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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-vdb">Debian Med / ncbi-vdb</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/commit/245dbdb2100e1ab86fbf62ed8e07f5d2079badb9">245dbdb2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-04T10:42:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add bug reference
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/commit/c8ff0c06110ecd261b5c1cfbad122a3bbe131dd6">c8ff0c06</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-04T10:42:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Revert attempt to build with DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/commit/e085572c47df45cca29b262ddc29032a5b6a6eb5">e085572c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-04T12:14:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disable patch that would be needed for -Wl,-z,defs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-vdb/commit/ddf9c5ab425b7b594f9aa344ea3d3692fadacd29">ddf9c5ab</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-04T12:21:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#cf39ab68d9d81e8ea74886f9556a67f049e65150">
debian/patches/fix_linking.patch
</a>
</li>
<li class="file-stats">
<a href="#d862affde6e3a48b6f7fe170aa79fcf08b61638b">
debian/patches/i386-uint64_msbit.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/compare/8800585355ba19a73a500e03458ee799694188aa...ddf9c5ab425b7b594f9aa344ea3d3692fadacd29#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ncbi-vdb (2.9.2-1+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ncbi-vdb (2.9.2-1+dfsg-1) <span class="idiff left right">unstable</span>; 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" 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">@@ -8,14 +8,17 @@ ncbi-vdb (2.9.2-1+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * d/rules:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> - DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs -Wl,--as-needed</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> This should prevent successful build of a broken library (thanks</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> for the hint to Steve Langasek in #907358)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> - DEB_LDFLAGS_MAINT_APPEND := -Wl,--as-needed</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> - Considered using</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> which should prevent successful build of a broken library (thanks</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> for the hint to Steve Langasek) Unfortunately this uncovers several</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> other build failures - volunteers to provide the correct linker</span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> flags are welcome</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> - dh_auto_build --no-parallel</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> TODO: Try to fix linking but failed</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="LC18" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, <span class="idiff left right">28 Aug 2018 07:55:59</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, <span class="idiff left right">04 Sep 2018 14:14:44</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">ncbi-vdb (2.9.1-1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<li id="cf39ab68d9d81e8ea74886f9556a67f049e65150">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/compare/8800585355ba19a73a500e03458ee799694188aa...ddf9c5ab425b7b594f9aa344ea3d3692fadacd29#cf39ab68d9d81e8ea74886f9556a67f049e65150"><strong>debian/patches/fix_linking.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: When using</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> which should prevent successful build of a broken library this patch is needed</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> but not sufficient to build the project successfully. There are at least one</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> further library that needs additional linking options. Any volunteer who wants</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> to provide a complete patch that enables linking with -Wl,-z,defs is welcome</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">Last-Update: Tue, 28 Aug 2018 07:55:59 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libs/hdf5/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libs/hdf5/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -112,7 +112,9 @@ ifdef HDF5_LIBDIR</span></span>
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<li id="d862affde6e3a48b6f7fe170aa79fcf08b61638b">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/compare/8800585355ba19a73a500e03458ee799694188aa...ddf9c5ab425b7b594f9aa344ea3d3692fadacd29#d862affde6e3a48b6f7fe170aa79fcf08b61638b"><strong>debian/patches/i386-uint64_msbit.patch</strong></a>
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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">@@ -4,6 +4,7 @@ Description: add missing implementation of uint64_msbit for i386</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> x86_64.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Author: Steve Langasek <steve.langasek@ubuntu.com></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">Last-Modified: 2018-08-26</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/907358</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h</span></span>
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<td class="diff-line-num new_line" data-linenumber="10" 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/ncbi-vdb/compare/8800585355ba19a73a500e03458ee799694188aa...ddf9c5ab425b7b594f9aa344ea3d3692fadacd29#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">@@ -10,4 +10,4 @@ add_-msse2.patch</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">use_debian_packaged_libmbedx.patch</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">mbedtls_ssl_init.patch</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">i386-uint64_msbit.patch</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">fix_linking.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"><span class="idiff left right"># </span>fix_linking.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ncbi-vdb/compare/8800585355ba19a73a500e03458ee799694188aa...ddf9c5ab425b7b594f9aa344ea3d3692fadacd29#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,7 +18,9 @@ LIBINSTALLDIR := debian/tmp/usr/$(DEB_SOURCE)/$(OS)/gcc/$(VDB_ARCH)/dbg/lib</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">LIBPKG := libncbi-vdb2</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">SCHEMADIR := debian/$(LIBPKG)/usr/lib/$(DEB_SOURCE)</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">export DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs -Wl,--as-needed</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># See debian/patches/fix-linking</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># export DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs -Wl,--as-needed</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">export DEB_LDFLAGS_MAINT_APPEND := -Wl,--as-needed</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> dh $@</span>
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