Your message dated Fri, 06 Dec 2019 22:21:22 +0000
with message-id <[email protected]>
and subject line Bug#943311: fixed in hyphy 2.5.1+dfsg-1
has caused the Debian Bug report #943311,
regarding hyphy: please add pkg-config to Build-Depends for cross compilation
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
943311: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=943311
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: hyphy
Version: 2.3.14+dfsg-2
Tags: patch
User: [email protected]
Usertags: ftcbfs
hyphy fails to cross build from source, because it fails finding mpi.
This happens, because cmake's FindMPI.cmake uses compiler wrappers such
as mpicc to discover mpi. Such compiler wrappers cannot work at all for
cross building and they will not be supported on Debian at all. Beyond
breaking cross compilation, compiler wrappers become a pain when you
need two of them (e.g. ccache/distcc/mpicc/...). As such they should be
avoided and the natural solution for this case is using pkg-config,
which is well-supported by all major mpi providers since ages. Making
FindMPI.cmake use pkg-config is a separate issue outside the scope of
hyphy and there will be a separate bug about that. However, hyphy needs
to depend on pkg-config. Therefore, please add pkg-config to
Build-Depends. You can make this dependency conditional to cross
compilation by annotating it with <cross> if you like, because we'll
keep using mpicc for the native case. I don't think the unconditional
dependency hurts. Please consider applying the attached patch and
understand that it is only half of the picture: The required changes to
cmake are still to be filed. Applying this patch early will make it
easier to develop the cmake patch. I'm attaching my first draft for
reference only.
Helmut
diff --minimal -Nru hyphy-2.3.14+dfsg/debian/changelog
hyphy-2.3.14+dfsg/debian/changelog
--- hyphy-2.3.14+dfsg/debian/changelog 2019-07-05 15:45:06.000000000 +0200
+++ hyphy-2.3.14+dfsg/debian/changelog 2019-10-23 09:00:30.000000000 +0200
@@ -1,3 +1,11 @@
+hyphy (2.3.14+dfsg-2.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross
+ compilation. (Closes: #-1)
+
+ -- Helmut Grohne <[email protected]> Wed, 23 Oct 2019 09:00:30 +0200
+
hyphy (2.3.14+dfsg-2) unstable; urgency=medium
[ Saira Hussain ]
diff --minimal -Nru hyphy-2.3.14+dfsg/debian/control
hyphy-2.3.14+dfsg/debian/control
--- hyphy-2.3.14+dfsg/debian/control 2019-07-05 15:45:06.000000000 +0200
+++ hyphy-2.3.14+dfsg/debian/control 2019-10-23 08:19:10.000000000 +0200
@@ -8,7 +8,8 @@
mpi-default-dev,
libcurl4-gnutls-dev | libcurl4-dev,
libssl-dev,
- libsqlite3-dev
+ libsqlite3-dev,
+ pkg-config,
Standards-Version: 4.3.1
Vcs-Browser: https://salsa.debian.org/med-team/hyphy
Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
--- cmake-3.13.4.orig/Modules/FindMPI.cmake
+++ cmake-3.13.4/Modules/FindMPI.cmake
@@ -247,6 +247,7 @@
cmake_policy(SET CMP0057 NEW) # if IN_LIST
include(${CMAKE_CURRENT_LIST_DIR}/FindPackageHandleStandardArgs.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/FindPkgConfig.cmake)
# Generic compiler names
set(_MPI_C_GENERIC_COMPILER_NAMES mpicc mpcc mpicc_r mpcc_r)
@@ -1459,7 +1460,40 @@
if(NOT MPI_PINNED_COMPILER AND NOT MPI_${LANG}_WRAPPER_FOUND)
