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01/04: gnu: khmer: Fix build with Python 3.8.
From: |
guix-commits |
Subject: |
01/04: gnu: khmer: Fix build with Python 3.8. |
Date: |
Thu, 2 Dec 2021 12:50:12 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 31d372cd8a727008a2205e428d50d0e160659066
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Dec 2 18:24:31 2021 +0100
gnu: khmer: Fix build with Python 3.8.
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T.
[arguments]: Remove trailing #T from build phases; add build phase
'python-3.8-compatibility.
---
gnu/packages/bioinformatics.scm | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fe9e74b..443c405 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5040,23 +5040,26 @@ command, or queried for specific k-mers with
@code{jellyfish query}.")
(("# libraries = z,bz2")
"libraries = z,bz2")
(("include:third-party/zlib:third-party/bzip2")
- "include:"))
- #t))))
+ "include:"))))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-cc
- (lambda _ (setenv "CC" "gcc") #t))
-
+ (lambda _ (setenv "CC" "gcc")))
+ (add-after 'unpack 'python-3.8-compatibility
+ (lambda _
+ ;; Python 3.8 removed time.clock().
+ (substitute* "sandbox/sweep-reads.py"
+ (("time\\.clock")
+ "time.process_time"))))
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure .gz files are writable so that the
;; 'reset-gzip-timestamps' phase can do its work.
(let ((out (assoc-ref outputs "out")))
(for-each make-file-writable
- (find-files out "\\.gz$"))
- #t))))))
+ (find-files out "\\.gz$"))))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)