
- branch master updated (2d2e97b -> c959e5a), Ben Woodcroft, 2017/08/30
- 03/04: gnu: ruby-2.3.4: Fix CVE-2017-{0899,0900,0901,0902}., Ben Woodcroft, 2017/08/30
- 04/04: gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}., Ben Woodcroft, 2017/08/30
- 01/04: gnu: metabat: Update to 2.11.3.,
Ben Woodcroft <=
- 02/04: gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}., Ben Woodcroft, 2017/08/30
- Prev by Date:
04/04: gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}.
- Next by Date:
02/04: gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}.
- Previous by thread:
04/04: gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}.
- Next by thread:
02/04: gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}.
- Index(es):