[med-svn] [Git][med-team/sailfish][master] 3 commits: Remove useless '"'
Andreas Tille
gitlab at salsa.debian.org
Wed Mar 27 12:38:30 GMT 2019
Andreas Tille pushed to branch master at Debian Med / sailfish
Commits:
dfe665c7 by Andreas Tille at 2019-03-27T12:15:49Z
Remove useless '"'
- - - - -
00c888ae by Andreas Tille at 2019-03-27T12:37:37Z
Do not claim missing libdivsufsort
- - - - -
45768618 by Andreas Tille at 2019-03-27T12:37:52Z
Document problem with spdlog: Obviously a quite old version is used since it relies on files removed in 2016
- - - - -
3 changed files:
- debian/changelog
- debian/patches/dfsg-please.patch
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,17 @@
sailfish (0.10.1+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #nnnn)
+
+ TODO:
+ 1. Code relies on old version of spdlog since it tries to include
+ spdlog/details/format.h
+ I've searched spdlog upstream Git. This file was removed in
+
+ commit f5bde237dda771f41e876ef7c7affc51db9c58f6 (HEAD)
+ Author: gabime <gmelman1 at gmail.com>
+ Date: Fri Jul 15 18:35:43 2016 +0300
+
+ Updated fmt lib to version 0d5ef5c2a66026409b0cfbafa1d2f46cdc5aa4d0
+
-- Steffen Moeller <moeller at debian.org> Thu, 21 Mar 2019 22:47:18 +0100
=====================================
debian/patches/dfsg-please.patch
=====================================
@@ -4,15 +4,28 @@ Description: Make sure we build against Debian packaged libraries
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -287,6 +287,7 @@ ExternalProject_Add(libdivsufsort
- set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+@@ -272,6 +272,7 @@ message("BOOST LIBRAREIS = ${Boost_LIBRA
+
+ set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
++if(!DEBIAN_BUILD)
+ message("Build system will build libdivsufsort")
+ message("==================================================================")
+ include(ExternalProject)
+@@ -285,8 +286,11 @@ ExternalProject_Add(libdivsufsort
+ CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
+ )
+ set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
++else()
++message("Use Debian packaged libdivsufsort")
++endif()
+-
+if(!DEBIAN_BUILD)
message("Build system will fetch and build Jellyfish")
message("==================================================================")
ExternalProject_Add(libjellyfish
-@@ -303,6 +304,9 @@ ExternalProject_Add(libjellyfish
+@@ -303,6 +307,9 @@ ExternalProject_Add(libjellyfish
cp config.h <INSTALL_DIR>/include/jellyfish-2.2.3/jellyfish/ &&
cp config.h <INSTALL_DIR>/include/
)
@@ -22,7 +35,7 @@ Description: Make sure we build against Debian packaged libraries
find_package(TBB)
##
-@@ -311,6 +315,7 @@ find_package(TBB)
+@@ -311,6 +318,7 @@ find_package(TBB)
#
##
if(NOT TBB_FOUND)
@@ -30,7 +43,7 @@ Description: Make sure we build against Debian packaged libraries
set(TBB_WILL_RECONFIGURE TRUE)
# Set the appropriate compiler
-@@ -352,6 +357,9 @@ ExternalProject_Add_Step(libtbb reconfig
+@@ -352,6 +360,9 @@ ExternalProject_Add_Step(libtbb reconfig
DEPENDEES install
)
endif()
@@ -40,7 +53,7 @@ Description: Make sure we build against Debian packaged libraries
##
# Find HDF5, and prefer the static libs
-@@ -401,7 +409,7 @@ endif()
+@@ -401,7 +412,7 @@ endif()
message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
@@ -49,7 +62,7 @@ Description: Make sure we build against Debian packaged libraries
message("Build system will compile libgff")
message("==================================================================")
ExternalProject_Add(libgff
-@@ -416,6 +424,9 @@ ExternalProject_Add(libgff
+@@ -416,6 +427,9 @@ ExternalProject_Add(libgff
BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
)
@@ -59,7 +72,7 @@ Description: Make sure we build against Debian packaged libraries
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
-@@ -441,6 +452,8 @@ endif()
+@@ -441,6 +455,8 @@ endif()
if (NOT HAVE_FAST_MALLOC)
message("Build system will fetch and use JEMalloc")
@@ -68,7 +81,7 @@ Description: Make sure we build against Debian packaged libraries
message("==================================================================")
ExternalProject_Add(libjemalloc
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-@@ -456,10 +469,12 @@ if (NOT HAVE_FAST_MALLOC)
+@@ -456,10 +472,12 @@ if (NOT HAVE_FAST_MALLOC)
set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
set (HAVE_FAST_MALLOC TRUE)
endif ()
@@ -81,7 +94,7 @@ Description: Make sure we build against Debian packaged libraries
message("Build system will fetch and build SparseHash")
message("==================================================================")
ExternalProject_Add(libsparsehash
-@@ -472,6 +487,7 @@ ExternalProject_Add(libsparsehash
+@@ -472,6 +490,7 @@ ExternalProject_Add(libsparsehash
CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
INSTALL_COMMAND make install
)
=====================================
debian/upstream/metadata
=====================================
@@ -2,7 +2,7 @@ Reference:
Author: Rob Patro and Stephen M Mount and Carl Kingsford
Title: >
Sailfish enables alignment-free isoform quantification from RNA-seq reads
- using lightweight algorithms"
+ using lightweight algorithms
Journal: Nature Biotechnology
Year: 2014
Volume: 32
View it on GitLab: https://salsa.debian.org/med-team/sailfish/compare/46844d11123591f90fa2362ea031fb6100450f79...457686186c34f3fb7c8aa1092087d85ff8cca929
--
View it on GitLab: https://salsa.debian.org/med-team/sailfish/compare/46844d11123591f90fa2362ea031fb6100450f79...457686186c34f3fb7c8aa1092087d85ff8cca929
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190327/9c9b86f2/attachment-0001.html>
More information about the debian-med-commit
mailing list