[med-svn] [Git][med-team/trinityrnaseq][master] Build with glibc 2.27 (fix for cannot find -lieee)

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / trinityrnaseq


Commits:
9cead657 by Andreas Tille at 2018-02-17T09:06:32+01:00
Build with glibc 2.27 (fix for cannot find -lieee)

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/disable-libieee
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+trinityrnaseq (2.5.1+dfsg-2) unstable; urgency=medium
+
+  * Team upload.
+
+  [ Aurelien Jarno ]
+  * Build with glibc 2.27 (fix for cannot find -lieee)
+
+ -- Andreas Tille <tille at debian.org>  Sat, 17 Feb 2018 09:04:18 +0100
+
 trinityrnaseq (2.5.1+dfsg-1) unstable; urgency=medium
 
   * New upstream release. Updated watch file.


=====================================
debian/patches/disable-libieee
=====================================
--- /dev/null
+++ b/debian/patches/disable-libieee
@@ -0,0 +1,64 @@
+Author: Aurelien Jarno <aurel32 at debian.org>
+Last-Update: Sat, 17 Feb 2018 00:26:39 +0100
+Bug-Debian: https://bugs.debian.org/890631
+Description: Starting with glibc 2.27, support for the "ieee" library (part of
+ SVID specification) has been removed. The libieee.a library is therefore not
+ shipped anymore. In the trinityrnaseq case, GCC tries to link with this
+ library due to the use of the -mieee-fp option. Removing this option
+ from the Makefile is enough to fix the issue. This is what the patch does.
+
+--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_i386
++++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_i386
+@@ -11,7 +11,7 @@ XERCES_INC	= -ISpines
+ # Need to use old Compaq assembler:
+ SYS_OPT		+= 
+ 
+-SYS_LANG	+= -mieee-fp
++SYS_LANG	+= 
+ 
+ SYS_INCS	+=
+ 
+--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_i686
++++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_i686
+@@ -9,7 +9,7 @@ XERCES_LIB	= -L$(LIB) -lxerces-c1_5_1-i6
+ # Need to use old Compaq assembler:
+ SYS_OPT		+= 
+ 
+-SYS_LANG	+= -mieee-fp
++SYS_LANG	+= 
+ 
+ SYS_INCS	+=
+ 
+--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_i86pc
++++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_i86pc
+@@ -9,7 +9,7 @@ XERCES_LIB	= -L$(LIB) -lxerces-c1_5_1-i8
+ # Need to use old Compaq assembler:
+ SYS_OPT		+= 
+ 
+-SYS_LANG	+= -mieee-fp
++SYS_LANG	+= 
+ 
+ SYS_INCS	+=
+ 
+--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_x86_64
++++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_x86_64
+@@ -11,7 +11,7 @@ XERCES_INC	= -ISpines
+ # Need to use old Compaq assembler:
+ SYS_OPT		+= 
+ 
+-SYS_LANG	+= -mieee-fp
++SYS_LANG	+=
+ 
+ SYS_INCS	+=
+ 
+--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_x86_64_mpi
++++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_x86_64_mpi
+@@ -11,7 +11,7 @@ XERCES_INC	= -ISpines
+ # Need to use old Compaq assembler:
+ SYS_OPT		+= 
+ 
+-SYS_LANG	+= -mieee-fp
++SYS_LANG	+= 
+ 
+ SYS_INCS	+=
+ 


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -9,3 +9,4 @@ adjust-trimmomatic-adapters-path
 build_with_gcc6.patch
 NeedlemanWunschGotohBanded.patch
 remove_anaconda_hashbang
+disable-libieee



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/commit/9cead657dc8e6265d6370293e1ea6acc12d4364d

---
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/commit/9cead657dc8e6265d6370293e1ea6acc12d4364d
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