Bug#1062232: libbpp-phyl-omics: NMU diff for 64-bit time_t transition
Dear maintainer, Please find attached a final version of this patch for the time_t transition. This patch is being uploaded to unstable. Note that this adds a versioned build-dependency on dpkg-dev, to guard against accidental backports with a wrong ABI. Thanks! -- System Information: Debian Release: trixie/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 6.5.0-21-generic (SMP w/4 CPU threads; PREEMPT) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) diff -Nru libbpp-phyl-omics-2.4.1/debian/changelog libbpp-phyl-omics-2.4.1/debian/changelog --- libbpp-phyl-omics-2.4.1/debian/changelog2023-08-13 11:11:55.0 + +++ libbpp-phyl-omics-2.4.1/debian/changelog2024-02-29 09:28:21.0 + @@ -1,3 +1,10 @@ +libbpp-phyl-omics (2.4.1-5.1) unstable; urgency=medium + + * Non-maintainer upload. + * Rename libraries for 64-bit time_t transition. Closes: #1062232 + + -- Lukas Märdian Thu, 29 Feb 2024 09:28:21 + + libbpp-phyl-omics (2.4.1-5) unstable; urgency=medium * Team upload. diff -Nru libbpp-phyl-omics-2.4.1/debian/control libbpp-phyl-omics-2.4.1/debian/control --- libbpp-phyl-omics-2.4.1/debian/control 2023-08-13 11:11:41.0 + +++ libbpp-phyl-omics-2.4.1/debian/control 2024-02-29 09:28:21.0 + @@ -4,9 +4,9 @@ Andreas Tille Section: science Priority: optional -Build-Depends: debhelper-compat (= 13), +Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, - d-shlibs, + d-shlibs (>= 0.106~), libbpp-phyl-dev, libbpp-seq-omics-dev Standards-Version: 4.6.2 @@ -18,7 +18,7 @@ Package: libbpp-phyl-omics-dev Architecture: any Section: libdevel -Depends: libbpp-phyl-omics3 (= ${binary:Version}), +Depends: libbpp-phyl-omics3t64 (= ${binary:Version}), ${misc:Depends}, ${devlibs:Depends} Multi-Arch: same @@ -32,7 +32,10 @@ This package contains the static library and the header files of the Bio++ classes dedicated to genomic phylogeny. -Package: libbpp-phyl-omics3 +Package: libbpp-phyl-omics3t64 +Provides: ${t64:Provides} +Replaces: libbpp-phyl-omics3 +Conflicts: libbpp-phyl-omics3 (<< ${source:Version}) Architecture: any Multi-Arch: same Section: libs diff -Nru libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols --- libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols 2023-08-13 11:11:55.0 + +++ libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols 1970-01-01 00:00:00.0 + @@ -1,543 +0,0 @@ -libbpp-phyl-omics.so.3 libbpp-phyl-omics3 #MINVER# -* Build-Depends-Package: libbpp-phyl-omics-dev - _ZN3bpp10BppIntegerD0Ev@Base 2.4.1 - _ZN3bpp10BppIntegerD1Ev@Base 2.4.1 - _ZN3bpp11MafSequence33splitNameIntoSpeciesAndChromosomeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_S9_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11getRootNodeEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11newOutGroupEPS1_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11newOutGroupEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11setNodeNameEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11setRootNodeEPS1_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE12resetNodesIdEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE13getInnerNodesEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE14deleteNodeNameEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE14getTotalLengthEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE15getNodePropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE15setNodePropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8ClonableE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE16getBranchLengthsEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE16setBranchLengthsEd@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE17getBranchPropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE17setBranchPropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8ClonableE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE18removeNodePropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE19setDistanceToFatherEid@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE20removeBranchPropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE20setVoidBranchLengthsEd@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE22deleteDistanceToFatherEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE6rootAtEPS1_@Base 2.4.1 -
