Your message dated Tue, 21 Feb 2023 15:19:32 +0000
with message-id <[email protected]>
and subject line Bug#1030295: fixed in tomopy 1.10.4+ds1-8
has caused the Debian Bug report #1030295,
regarding tomopy: please fix build on atomic architectures
to be marked as done.
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If this is not the case it is now your responsibility to reopen the
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--
1030295: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1030295
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: tomopy
Version: 1.10.4+ds1-7
tags: patch
Hello, looks like tomopy is FTBFS on architectures where libatomic is needed
I created a patch from CheckAtomic.cmake (cmake-extras-modules package), and I
plan to submit upstream
diff -Nru tomopy-1.10.4+ds1/debian/patches/fix-build.patch
tomopy-1.10.4+ds1/debian/patches/fix-build.patch
--- tomopy-1.10.4+ds1/debian/patches/fix-build.patch 1970-01-01
00:00:00.000000000 +0000
+++ tomopy-1.10.4+ds1/debian/patches/fix-build.patch 2023-02-01
10:07:39.000000000 +0000
@@ -0,0 +1,146 @@
+Description: Link with latomic where needed
+Author: Gianfranco Costamagna <[email protected]>
+Bug-Debian: https://bugs.debian.org/
+Forwarded:
+Last-Update: 2023-02-01
+
+Index: tomopy-1.10.4+ds1/CMakeLists.txt
+===================================================================
+--- tomopy-1.10.4+ds1.orig/CMakeLists.txt
++++ tomopy-1.10.4+ds1/CMakeLists.txt
+@@ -40,6 +40,7 @@
+ include(BuildSettings)
+ include(Packages)
+ include(ClangFormat)
++include(CheckAtomic)
+
+
################################################################################
+ # tomopy source
+Index: tomopy-1.10.4+ds1/PTL/cmake/Modules/Packages.cmake
+===================================================================
+--- tomopy-1.10.4+ds1.orig/PTL/cmake/Modules/Packages.cmake
++++ tomopy-1.10.4+ds1/PTL/cmake/Modules/Packages.cmake
+@@ -165,6 +165,9 @@
+
+ endif()
+
++if(NOT HAVE_CXX_ATOMICS_WITHOUT_LIB OR NOT HAVE_CXX_ATOMICS64_WITHOUT_LIB)
++ list(APPEND EXTERNAL_LIBRARIES "atomic")
++endif()
+
+
################################################################################
+ #
+Index: tomopy-1.10.4+ds1/cmake/Modules/CheckAtomic.cmake
+===================================================================
+--- /dev/null
++++ tomopy-1.10.4+ds1/cmake/Modules/CheckAtomic.cmake
+@@ -0,0 +1,95 @@
++# SPDX-FileCopyrightText: 2003-2018 University of Illinois at
Urbana-Champaign.
++#
++# SPDX-License-Identifier: BSD-3-Clause
++
++#[=======================================================================[.rst:
++CheckAtomic
++-----------
++
++Check if the compiler supports std:atomic out of the box or if libatomic is
++needed for atomic support. If it is needed libatomicis added to
++``CMAKE_REQUIRED_LIBRARIES``. So after running CheckAtomic you can use
++std:atomic.
++
++Since 5.75.0.
++#]=======================================================================]
++
++include(CheckCXXSourceCompiles)
++include(CheckLibraryExists)
++
++# Sometimes linking against libatomic is required for atomic ops, if
++# the platform doesn't support lock-free atomics.
++
++function(check_working_cxx_atomics varname)
++ set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
++ set(CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS} -std=c++11")
++ check_cxx_source_compiles("
++ #include <atomic>
++ std::atomic<int> x;
++ std::atomic<short> y;
++ std::atomic<char> z;
++ int main() {
++ ++z;
++ ++y;
++ return ++x;
++ }
++ " ${varname})
++ set(CMAKE_REQUIRED_FLAGS ${OLD_CMAKE_REQUIRED_FLAGS})
++endfunction()
++
++function(check_working_cxx_atomics64 varname)
++ set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
++ set(CMAKE_REQUIRED_FLAGS "-std=c++11 ${CMAKE_REQUIRED_FLAGS}")
++ check_cxx_source_compiles("
++ #include <atomic>
++ #include <cstdint>
++ std::atomic<uint64_t> x (0);
++ int main() {
++ uint64_t i = x.load(std::memory_order_relaxed);
++ return 0;
++ }
++ " ${varname})
++ set(CMAKE_REQUIRED_FLAGS ${OLD_CMAKE_REQUIRED_FLAGS})
++endfunction()
++
++# Check for (non-64-bit) atomic operations.
