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<title>[119367] trunk/dports/science/arb</title>
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<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/119367">119367</a></dd>
<dt>Author</dt> <dd>mf2k@macports.org</dd>
<dt>Date</dt> <dd>2014-04-23 12:52:12 -0700 (Wed, 23 Apr 2014)</dd>
</dl>
<h3>Log Message</h3>
<pre>arb: Update to version 6.0-rc1. Mavericks build fix. (#43339)</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportssciencearbPortfile">trunk/dports/science/arb/Portfile</a></li>
<li><a href="#trunkdportssciencearbfilespatchARBconfigmakefilediff">trunk/dports/science/arb/files/patch-ARB-config.makefile.diff</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li><a href="#trunkdportssciencearbfilespatchARBARBDBdiff">trunk/dports/science/arb/files/patch-ARB-ARBDB.diff</a></li>
<li><a href="#trunkdportssciencearbfilespatchARBarbdiff">trunk/dports/science/arb/files/patch-ARB-arb.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportssciencearbPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/arb/Portfile (119366 => 119367)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/arb/Portfile 2014-04-23 18:24:33 UTC (rev 119366)
+++ trunk/dports/science/arb/Portfile 2014-04-23 19:52:12 UTC (rev 119367)
</span><span class="lines">@@ -5,8 +5,7 @@
</span><span class="cx">
</span><span class="cx"> name arb
</span><span class="cx"> epoch 1
</span><del>-version 5.5
-revision 2
</del><ins>+version 6.0-rc1
</ins><span class="cx"> categories science
</span><span class="cx"> maintainers mac.com:matt.cottrell
</span><span class="cx"> platforms darwin
</span><span class="lines">@@ -24,14 +23,15 @@
</span><span class="cx"> (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment \
</span><span class="cx"> for sequence data. Nucleic Acids Research. 32:1363-1371.
</span><span class="cx">
</span><del>-master_sites http://download.arb-home.de/release/arb_${version}/
-distname arbsrc
</del><ins>+license Restrictive/Distributable
+
+master_sites http://download.arb-home.de/build/$name-${version}/
+distname arb-${version}-source-hotfix1
</ins><span class="cx"> extract.suffix .tgz
</span><del>-dist_subdir ${name}/${version}
-worksrcdir arbsrc_9167
</del><ins>+worksrcdir arbsrc_11977
</ins><span class="cx">
</span><del>-checksums rmd160 f8b7b12cd9259b1b0f7cbbc29aca4f85585e8b9f \
- sha256 25246355ccaebff2e3350a553732636896f0f9f21eca3bb2bcf75cbeb7ac92a9
</del><ins>+checksums rmd160 9ef6edf8e2e386794cfc204519bb00f4394549ee \
+ sha256 cb9bcbd999d6f8b3c06bde70a1d1e5a61ca564e80c16da4bb01bb7820f396e10
</ins><span class="cx">
</span><span class="cx"> depends_build port:imake \
</span><span class="cx"> port:makedepend
</span><span class="lines">@@ -45,14 +45,16 @@
</span><span class="cx"> port:xfig \
</span><span class="cx"> port:gv \
</span><span class="cx"> port:xorg-libXaw \
</span><del>- port:gtime
</del><ins>+ port:gtime \
+ path:lib/pkgconfig/glib-2.0.pc:glib2 \
+ port:coreutils
</ins><span class="cx">
</span><ins>+
+
</ins><span class="cx"> patchfiles patch-ARB-config.makefile.diff \
</span><span class="cx"> patch-ARB-intro.fig.diff \
</span><del>- patch-ARB-glpng.h.diff \
- patch-ARB-glpng.c.diff \
- patch-ARB-RNA3D_Textures.cxx.diff \
- patch-ARB-Makefile.diff
</del><ins>+ patch-ARB-arb.diff \
+ patch-ARB-ARBDB.diff
</ins><span class="cx">
</span><span class="cx"> configure {
</span><span class="cx"> if {${build_arch} eq "ppc" || ${build_arch} eq "i386"} {
</span><span class="lines">@@ -63,43 +65,15 @@
</span><span class="cx">
</span><span class="cx"> file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
</span><span class="cx"> reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile
</span><del>- file copy ${filespath}/arb_macsetup ${worksrcpath}/bin
- reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/bin/arb_macsetup ${worksrcpath}/SH/arb
- reinplace "s|@@GPP@@|${configure.cxx}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL
- reinplace "s|@@LIBPERLDIR@@|[exec ${prefix}/bin/perl -e "use Config; print \$Config{archlib};"]/CORE|g" ${worksrcpath}/PERL2ARB/DARWIN.PL
- reinplace -locale C "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \
- ${worksrcpath}/util/arb_check_build_env.pl \
- ${worksrcpath}/arb_install.sh \
- ${worksrcpath}/WINDOW/AW_status.cxx \
- ${worksrcpath}/SH/example_batch_probe_match.sh \
- ${worksrcpath}/GDEHELP/genhelp.sh \
- ${worksrcpath}/GDEHELP/genhelptree.sh \
- ${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh \
- ${worksrcpath}/HELP_SOURCE/Makefile \
- ${worksrcpath}/AISC_COM/AISC/Makefile \
- ${worksrcpath}/GDEHELP/Makefile \
- ${worksrcpath}/HELP_SOURCE/genhelp/Makefile \
- ${worksrcpath}/GDEHELP/Makefile.helpfiles
</del><ins>+ reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/SH/arb_macsetup
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> build.env-append PREFIX=${prefix} \
</span><span class="cx"> ARBHOME=${worksrcpath} \
</span><span class="cx"> PATH=${worksrcpath}/bin:$env(PATH)
</span><span class="cx">
</span><del>-# https://trac.macports.org/ticket/33756
-compiler.blacklist *clang*
-
-platform darwin {
- if {${os.major} >= 13} {
- depends_lib
- depends_run
- pre-fetch {
- ui_error "$name does not build on Mavericks or later."