Bug#1062232: libbpp-phyl-omics: NMU diff for 64-bit time_t transition
Ahem. Really attached now. On Fri, Feb 23, 2024 at 11:08:42PM -0800, Steve Langasek wrote: > Hello, > > The package that was previously uploaded to experimental was unfortunately > broken because we did not notice that the package uses d-shlibs and > therefore needs additional changes. (Most packages using d-shlibs simply > failed to build without additional changes; libbpp-phyl-omics built but > produced an empty package.) > > Please find a fixed patch attached. > > -- > Steve Langasek Give me a lever long enough and a Free OS > Debian Developer to set it on, and I can move the world. > Ubuntu Developer https://www.debian.org/ > slanga...@ubuntu.com vor...@debian.org -- Steve Langasek Give me a lever long enough and a Free OS Debian Developer to set it on, and I can move the world. Ubuntu Developer https://www.debian.org/ slanga...@ubuntu.com vor...@debian.org diff -Nru libbpp-phyl-omics-2.4.1/debian/changelog libbpp-phyl-omics-2.4.1/debian/changelog --- libbpp-phyl-omics-2.4.1/debian/changelog2023-08-13 11:11:55.0 + +++ libbpp-phyl-omics-2.4.1/debian/changelog2024-02-24 07:11:14.0 + @@ -1,3 +1,16 @@ +libbpp-phyl-omics (2.4.1-5.1~exp2) experimental; urgency=medium + + * Bump d-shlibs build-dependency for --t64 support. + + -- Steve Langasek Sat, 24 Feb 2024 07:11:14 + + +libbpp-phyl-omics (2.4.1-5.1~exp1) experimental; urgency=medium + + * Non-maintainer upload. + * Rename libraries for 64-bit time_t transition. + + -- Steve Langasek Wed, 31 Jan 2024 19:55:07 + + libbpp-phyl-omics (2.4.1-5) unstable; urgency=medium * Team upload. diff -Nru libbpp-phyl-omics-2.4.1/debian/control libbpp-phyl-omics-2.4.1/debian/control --- libbpp-phyl-omics-2.4.1/debian/control 2023-08-13 11:11:41.0 + +++ libbpp-phyl-omics-2.4.1/debian/control 2024-02-24 07:11:11.0 + @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper-compat (= 13), cmake, - d-shlibs, + d-shlibs (>= 0.106~), libbpp-phyl-dev, libbpp-seq-omics-dev Standards-Version: 4.6.2 @@ -18,7 +18,7 @@ Package: libbpp-phyl-omics-dev Architecture: any Section: libdevel -Depends: libbpp-phyl-omics3 (= ${binary:Version}), +Depends: libbpp-phyl-omics3t64 (= ${binary:Version}), ${misc:Depends}, ${devlibs:Depends} Multi-Arch: same @@ -32,7 +32,10 @@ This package contains the static library and the header files of the Bio++ classes dedicated to genomic phylogeny. -Package: libbpp-phyl-omics3 +Package: libbpp-phyl-omics3t64 +Provides: ${t64:Provides} +Replaces: libbpp-phyl-omics3 +Conflicts: libbpp-phyl-omics3 (<< ${source:Version}) Architecture: any Multi-Arch: same Section: libs diff -Nru libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols --- libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols 2023-08-13 11:11:55.0 + +++ libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols 1970-01-01 00:00:00.0 + @@ -1,543 +0,0 @@ -libbpp-phyl-omics.so.3 libbpp-phyl-omics3 #MINVER# -* Build-Depends-Package: libbpp-phyl-omics-dev - _ZN3bpp10BppIntegerD0Ev@Base 2.4.1 - _ZN3bpp10BppIntegerD1Ev@Base 2.4.1 - _ZN3bpp11MafSequence33splitNameIntoSpeciesAndChromosomeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_S9_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11getRootNodeEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11newOutGroupEPS1_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11newOutGroupEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11setNodeNameEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11setRootNodeEPS1_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE12resetNodesIdEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE13getInnerNodesEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE14deleteNodeNameEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE14getTotalLengthEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE15getNodePropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE15setNodePropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8ClonableE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE16getBranchLengthsEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE16setBranchLengthsEd@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE17getBranchPropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE17setBranchPropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8ClonableE@Base 2.4.1 -
