Source: jellyfish
Version: 2.3.1-2
Severity: important
Tags: patch pending sid trixie
User: debian-...@lists.debian.org
Usertags: time-t
NOTICE: these changes must not be uploaded to unstable yet!
Dear maintainer,
As part of the 64-bit time_t transition required to support 32-bit
architectures in 2038 and beyond
(https://wiki.debian.org/ReleaseGoals/64bit-time), we have identified
jellyfish as a source package shipping runtime libraries whose ABI
either is affected by the change in size of time_t, or could not be
analyzed via abi-compliance-checker (and therefore to be on the safe
side we assume is affected).
To ensure that inconsistent combinations of libraries with their
reverse-dependencies are never installed together, it is necessary to
have a library transition, which is most easily done by renaming the
runtime library package.
Since turning on 64-bit time_t is being handled centrally through a change
to the default dpkg-buildflags (https://bugs.debian.org/1037136), it is
important that libraries affected by this ABI change all be uploaded close
together in time. Therefore I have prepared a 0-day NMU for jellyfish
which will initially be uploaded to experimental if possible, then to
unstable after packages have cleared binary NEW.
Please find the patch for this NMU attached.
If you have any concerns about this patch, please reach out ASAP. Although
this package will be uploaded to experimental immediately, there will be a
period of several days before we begin uploads to unstable; so if information
becomes available that your package should not be included in the transition,
there is time for us to amend the planned uploads.
-- System Information:
Debian Release: trixie/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1,
'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.5.0-14-generic (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru jellyfish-2.3.1/debian/changelog jellyfish-2.3.1/debian/changelog
--- jellyfish-2.3.1/debian/changelog 2024-01-01 10:43:16.000000000 +0000
+++ jellyfish-2.3.1/debian/changelog 2024-02-17 18:32:32.000000000 +0000
@@ -1,3 +1,11 @@
+jellyfish (2.3.1-2.1) experimental; urgency=medium
+
+ * Non-maintainer upload.
+ * Rename libraries for 64-bit time_t transition.
+ * Bump d-shlibs build-dep for t64 support.
+
+ -- Steve Langasek <vor...@debian.org> Sat, 17 Feb 2024 18:32:32 +0000
+
jellyfish (2.3.1-2) unstable; urgency=medium
[ Zhang Na ]
diff -Nru jellyfish-2.3.1/debian/control jellyfish-2.3.1/debian/control
--- jellyfish-2.3.1/debian/control 2024-01-01 10:17:41.000000000 +0000
+++ jellyfish-2.3.1/debian/control 2024-02-17 18:32:32.000000000 +0000
@@ -7,7 +7,7 @@
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- d-shlibs,
+ d-shlibs (>= 0.106~),
autoconf-archive,
yaggo,
pkg-config,
@@ -32,7 +32,7 @@
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 loong64
Depends: ${shlibs:Depends},
${misc:Depends},
- libjellyfish-2.0-2 (= ${binary:Version})
+ libjellyfish-2.0-2t64 (= ${binary:Version})
Description: count k-mers in DNA sequences
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
@@ -48,7 +48,10 @@
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
-Package: libjellyfish-2.0-2
+Package: libjellyfish-2.0-2t64
+Provides: ${t64:Provides}
+Replaces: libjellyfish-2.0-2
+Conflicts: libjellyfish-2.0-2 (<< ${source:Version})
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 loong64
Multi-Arch: same
Section: libs
@@ -76,7 +79,7 @@
Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 loong64
Section: libdevel
Depends: ${misc:Depends},
- libjellyfish-2.0-2 (= ${binary:Version})
+ libjellyfish-2.0-2t64 (= ${binary:Version})
Description: count k-mers in DNA sequences (development files of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
diff -Nru jellyfish-2.3.1/debian/libjellyfish-2.0-2.lintian-overrides
jellyfish-2.3.1/debian/libjellyfish-2.0-2.lintian-overrides
--- jellyfish-2.3.1/debian/libjellyfish-2.0-2.lintian-overrides 2024-01-01
10:16:41.000000000 +0000
+++ jellyfish-2.3.1/debian/libjellyfish-2.0-2.lintian-overrides 1970-01-01
00:00:00.000000000 +0000
@@ -1,2 +0,0 @@
-# Upstream decided to use a dynamic library without really intending to make
this a development package
-libjellyfish-2.0-2: no-symbols-control-file usr/lib/*/libjellyfish-*.so.*
diff -Nru jellyfish-2.3.1/debian/libjellyfish-2.0-2t64.lintian-overrides
jellyfish-2.3.1/debian/libjellyfish-2.0-2t64.lintian-overrides
--- jellyfish-2.3.1/debian/libjellyfish-2.0-2t64.lintian-overrides
1970-01-01 00:00:00.000000000 +0000
+++ jellyfish-2.3.1/debian/libjellyfish-2.0-2t64.lintian-overrides
2024-02-17 18:32:32.000000000 +0000
@@ -0,0 +1,3 @@
+# Upstream decided to use a dynamic library without really intending to make
this a development package
+libjellyfish-2.0-2t64: no-symbols-control-file usr/lib/*/libjellyfish-*.so.*
+libjellyfish-2.0-2t64: package-name-doesnt-match-sonames libjellyfish-2.0-2
diff -Nru jellyfish-2.3.1/debian/rules jellyfish-2.3.1/debian/rules
--- jellyfish-2.3.1/debian/rules 2024-01-01 10:16:41.000000000 +0000
+++ jellyfish-2.3.1/debian/rules 2024-02-17 18:32:32.000000000 +0000
@@ -43,6 +43,7 @@
chrpath --delete
debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
dh_install
d-shlibmove --commit \
+ --t64 \
--multiarch \
--devunversioned \
--movedev
"debian/tmp/usr/include/$(DEB_SOURCE)*/$(DEB_SOURCE)/*.hpp"
usr/include/$(DEB_SOURCE) \
