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07/11: gnu: rsem: Update to 1.3.3.
From: |
guix-commits |
Subject: |
07/11: gnu: rsem: Update to 1.3.3. |
Date: |
Sat, 4 Dec 2021 10:02:35 -0500 (EST) |
rekado pushed a commit to branch core-updates-frozen
in repository guix.
commit a4e7475edcb58d11e2ebb545a63f4b32ad7bfbd9
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Sat Dec 4 15:27:39 2021 +0100
gnu: rsem: Update to 1.3.3.
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3.
[arguments]: Build with gnu++11 standard; patch sources for compatibility.
---
gnu/packages/bioinformatics.scm | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ee03d44..bf8aff8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6117,7 +6117,7 @@ phylogenies.")
(define-public rsem
(package
(name "rsem")
- (version "1.3.1")
+ (version "1.3.3")
(source
(origin
(method git-fetch)
@@ -6125,7 +6125,7 @@ phylogenies.")
(url "https://github.com/deweylab/RSEM")
(commit (string-append "v" version))))
(sha256
- (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
+ (base32 "1yl4i7z20n2p84j1lmk15aiak3yqc6fiw0q5a4pndw7pxfiq3rzp"))
(file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
@@ -6149,12 +6149,22 @@ phylogenies.")
#:phases
(modify-phases %standard-phases
;; No "configure" script.
- ;; Do not build bundled samtools library.
(replace 'configure
(lambda _
(substitute* "Makefile"
(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
- (("^\\$\\(SAMLIBS\\).*") ""))))
+ ;; Do not build bundled samtools library.
+ (("^\\$\\(SAMLIBS\\).*") "")
+ ;; Needed for Boost
+ (("gnu\\+\\+98") "gnu++11"))
+ ;; C++11 compatibility
+ (substitute* "buildReadIndex.cpp"
+ (("success = \\(getline")
+ "success = (bool)(getline"))
+ (substitute* '("PairedEndHit.h"
+ "SingleHit.h")
+ (("return \\(in>>sid>>pos")
+ "return (bool)(in>>sid>>pos"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
- branch core-updates-frozen updated (114eb98 -> cc491ea), guix-commits, 2021/12/04
- 08/11: gnu: plink: Remove trailing #T., guix-commits, 2021/12/04
- 09/11: gnu: plink: Remove reference to %build-inputs., guix-commits, 2021/12/04
- 03/11: gnu: prodigal: Remove reference to %outputs., guix-commits, 2021/12/04
- 01/11: gnu: prank: Remove trailing #T., guix-commits, 2021/12/04
- 07/11: gnu: rsem: Update to 1.3.3.,
guix-commits <=
- 06/11: gnu: rsem: Remove trailing #T., guix-commits, 2021/12/04
- 10/11: gnu: plink-ng: Replace reference to %outputs., guix-commits, 2021/12/04
- 02/11: gnu: prank: Bind INPUTS in 'install phase., guix-commits, 2021/12/04
- 04/11: gnu: rsem: Remove trailing #T from snippet., guix-commits, 2021/12/04
- 05/11: gnu: rsem: Remove references to %build-inputs., guix-commits, 2021/12/04
- 11/11: gnu: plink-ng: Enable tests., guix-commits, 2021/12/04