# If MPI_PINNED_COMPILER wasn't given, and the MPI compiler we potentially found didn't work, we withdraw it.
set(MPI_${LANG}_COMPILER "MPI_${LANG}_COMPILER-NOTFOUND" CACHE FILEPATH "MPI compiler for ${LANG}" FORCE)
- if(NOT MPI_SKIP_GUESSING)
+
+ if(LANG STREQUAL "C")
+ set(_MPI_PKG "mpi-c")
+ elseif(LANG STREQUAL "CXX")
+ set(_MPI_PKG "mpi-cxx")
+ elseif(LANG STREQUAL "Fortran")
+ set(_MPI_PKG "mpi-fort")
+ else()
+ set(_MPI_PKG "")
+ endif()
+ if(_MPI_PKG)
+ pkg_check_modules("MPI_${LANG}_PKG" "${_MPI_PKG}")
+ if("${MPI_${LANG}_PKG_FOUND}")
+ set(MPI_${LANG}_COMPILE_OPTIONS ${MPI_${LANG}_PKG_CFLAGS} CACHE STRING "MPI ${LANG} compilation options" FORCE)
+ set(MPI_${LANG}_INCLUDE_PATH ${MPI_${LANG}_PKG_INCLUDE_DIRS} CACHE STRING "MPI ${LANG} include directories" FORCE)
+ set(MPI_${LANG}_LINK_FLAGS ${MPI_${LANG}_PKG_LDFLAGS} CACHE STRING "MPI ${LANG} linker flags" FORCE)
+ set(MPI_${LANG}_LIB_NAMES ${MPI_${LANG}_PKG_LIBRARIES} CACHE STRING "MPI ${LANG} libraries to link against" FORCE)
+ foreach(_MPI_LIB IN LISTS MPI_${LANG}_LIB_NAMES)
+ if(_MPI_LIB)
+ get_filename_component(_MPI_PLAIN_LIB_NAME "${_MPI_LIB}" NAME_WE)
+ get_filename_component(_MPI_LIB_NAME "${_MPI_LIB}" NAME)
+ get_filename_component(_MPI_LIB_DIR "${_MPI_LIB}" DIRECTORY)
+ find_library(MPI_${_MPI_PLAIN_LIB_NAME}_LIBRARY
+ NAMES "${_MPI_LIB_NAME}" "lib${_MPI_LIB_NAME}"
+ HINTS ${_MPI_LIB_DIR}
+ DOC "Location of the ${_MPI_PLAIN_LIB_NAME} library for MPI"
+ )
+ mark_as_advanced(MPI_${_MPI_PLAIN_LIB_NAME}_LIBRARY)
+ endif()
+ endforeach()
+ endif()
+ endif()
+
+ if(NOT MPI_SKIP_GUESSING AND NOT "${MPI_${LANG}_PKG_FOUND}")
# For C++, we may use the settings for C. Should a given compiler wrapper for C++ not exist, but one for C does, we copy over the
# settings for C. An MPI distribution that is in this situation would be IBM Platform MPI.
if("${LANG}" STREQUAL "CXX" AND MPI_C_WRAPPER_FOUND)
--- End Message ---
--- Begin Message ---
Source: hyphy
Source-Version: 2.5.1+dfsg-1
We believe that the bug you reported is fixed in the latest version of
hyphy, 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.
Andreas Tille <[email protected]> (supplier of updated hyphy 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: SHA256
Format: 1.8
Date: Fri, 06 Dec 2019 22:47:47 +0100
Source: hyphy
Binary: hyphy-pt hyphy-mpi hyphy-common
Architecture: source
Version: 2.5.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
hyphy-common - Hypothesis testing using Phylogenies (common files)
hyphy-mpi - Hypothesis testing using Phylogenies (MPI version)
hyphy-pt - Hypothesis testing using Phylogenies (pthreads version)
Closes: 909707 943311
Changes:
hyphy (2.5.1+dfsg-1) unstable; urgency=medium
.
[ Helmut Grohne ]
* Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross
compilation. (Closes: #943311)
.
[ Andreas Tille ]
* New upstream version
* debhelper-compat 12
* Secure URI in copyright format
* Remove trailing whitespace in debian/changelog
* New upstream version
* Standards-Version: 4.4.1
* Use secure URI in Homepage field.
* Remove patches msse_option_only_if_available.patch that are missing
from debian/patches/series.
* Skip GTEST target for the moment since this is currently in flux
see https://github.com/veg/hyphy/issues/1058
* No need to rename executables any more since upstream is doing this now
* Autopkgtest exists since last release - so close bug
Closes: #909707
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