Source: htslib
Version: 1.18+ds-1
Severity: serious
Tags: patch pending
Justification: library ABI skew on upgrade
User: debian-...@lists.debian.org
Usertags: time-t
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
htslib 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 htslib
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'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.5.0-15-generic (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: 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: unable to detect
diff -Nru htslib-1.18+ds/debian/changelog htslib-1.18+ds/debian/changelog
--- htslib-1.18+ds/debian/changelog 2023-11-07 18:46:30.0 +
+++ htslib-1.18+ds/debian/changelog 2024-02-01 05:58:50.0 +
@@ -1,3 +1,10 @@
+htslib (1.18+ds-1.1) experimental; urgency=medium
+
+ * Non-maintainer upload.
+ * Rename libraries for 64-bit time_t transition.
+
+ -- Graham Inggs Thu, 01 Feb 2024 05:58:50 +
+
htslib (1.18+ds-1) unstable; urgency=medium
* Migrate htslib 1.18 from experimental to unstable.
diff -Nru htslib-1.18+ds/debian/control htslib-1.18+ds/debian/control
--- htslib-1.18+ds/debian/control 2023-08-23 16:38:26.0 +
+++ htslib-1.18+ds/debian/control 2024-02-01 05:58:50.0 +
@@ -21,18 +21,19 @@
Homepage: https://github.com/samtools/htslib
Rules-Requires-Root: no
-Package: libhts3
+Package: libhts3t64
+Provides: ${t64:Provides}
Architecture: any
Multi-Arch: same
Section: libs
Depends: ${misc:Depends},
${shlibs:Depends}
Pre-Depends: ${misc:Pre-Depends}
-Breaks: libtabixpp (<< 1.0.0-5~),
+Breaks: libhts3 (<< ${source:Version}), libtabixpp (<< 1.0.0-5~),
libhts-dev (<< 1.13~),
samtools (<< 1.17~),
ivar (<< 1.3.1~)
-Replaces: libhts-dev (<< 1.13~)
+Replaces: libhts3, libhts-dev (<< 1.13~)
Description: C library for high-throughput sequencing data formats
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call
@@ -48,7 +49,7 @@
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libhts3 (= ${binary:Version}),
+Depends: libhts3t64 (= ${binary:Version}),
libcurl4-gnutls-dev,
libdeflate-dev,
liblzma-dev,
diff -Nru htslib-1.18+ds/debian/libhts3.install
htslib-1.18+ds/debian/libhts3.install
--- htslib-1.18+ds/debian/libhts3.install 2022-10-19 14:55:31.0
+
+++ htslib-1.18+ds/debian/libhts3.install 1970-01-01 00:00:00.0
+
@@ -1,3 +0,0 @@
-usr/lib/${DEB_HOST_MULTIARCH}/libhts.so.* usr/lib/${DEB_HOST_MULTIARCH}
-usr/lib/${DEB_HOST_MULTIARCH}/htslib usr/lib/${DEB_HOST_MULTIARCH}
-usr/share/man/man5/* usr/share/man/man5
diff -Nru htslib-1.18+ds/debian/libhts3.manpages
htslib-1.18+ds/debian/libhts3.manpages
--- htslib-1.18+ds/debian/libhts3.manpages 2022-07-03 07:14:15.0
+
+++ htslib-1.18+ds/debian/libhts3.manpages 1970-01-01 00:00:00.0
+
@@ -1 +0,0 @@
-htslib-s3-plugin.7
diff -Nru htslib-1.18+ds/debian/libhts3.symbols
htslib-1.18+ds/debian/libhts3.symbols
--- htslib-1.18+ds/debian/libhts3.symbols 2023-08-23 16:36:56.0
+
+++ htslib-1.18+ds/debian/libhts3.symbols 1970-01-01 00:00:00.0
+
@@ -1,930 +0,0 @@
-libhts.so.3 libhts3 #MINVER#
-* Build-Depends-Package: libhts-dev
- HTSLIB_1.0@HTSLIB_1.0 1.17
- HTSLIB_1.10@HTSLIB_1.10 1.17
-
