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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/fasta3">Debian Med / fasta3</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fasta3/commit/d61cb91bbfbcdbe918b8720a22af87b34550aef8">d61cb91b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-01-06T12:22:17+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparing for upload
</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#f6361e25b2927c77444e8b661a216d7f56f9d1f8">
debian/patches/Makefile.patch
</a>
</li>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fasta3/commit/d61cb91bbfbcdbe918b8720a22af87b34550aef8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">fasta3 (36.3.8h-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">fasta3 (36.3.8h-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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> TODO: Do we really need to use non-free smith waterman code?</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> There is a free libssw. Please contact upstream!</span>
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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="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 19 Aug 2019 21:45:02 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> TODO: Do we really need to use non-free smith waterman code?</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> There is a free libssw. Please contact upstream!</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"> [ Steffen Moeller]</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Fixed patches - somehow one Makefile.common was removed but needed</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> that led to a FTBFS.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Mon, 06 Jan 2020 12:20:34 +0100</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">fasta3 (36.3.8g-1) unstable; urgency=low</span>
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<a href="https://salsa.debian.org/med-team/fasta3/commit/d61cb91bbfbcdbe918b8720a22af87b34550aef8#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -6,7 +6,7 @@ XS-Autobuild: no</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/fasta3</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/fasta3.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: http://fasta.bioch.virginia.edu</span>
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<a href="https://salsa.debian.org/med-team/fasta3/commit/d61cb91bbfbcdbe918b8720a22af87b34550aef8#f6361e25b2927c77444e8b661a216d7f56f9d1f8"><strong>debian/patches/Makefile.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">@@ -29,58 +29,3 @@ Description: Makefile</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS += -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> # -I/usr/include/mysql -DMYSQL_DB</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> # -DSUPERFAMNUM -DSFCHAR="'|'" </span></pre>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/make/Makefile36m.common</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="p">@@ -1,51 +0,0 @@</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# $Name: $ - $Id: Makefile36m.common 1250 2014-01-24 21:33:39Z wrp $</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# commands common to all architectures</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# if your architecture does not support "include", append at the end.</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-COMP_LIBO=comp_mlib9.o # reads database into memory for multi-query without delay</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-COMP_THRO=comp_mthr9.o # threaded version</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-WORK_THRO=work_thr2.o</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-GETSEQO = </span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# standard nxgetaa, no memory mapping for 0 - 6</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#LGETLIB=getseq.o lgetlib.o</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#NGETLIB=nmgetlib</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# memory mapping for 0FASTA, 5PIRVMS, 6GCGBIN</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LGETLIB= $(GETSEQO) lgetlib.o lgetaa_m.o</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-NGETLIB=nmgetlib</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# use ncbl_lib.c for BLAST1.4 support instead of ncbl2_mlib.c</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#NCBL_LIB=ncbl_lib.o</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# this option should support both formats (BLAST1.4 not currently supported): </span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#NCBL_LIB=ncbl_lib.o ncbl2_mlib.o</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# normally use ncbl2_mlib.c</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#NCBL_LIB=ncbl2_mlib.o</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#LIB_M= -lm</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# this option supports NCBI BLAST2 and mySQL</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# it requires "-I/usr/include/mysql -DMYSQL_DB" in CFLAGS</span></span>
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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# and "-L/usr/lib64/mysql -lmysqlclient -lz" in LIB_M</span></span>
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<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# some systems may also require a LD_LIBRARY_PATH change</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIB_M= -lm </span></span>
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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#LIB_M= -L/usr/lib64/mysql -lmysqlclient -lm # -lz </span></span>
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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-NCBL_LIB=ncbl2_mlib.o</span></span>
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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#NCBL_LIB=ncbl2_mlib.o mysql_lib.o</span></span>
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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# threaded as _t, serial</span></span>
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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# include ../make/Makefile.pcom</span></span>
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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# threaded without _t</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-include ../make/Makefile.pcom_t</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# serial only </span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# include ../make/Makefile.pcom_s</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-include ../make/Makefile.fcom</span></span></pre>
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