Bug#1062232: libbpp-phyl-omics: NMU diff for 64-bit time_t transition
Hello, The package that was previously uploaded to experimental was unfortunately broken because we did not notice that the package uses d-shlibs and therefore needs additional changes. (Most packages using d-shlibs simply failed to build without additional changes; libbpp-phyl-omics built but produced an empty package.) Please find a fixed patch attached. -- Steve Langasek Give me a lever long enough and a Free OS Debian Developer to set it on, and I can move the world. Ubuntu Developer https://www.debian.org/ slanga...@ubuntu.com vor...@debian.org signature.asc Description: PGP signature
Bug#1062232: libbpp-phyl-omics: NMU diff for 64-bit time_t transition
Source: libbpp-phyl-omics Version: 2.4.1-5 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 libbpp-phyl-omics 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 libbpp-phyl-omics 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'), (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 libbpp-phyl-omics-2.4.1/debian/changelog libbpp-phyl-omics-2.4.1/debian/changelog --- libbpp-phyl-omics-2.4.1/debian/changelog2023-08-13 11:11:55.0 + +++ libbpp-phyl-omics-2.4.1/debian/changelog2024-01-31 19:54:16.0 + @@ -1,3 +1,10 @@ +libbpp-phyl-omics (2.4.1-5.1) experimental; urgency=medium + + * Non-maintainer upload. + * Rename libraries for 64-bit time_t transition. + + -- Steve Langasek Wed, 31 Jan 2024 19:54:16 + + libbpp-phyl-omics (2.4.1-5) unstable; urgency=medium * Team upload. diff -Nru libbpp-phyl-omics-2.4.1/debian/control libbpp-phyl-omics-2.4.1/debian/control --- libbpp-phyl-omics-2.4.1/debian/control 2023-08-13 11:11:41.0 + +++ libbpp-phyl-omics-2.4.1/debian/control 2024-01-31 19:54:16.0 + @@ -18,7 +18,7 @@ Package: libbpp-phyl-omics-dev Architecture: any Section: libdevel -Depends: libbpp-phyl-omics3 (= ${binary:Version}), +Depends: libbpp-phyl-omics3t64 (= ${binary:Version}), ${misc:Depends}, ${devlibs:Depends} Multi-Arch: same @@ -32,7 +32,10 @@ This package contains the static library and the header files of the Bio++ classes dedicated to genomic phylogeny. -Package: libbpp-phyl-omics3 +Package: libbpp-phyl-omics3t64 +Provides: ${t64:Provides} +Replaces: libbpp-phyl-omics3 +Breaks: libbpp-phyl-omics3 (<< ${source:Version}) Architecture: any Multi-Arch: same Section: libs diff -Nru libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols --- libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols 2023-08-13 11:11:55.0 + +++ libbpp-phyl-omics-2.4.1/debian/libbpp-phyl-omics3.symbols 1970-01-01 00:00:00.0 + @@ -1,543 +0,0 @@ -libbpp-phyl-omics.so.3 libbpp-phyl-omics3 #MINVER# -* Build-Depends-Package: libbpp-phyl-omics-dev - _ZN3bpp10BppIntegerD0Ev@Base 2.4.1 - _ZN3bpp10BppIntegerD1Ev@Base 2.4.1 - _ZN3bpp11MafSequence33splitNameIntoSpeciesAndChromosomeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_S9_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11getRootNodeEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11newOutGroupEPS1_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11newOutGroupEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11setNodeNameEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE11setRootNodeEPS1_@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE12resetNodesIdEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE13getInnerNodesEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE14deleteNodeNameEi@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE14getTotalLengthEv@Base 2.4.1 - _ZN3bpp12TreeTemplateINS_4NodeEE15getNodePropertyEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1 -