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Hi Release team,
thanks for Trixie, I enjoy it at home and at work, from where I send this email.
I am sorry that we could not fix for #1111758 on time for Trixie. I wonder what is the next step. Can you just migrate 2.22.0+ds-3 from Testing for the next point release, or do you need an upload? One more solution is just to ignore the issue, since the patch
is basically putting the dust under the carpet…
Here is the debdiff.
diff -Nru r-bioc-beachmat-2.22.0+ds/debian/changelog r-bioc-beachmat-2.22.0+ds/debian/changelog
--- r-bioc-beachmat-2.22.0+ds/debian/changelog 2025-01-13 05:38:05.000000000 +0900
+++ r-bioc-beachmat-2.22.0+ds/debian/changelog 2025-08-28 01:16:33.000000000 +0900
@@ -1,3 +1,11 @@
+r-bioc-beachmat (2.22.0+ds-3) unstable; urgency=medium
+
+ * Team upload.
+ * Patch up part of a test that depends on the "beachmat.hdf5" R
+ package, which is not yet in Debian. Closes: #1111758
+
+ -- Michael R. Crusoe <crusoe@debian.org> Wed, 27 Aug 2025 18:16:33 +0200
+
r-bioc-beachmat (2.22.0+ds-2) unstable; urgency=medium
* Team upload.
diff -Nru r-bioc-beachmat-2.22.0+ds/debian/patches/series r-bioc-beachmat-2.22.0+ds/debian/patches/series
--- r-bioc-beachmat-2.22.0+ds/debian/patches/series 1970-01-01 09:00:00.000000000 +0900
+++ r-bioc-beachmat-2.22.0+ds/debian/patches/series 2025-08-27 22:43:00.000000000 +0900
@@ -0,0 +1 @@
+skip-missing-beachmat.hdf5
diff -Nru r-bioc-beachmat-2.22.0+ds/debian/patches/skip-missing-beachmat.hdf5 r-bioc-beachmat-2.22.0+ds/debian/patches/skip-missing-beachmat.hdf5
--- r-bioc-beachmat-2.22.0+ds/debian/patches/skip-missing-beachmat.hdf5 1970-01-01 09:00:00.000000000 +0900
+++ r-bioc-beachmat-2.22.0+ds/debian/patches/skip-missing-beachmat.hdf5 2025-08-27 22:44:00.000000000 +0900
@@ -0,0 +1,15 @@
+Author: Michael R. Crusoe <crusoe@debian.org>
+Description: skip part of a test that depends on the unpackaged beachmat.hdf5
+Forwarded: not-needed
+--- r-bioc-beachmat.orig/tests/testthat/test-initializeCpp-other.R
++++ r-bioc-beachmat/tests/testthat/test-initializeCpp-other.R
+@@ -150,9 +150,6 @@
+
+ ptr <- initializeCpp(mat2)
+ am_i_ok(mat, ptr)
+-
+- # Package is automatically loaded to expose the specialized methods.
+- expect_true(isNamespaceLoaded("beachmat.hdf5"))
+ })
+
+ test_that("initialization works correctly with an unknown DelayedArray", {
Have a nice day,
Charles
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