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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mecat2">Debian Med / mecat2</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/mecat2/-/commit/98eeb38062772bb771034fa6fade16f18fcb4fa7">98eeb380</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-06-29T15:49:14+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some build depends and modify Makefiles to use libraries already in Debian
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<h4>3 changed files:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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+
debian/patches/use_system_packaged_libs.patch
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/98eeb38062772bb771034fa6fade16f18fcb4fa7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mecat2</span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mecat2.git</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/98eeb38062772bb771034fa6fade16f18fcb4fa7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">use_system_packaged_libs.patch</span></pre>
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<li id="e48565eeed468e118e5f54e2aa707c40d443cefe">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/98eeb38062772bb771034fa6fade16f18fcb4fa7#e48565eeed468e118e5f54e2aa707c40d443cefe"><strong>debian/patches/use_system_packaged_libs.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: use libraries that are already pre-packaged in Debian</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Modify the Makefiles so that we instead use libraries that are already within Debian as a package, and not one in some third_party/ directory to build (removed).</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me> </span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-06-29</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- mecat2.orig/Makefile</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mecat2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,6 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> PWD := $(shell pwd)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> OS_TYPE := $(shell echo `uname`)</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> MACHINE_TYPE := $(shell echo `uname -m`)</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MACHINE_TYPE_2 := $(shell echo `uname -m`)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> ifeq (${MACHINE_TYPE}, x86_64)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> MACHINE_TYPE = amd64</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -8,13 +9,6 @@</span></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"> BUILD_TOP_DIR := ${PWD}/${OS_TYPE}-${MACHINE_TYPE}</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_VERSION ?= 1.10.4</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_INSTALL = ${BUILD_TOP_DIR}/hdf5</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_SOURCE = ${BUILD_TOP_DIR}/hdf5-${HDF5_VERSION}</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_INCLUDE = ${HDF5_INSTALL}/include</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HDF5_LIB = ${HDF5_INSTALL}/lib/libhdf5.a</span></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;">-HDF5_TAR_GZ = ${BUILD_TOP_DIR}/hdf5-$(HDF5_VERSION).tar.gz</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;">-</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> DEXTRACTOR_BIN_NAME = dexqv dexta dextract undexqv undexta</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> DEXTRACTOR_BIN = $(patsubst %, ${BUILD_DIR}/%, $(DEXTRACTOR_BIN_NAME))</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -28,8 +22,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> cd src && make clean</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> cd DEXTRACTOR && make -f ../dextract_makefile clean</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm ${HDF5_INSTALL} -rf</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;">- rm ${HDF5_SOURCE} -rf</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> rm ${DEXTRACTOR_BIN} -f</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> dextractor: ${BUILD_TOP_DIR}/bin/dexqv ${BUILD_TOP_DIR}/bin/dexta ${BUILD_TOP_DIR}/bin/dextract ${BUILD_TOP_DIR}/bin/undexqv ${BUILD_TOP_DIR}/bin/undexta</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="p">@@ -37,18 +29,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> ${DEXTRACTOR_BIN}: ${HDF5_LIB}</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> mkdir -p ${BUILD_DIR} </span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd DEXTRACTOR && make -f ../dextract_makefile HDF5_INCLUDE=${HDF5_INCLUDE} HDF5_LIB=${HDF5_LIB} </span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd DEXTRACTOR && make -f ../dextract_makefile HDF5_INCLUDE=/usr/include/hdf5/serial/ HDF5_LIB=/usr/lib/${MACHINE_TYPE_2}-linux-gnu/hdf5/serial/ </span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> cd DEXTRACTOR && cp ${DEXTRACTOR_BIN_NAME} ${BUILD_DIR}</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-${HDF5_LIB}: ${HDF5_TAR_GZ}</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tar -xzf ${BUILD_TOP_DIR}/hdf5-$(HDF5_VERSION).tar.gz -C ${BUILD_TOP_DIR} || exit 255</span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" 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="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd ${BUILD_TOP_DIR}/hdf5-$(HDF5_VERSION) && \</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ./configure --enable-threadsafe --disable-hl --libdir=`pwd`/../hdf5/lib --includedir=`pwd`/../hdf5/include --prefix=`pwd`/../hdf5 && \</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- make -j ${MAKEFLAGS} && make install</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-${HDF5_TAR_GZ}:</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;">- mkdir -p ${BUILD_DIR} </span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- version_major_minor=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cp third_party/hdf5-1.10.4.tar.gz ${BUILD_TOP_DIR}/</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mecat2.orig/dextract_makefile</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mecat2/dextract_makefile</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="p">@@ -6,8 +6,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> all: dextract dexta undexta dexqv undexqv</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> dextract:</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c -lhdf5 -lz</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c ${HDF5_LIB} -lpthread -lz -ldl -lm</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c -lhdf5 -lz -lpthread -lm -ldl</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c ${HDF5_LIB} -lpthread -lz -ldl -lm</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> dexta:</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> ${CC} ${CFLAGS} -o dexta dexta.c DB.c QV.c</span></pre>
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