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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinityrnaseq">Debian Med / trinityrnaseq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6">10f51f60</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-04T15:59:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs
and add LDFALGS CPPFLAGS and unshadow CFALGS for seqtk-trinity-0.0.2
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
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+
debian/patches/hardening
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<li class="file-stats">
<a href="#5b7194c7e8e3451f085699bcc06c43a54154e5cc">
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+
debian/patches/seqtk-trinity-hardening
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.6.6+dfsg-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Eliminate warning about missing hardening flags</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 04 Jan 2019 07:58:22 -0800</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">trinityrnaseq (2.6.6+dfsg-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * -examples: Don't hardcode number of --CPU (especially above 2). Fixes the</span>
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<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Chrysalis/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Chrysalis/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -466,7 +466,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> # How to compile C++ files:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> .cc.o:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> @ mkdir -p $(OBJ)/${@D}</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CPLUSPLUS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CPLUSPLUS) $(CXXFLAGS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ##############################################################################</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> ## ADDITIONAL TARGETS:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity-plugins/scaffold_iworm_contigs/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,7 +2,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> prefix = ../htslib</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> ScaffoldIwormContigs:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) $(CPPFLAGS) $(CXXFLAGS) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> rm -f scaffold_iworm_contigs</span></pre>
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<li id="5b7194c7e8e3451f085699bcc06c43a54154e5cc">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6#5b7194c7e8e3451f085699bcc06c43a54154e5cc"><strong>debian/patches/seqtk-trinity-hardening</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: Add LDFALGS CPPFLAGS and unshadw CFALGS for seqtk-trinity-0.0.2</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity-plugins/seqtk-trinity-0.0.2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity-plugins/seqtk-trinity-0.0.2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,10 +1,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> CC=gcc</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=-g -Wall -O2 -Wno-unused-function</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+=-g -Wall -O2 -Wno-unused-function</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> all:seqtk-trinity</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> seqtk-trinity:seqtk.c khash.h kseq.h</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) seqtk.c -o $@ -lz -lm</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,3 +14,4 @@ disable-libieee</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">python3</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">better_java_version_check</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">unfix_num_of_cores</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">hardening</span></pre>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,9 +27,11 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> $(shell dpkg-buildflags --export=configure); done</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> patch -p1 < debian/patches/seqtk-trinity-hardening</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> for target in ${SOURCE_DIRECTORIES_ALL}; do dh_auto_build \</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> -O--sourcedirectory=$${target}; done</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> for target in ${SOURCE_DIRECTORIES}; do dh_auto_clean \</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> --sourcedirectory=$${target}; done</span>
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