On 25/07/15 19:02, Andreas Enge wrote:
Hello,
unfortunately, it seems to fail in 32 bit (i686 and mips):
http://hydra.gnu.org/eval/105733#tabs-new
with lots of messages of the kind
In file included from ../../utils//general/BedtoolsTypes.h:20:0,
from ContextBase.h:21,
from ContextIntersect.h:11,
from ContextIntersect.cpp:8:
../../utils//general/QuickString.h:41:15: error: ‘QuickString&
QuickString::operator=(size_t)’ cannot be overloaded
QuickString &operator = (size_t);
Helpfully this is fixed in upstream though it hasn't yet made it to a
release. Attached is a new patch that hopefully will help.
ben
>From 47519e0145298c00e4bfa672d92b9f700d12f5ad Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
Date: Sat, 25 Jul 2015 22:54:19 +1000
Subject: [PATCH] gnu: bedtools: Update to 2.24.0.
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
---
gnu/packages/bioinformatics.scm | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 78cd3ce..738d559 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -148,7 +148,7 @@ computational cluster.")
(define-public bedtools
(package
(name "bedtools")
- (version "2.22.0")
+ (version "2.24.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/archive/v";
@@ -156,7 +156,10 @@ computational cluster.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+ "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
+ ;; Fixed in upstream, see
+ ;; https://github.com/arq5x/bedtools2/issues/271
+ (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
(build-system gnu-build-system)
(native-inputs `(("python" ,python-2)))
(inputs `(("samtools" ,samtools)
--
2.4.3
