[med-svn] [Git][med-team/pbcopper][master] 5 commits: d/patches/gcc-13: fix build failures (Closes: #1041127)
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Aug 9 14:52:58 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / pbcopper
Commits:
d7fe2ed1 by Michael R. Crusoe at 2023-08-09T15:42:55+02:00
d/patches/gcc-13: fix build failures (Closes: #1041127)
- - - - -
9e022016 by Michael R. Crusoe at 2023-08-09T15:43:32+02:00
d/control: use newer boost version for c++20 compat
- - - - -
ccf1808c by Michael R. Crusoe at 2023-08-09T15:43:34+02:00
d/patches: mark Debian specific patches as not needing forwarding.
- - - - -
ef057d48 by Michael R. Crusoe at 2023-08-09T15:50:00+02:00
d/control: rename library package to match soversion (2.2.0)
- - - - -
a620bcd6 by Michael R. Crusoe at 2023-08-09T15:51:08+02:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc-13
- debian/patches/series
- debian/patches/skip_test_Parallel_FireAndForget.patch
- debian/patches/static+shared_lib.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,18 @@
-pbcopper (2.2.0+dfsg-1) UNRELEASED; urgency=medium
+pbcopper (2.2.0+dfsg-1) unstable; urgency=medium
+ * Team upload.
+
+ [ Andreas Tille ]
* New upstream version
* Standards-Version: 4.6.2 (routine-update)
- TODO: Build error
- -- Andreas Tille <tille at debian.org> Thu, 19 Jan 2023 14:00:14 +0100
+ [ Michael R. Crusoe ]
+ * d/patches/gcc-13: fix build failures (Closes: #1041127)
+ * d/control: use newer boost version for c++20 compat
+ * d/patches: mark Debian specific patches as not needing forwarding.
+ * d/control: rename library package to match soversion (2.2.0
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 09 Aug 2023 15:48:38 +0200
pbcopper (2.0.0+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),
meson,
cmake,
pkg-config,
- libboost-dev,
+ libboost1.81-dev,
googletest,
libgtest-dev,
libsimde-dev
@@ -18,14 +18,12 @@ Vcs-Git: https://salsa.debian.org/med-team/pbcopper.git
Homepage: https://github.com/PacificBiosciences/pbcopper
Rules-Requires-Root: no
-Package: libpbcopper2.0.0
+Package: libpbcopper2.2.0
Architecture: any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha
Multi-Arch: same
Section: libs
Depends: ${misc:Depends},
${shlibs:Depends}
-Breaks: libpbcopper1.3.0 (>= 1.6)
-Replaces: libpbcopper1.3.0 (>= 1.6)
Description: data structures, algorithms, and utilities for C++ applications
pbcopper provides general tools for C++ applications. It is developed
for use by applications of the Pacific Biosciences SMRT Analysis
@@ -37,7 +35,7 @@ Package: libpbcopper-dev
Architecture: any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha
Multi-Arch: same
Section: libdevel
-Depends: libpbcopper2.0.0 (= ${binary:Version}),
+Depends: libpbcopper2.2.0 (= ${binary:Version}),
${misc:Depends},
${shlibs:Depends}
Description: data structures, algorithms, and utilities for C++ applications -- header files
=====================================
debian/patches/gcc-13
=====================================
@@ -0,0 +1,41 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: gcc-13 fixes
+Forwarded: https://github.com/PacificBiosciences/pbcopper/pull/13
+--- pbcopper.orig/include/pbcopper/align/LocalAlignment.h
++++ pbcopper/include/pbcopper/align/LocalAlignment.h
+@@ -9,6 +9,7 @@
+
+ #include <string>
+ #include <vector>
++#include <cstdint>
+
+ namespace PacBio {
+ namespace Align {
+--- pbcopper.orig/include/pbcopper/cli2/OptionValue.h
++++ pbcopper/include/pbcopper/cli2/OptionValue.h
+@@ -6,6 +6,7 @@
+ #include <iosfwd>
+ #include <string>
+ #include <variant>
++#include <cstdint>
+
+ // clang-format off
+
+--- pbcopper.orig/include/pbcopper/utility/Random.h
++++ pbcopper/include/pbcopper/utility/Random.h
+@@ -4,6 +4,7 @@
+
+ #include <algorithm>
+ #include <iterator>
++#include <cstdint>
+
+ namespace PacBio {
+ namespace Utility {
+--- pbcopper.orig/src/utility/Random.cpp
++++ pbcopper/src/utility/Random.cpp
+@@ -1,4 +1,5 @@
+ #include <pbcopper/utility/Random.h>
++#include <cstdint>
+
+ namespace PacBio {
+ namespace Utility {
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
simde.patch
static+shared_lib.patch
skip_test_Parallel_FireAndForget.patch
+gcc-13
=====================================
debian/patches/skip_test_Parallel_FireAndForget.patch
=====================================
@@ -1,5 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 24 Feb 2022 17:45:52 +0100
+Forwarded: not-needed
Description: Simply skip test producing
[ FAILED ] 2 tests, listed below:
[ FAILED ] Parallel_FireAndForget.exceptionProduceWith
=====================================
debian/patches/static+shared_lib.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 26 May 2020 12:54:54 +0200
Description: Enable building shared and static lib
+Forwarded: not-needed
--- a/meson.build
+++ b/meson.build
=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
#export DH_VERBOSE = 1
# needed to build consensuscore2
-export DEB_CXXFLAGS_MAINT_APPEND=-fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3
+export DEB_CXXFLAGS_MAINT_APPEND=-fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++20
# The package FTBFS if we don't call the build directory "build"
%:
View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/compare/586655ffa1aa2db4578957e91bc830320adf8913...a620bcd68b9cc87359273bc2e9356be89c72adc5
--
View it on GitLab: https://salsa.debian.org/med-team/pbcopper/-/compare/586655ffa1aa2db4578957e91bc830320adf8913...a620bcd68b9cc87359273bc2e9356be89c72adc5
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