I've noticed that `guix refresh -u` will update extraneous packages if
they happen to have the same version and be in the same module.
For example, from commit d694230ab, you can reproduce the bug:
$ ./pre-inst-env guix environment guix -- ./pre-inst-env guix refresh -u
python-pytest
$ git diff
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3dd3862..ae14404 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -796,7 +796,7 @@ Python 3 support.")
(define-public python-pycrypto
(package
(name "python-pycrypto")
- (version "2.6.1")
+ (version "2.8.7")
(source
(origin
(method url-fetch)
@@ -1565,7 +1565,7 @@ code introspection, and logging.")
(define-public python-pytest
(package
(name "python-pytest")
- (version "2.6.1")
+ (version "2.8.7")
(source
(origin
(method url-fetch)
@@ -1574,7 +1574,7 @@ code introspection, and logging.")
version ".tar.gz"))
(sha256
(base32
- "0g2w4p0n42wvz8rq4k6gnzpkakgz3g8sfanxk8jrsra9675snkcr"))
+ "1bwb06g64x2gky8x5hcrfpg6r351xwvafimnhm5qxq7wajz8ck7w"))
(modules '((guix build utils)))
(snippet
;; One of the tests involves the /usr directory, so it fails.
