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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinityrnaseq">Debian Med / trinityrnaseq</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/9cead657dc8e6265d6370293e1ea6acc12d4364d">9cead657</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-02-17T09:06:32+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build with glibc 2.27 (fix for cannot find -lieee)
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#e0c7ec6f3c3943671a6cb8ed1e9707d82dc2a211">
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+
debian/patches/disable-libieee
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/9cead657dc8e6265d6370293e1ea6acc12d4364d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.5.1+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Aurelien Jarno ]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Build with glibc 2.27 (fix for cannot find -lieee)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 17 Feb 2018 09:04:18 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">trinityrnaseq (2.5.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * New upstream release. Updated watch file.</span>
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<li id="e0c7ec6f3c3943671a6cb8ed1e9707d82dc2a211">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/9cead657dc8e6265d6370293e1ea6acc12d4364d#e0c7ec6f3c3943671a6cb8ed1e9707d82dc2a211"><strong>debian/patches/disable-libieee</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Author: Aurelien Jarno <aurel32@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Last-Update: Sat, 17 Feb 2018 00:26:39 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Debian: https://bugs.debian.org/890631</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Description: Starting with glibc 2.27, support for the "ieee" library (part of</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> SVID specification) has been removed. The libieee.a library is therefore not</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> shipped anymore. In the trinityrnaseq case, GCC tries to link with this</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> library due to the use of the -mieee-fp option. Removing this option</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> from the Makefile is enough to fix the issue. This is what the patch does.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_i386</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">+++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_i386</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">@@ -11,7 +11,7 @@ XERCES_INC = -ISpines</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> # Need to use old Compaq assembler:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> SYS_OPT += </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">-SYS_LANG += -mieee-fp</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">+SYS_LANG += </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> SYS_INCS +=</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_i686</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">+++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_i686</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">@@ -9,7 +9,7 @@ XERCES_LIB = -L$(LIB) -lxerces-c1_5_1-i6</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> # Need to use old Compaq assembler:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> SYS_OPT += </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">-SYS_LANG += -mieee-fp</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">+SYS_LANG += </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> SYS_INCS +=</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_i86pc</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">+++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_i86pc</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">@@ -9,7 +9,7 @@ XERCES_LIB = -L$(LIB) -lxerces-c1_5_1-i8</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> # Need to use old Compaq assembler:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> SYS_OPT += </span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">-SYS_LANG += -mieee-fp</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">+SYS_LANG += </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> </span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> SYS_INCS +=</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_x86_64</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">+++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_x86_64</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">@@ -11,7 +11,7 @@ XERCES_INC = -ISpines</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> # Need to use old Compaq assembler:</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> SYS_OPT += </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> </span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">-SYS_LANG += -mieee-fp</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">+SYS_LANG +=</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> SYS_INCS +=</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">--- trinityrnaseq-2.5.1+dfsg.orig/Chrysalis/Makefile_g++_x86_64_mpi</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">+++ trinityrnaseq-2.5.1+dfsg/Chrysalis/Makefile_g++_x86_64_mpi</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">@@ -11,7 +11,7 @@ XERCES_INC = -ISpines</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> # Need to use old Compaq assembler:</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> SYS_OPT += </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">-SYS_LANG += -mieee-fp</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">+SYS_LANG += </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> SYS_INCS +=</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> </span></pre>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/9cead657dc8e6265d6370293e1ea6acc12d4364d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,3 +9,4 @@ adjust-trimmomatic-adapters-path</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">build_with_gcc6.patch</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">NeedlemanWunschGotohBanded.patch</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">remove_anaconda_hashbang</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">disable-libieee</span></pre>
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