Bug#1115192: trixie-pu: package r-bioc-beachmat/2.22.0+ds-3~deb13u1

[Charles Plessy <plessy@debian.org>]

Package: release.debian.org
Severity: normal
Tags: trixie
X-Debbugs-Cc: r-bioc-beachmat@packages.debian.org, debian-r@lists.debian.org, plessy@debian.org
Control: affects -1 + src:r-bioc-beachmat
User: release.debian.org@packages.debian.org
Usertags: pu

Hello,

I am sorry that we could not fix for #1111758 on time for Trixie.  As we
can not migrate 2.22.0+ds-3 from Testing for the next point release, how
about an upload with the following debdiff?

[ Checklist ]
  [x] *all* changes are documented in the d/changelog
  [x] I reviewed all changes and I approve them
  [x] attach debdiff against the package in (old)stable
  [x] the issue is verified as fixed in unstable

[ Changes ]

index 068fccb..16ee884 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+r-bioc-beachmat (2.22.0+ds-3~deb13u1) trixie; urgency=medium
+
+  * Team upload.
+
+  [ Michael R. Crusoe ]
+  * Patch up part of a test that depends on the "beachmat.hdf5" R
+    package, which is not yet in Debian. Closes: #1111758
+
+ -- Charles Plessy <plessy@debian.org>  Sun, 14 Sep 2025 16:38:29 +0900
+
 r-bioc-beachmat (2.22.0+ds-2) unstable; urgency=medium
 
   * Team upload.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..6183596
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+skip-missing-beachmat.hdf5
diff --git a/debian/patches/skip-missing-beachmat.hdf5 b/debian/patches/skip-missing-beachmat.hdf5
new file mode 100644
index 0000000..6dd66d2
--- /dev/null
+++ b/debian/patches/skip-missing-beachmat.hdf5
@@ -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

-- 
Charles Plessy                         Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team         http://www.debian.org/devel/debian-med
Tooting from work,               https://fediscience.org/@charles_plessy
Tooting from home,                 https://framapiaf.org/@charles_plessy