++if(MSVC)
++ set(HAVE_CXX_ATOMICS_WITHOUT_LIB True)
++elseif(LLVM_COMPILER_IS_GCC_COMPATIBLE)
++ # First check if atomics work without the library.
++ check_working_cxx_atomics(HAVE_CXX_ATOMICS_WITHOUT_LIB)
++ # If not, check if the library exists, and atomics work with it.
++ if(NOT HAVE_CXX_ATOMICS_WITHOUT_LIB)
++ check_library_exists(atomic __atomic_fetch_add_4 "" HAVE_LIBATOMIC)
++ if(HAVE_LIBATOMIC)
++ list(APPEND CMAKE_REQUIRED_LIBRARIES "atomic")
++ check_working_cxx_atomics(HAVE_CXX_ATOMICS_WITH_LIB)
++ if (NOT HAVE_CXX_ATOMICS_WITH_LIB)
++ message(FATAL_ERROR "Host compiler must support std::atomic!")
++ endif()
++ else()
++ message(FATAL_ERROR "Host compiler appears to require libatomic, but cannot
find it.")
++ endif()
++ endif()
++endif()
++
++# Check for 64 bit atomic operations.
++if(MSVC)
++ set(HAVE_CXX_ATOMICS64_WITHOUT_LIB True)
++elseif(LLVM_COMPILER_IS_GCC_COMPATIBLE)
++ # First check if atomics work without the library.
++ check_working_cxx_atomics64(HAVE_CXX_ATOMICS64_WITHOUT_LIB)
++ # If not, check if the library exists, and atomics work with it.
++ if(NOT HAVE_CXX_ATOMICS64_WITHOUT_LIB)
++ check_library_exists(atomic __atomic_load_8 "" HAVE_CXX_LIBATOMICS64)
++ if(HAVE_CXX_LIBATOMICS64)
++ list(APPEND CMAKE_REQUIRED_LIBRARIES "atomic")
++ check_working_cxx_atomics64(HAVE_CXX_ATOMICS64_WITH_LIB)
++ if (NOT HAVE_CXX_ATOMICS64_WITH_LIB)
++ message(FATAL_ERROR "Host compiler must support 64-bit std::atomic!")
++ endif()
++ else()
++ message(FATAL_ERROR "Host compiler appears to require libatomic for 64-bit
operations, but cannot find it.")
++ endif()
++ endif()
++endif()
+Index: tomopy-1.10.4+ds1/cmake/Modules/Packages.cmake
+===================================================================
+--- tomopy-1.10.4+ds1.orig/cmake/Modules/Packages.cmake
++++ tomopy-1.10.4+ds1/cmake/Modules/Packages.cmake
+@@ -280,6 +280,9 @@
+
+ endif()
+
++if(NOT HAVE_CXX_ATOMICS_WITHOUT_LIB OR NOT HAVE_CXX_ATOMICS64_WITHOUT_LIB)
++ list(APPEND TOMOPY_EXTERNAL_LIBRARIES "atomic")
++endif()
+
+
################################################################################
+ #
diff -Nru tomopy-1.10.4+ds1/debian/patches/series
tomopy-1.10.4+ds1/debian/patches/series
--- tomopy-1.10.4+ds1/debian/patches/series 2023-01-31 10:21:12.000000000
+0000
+++ tomopy-1.10.4+ds1/debian/patches/series 2023-02-01 10:07:39.000000000
+0000
@@ -2,3 +2,4 @@
0002-Don-t-try-to-git-clone-the-PTL-submodule.patch
cmake-args.patch
0004-Check-for-appropriate-version-of-libufo.patch
+fix-build.patch
thanks for considering it,
Gianfranco
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: tomopy
Source-Version: 1.10.4+ds1-8
Done: Roland Mas <[email protected]>
We believe that the bug you reported is fixed in the latest version of
tomopy, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Roland Mas <[email protected]> (supplier of updated tomopy package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 21 Feb 2023 15:40:46 +0100
Source: tomopy
Binary: python3-tomopy python3-tomopy-dbgsym
Architecture: source amd64
Version: 1.10.4+ds1-8
Distribution: unstable
Urgency: medium
Maintainer: Debian PaN Maintainers
<[email protected]>
Changed-By: Roland Mas <[email protected]>
Description:
python3-tomopy - Python package for tomographic data processing and image
reconstr
Closes: 1030295
Changes:
tomopy (1.10.4+ds1-8) unstable; urgency=medium
.
* Bug fix: "please fix build on atomic architectures", thanks to
Gianfranco Costamagna (Closes: #1030295).
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