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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/f74239245cd2384c4d335dbdc9969e5d5e9e397c">f7423924</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-15T20:15:02+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix baseline violation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/5ea52480022f8c6cd8999a6b5ed815d36c91b3e1">5ea52480</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-15T20:15:39+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: No tab in license text
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9">ff006171</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-15T20:48:36+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lintian override for script-with-language-extension
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="new-file">
+
debian/lintian-overrides
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<li class="file-stats">
<a href="#467246cedaa3eaa73fb42ba66b56cea7cd398700">
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+
debian/patches/baseline.patch
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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/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.24+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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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix baseline violation</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #974850</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * No tab in license text (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Lintian override for script-with-language-extension</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> Sun, 15 Nov 2020 20:15:41 +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">proteinortho (6.0.24+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"> * Team upload.</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,7 @@ Upstream-Name: Proteinortho</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Marcus Lechner <lechner@staff.uni-marburg.de></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://www.bioinf.uni-leipzig.de/Software/proteinortho/</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Files-Excluded: */BUILD</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>*/lapack-*.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>*/lapack-*.tar.gz</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">Files: *</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: 2009-2014 Marcus Lechner <lechner@staff.uni-marburg.de></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">proteinortho: script-with-language-extension usr/bin/proteinortho*.pl</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">proteinortho: script-with-language-extension usr/bin/proteinortho_ffadj_mcs.py</span></pre>
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<li id="467246cedaa3eaa73fb42ba66b56cea7cd398700">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9#467246cedaa3eaa73fb42ba66b56cea7cd398700"><strong>debian/patches/baseline.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix baseline violation</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/974850</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Sun, 15 Nov 2020 20:11:22 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -158,10 +158,10 @@</span> ifeq ($(USELAPACK),TRUE)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ifeq ($(USEPRECOMPILEDLAPACK),TRUE)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ifeq ($(STATIC),TRUE)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive... (this should now work for OSX).$(NC)"; \</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "......$(ORANGE)-march=native -mtune=native failed, I try without them again.$(NC)"; \</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "......$(ORANGE) failed, I try without them again.$(NC)"; \</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> echo "......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"; \</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -178,8 +178,8 @@</span> ifeq ($(STATIC),TRUE)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) )</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- echo "......$(ORANGE)-march=native -mtune=native failed, I try without them again.$(NC)"; \</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "......$(ORANGE) failed, I try without them again.$(NC)"; \</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/af2d491e9b7426efc8a261bc270d27896b821bef...ff006171fa68e37ec21dfef0cd1c5b9e53bc93f9#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">deb_diamond</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">baseline.patch</span></pre>
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