- error "unsupported platform"
- }
- }
-}
-
</del><ins>+compiler.blacklist *llvm-gcc-4.2
+
</ins><span class="cx"> build.args GCC=${configure.cc} \
</span><span class="cx"> GPP=${configure.cxx}
</span><span class="cx">
</span><span class="lines">@@ -126,7 +100,6 @@
</span><span class="cx"> ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server
</span><span class="cx">
</span><span class="cx"> xinstall -m 777 -d ${destroot}${prefix}/share/arb/lib/pts
</span><del>-
</del><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> # to be investigated later
</span><span class="lines">@@ -223,5 +196,5 @@
</span><span class="cx"> "
</span><span class="cx">
</span><span class="cx"> livecheck.type regex
</span><del>-livecheck.url http://download.arb-home.de/release/
-livecheck.regex ${name}_(\[0-9.\]+)/
</del><ins>+livecheck.url http://download.arb-home.de/build/
+livecheck.regex ${name}-(\[0-9.\]+)-rc1-source/${extract.suffix}
</ins></span></pre></div>
<a id="trunkdportssciencearbfilespatchARBARBDBdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/arb/files/patch-ARB-ARBDB.diff (0 => 119367)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/arb/files/patch-ARB-ARBDB.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-ARBDB.diff 2014-04-23 19:52:12 UTC (rev 119367)
</span><span class="lines">@@ -0,0 +1,20 @@
</span><ins>+Index: ARBDB/arbdb.cxx
+===================================================================
+--- ARBDB/arbdb.cxx (revision 11958)
++++ ARBDB/arbdb.cxx (working copy)
+@@ -447,6 +447,7 @@
+ return inside_shell;
+ }
+
++#if 0
+ struct GB_test_shell_closed {
+ ~GB_test_shell_closed() {
+ if (GB_shell::in_shell()) { // leave that call
+@@ -455,6 +456,7 @@
+ }
+ };
+ static GB_test_shell_closed test;
++#endif
+
+ #if defined(UNIT_TESTS)
+ static bool closed_open_shell_for_unit_tests() {
</ins></span></pre></div>
<a id="trunkdportssciencearbfilespatchARBarbdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/arb/files/patch-ARB-arb.diff (0 => 119367)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/arb/files/patch-ARB-arb.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-arb.diff 2014-04-23 19:52:12 UTC (rev 119367)
</span><span class="lines">@@ -0,0 +1,11 @@
</span><ins>+--- SH/arb.orig 2013-03-02 09:47:45.000000000 -0500
++++ SH/arb 2013-03-02 14:09:54.000000000 -0500
+@@ -62,7 +62,7 @@
+ esac
+
+ # use ARBHOME defined by location of script (comment out for old behavior)
+-ARBHOME=$ARBHOME_OF_SCRIPT
++#ARBHOME=$ARBHOME_OF_SCRIPT
+
+ echo "Using ARBHOME='$ARBHOME'"
+
</ins></span></pre></div>
<a id="trunkdportssciencearbfilespatchARBconfigmakefilediff"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/arb/files/patch-ARB-config.makefile.diff (119366 => 119367)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/arb/files/patch-ARB-config.makefile.diff 2014-04-23 18:24:33 UTC (rev 119366)
+++ trunk/dports/science/arb/files/patch-ARB-config.makefile.diff 2014-04-23 19:52:12 UTC (rev 119367)
</span><span class="lines">@@ -1,15 +1,15 @@
</span><del>---- config.makefile.template.orig 2012-11-17 07:59:37.000000000 -0500
-+++ config.makefile.template 2012-11-17 20:32:26.000000000 -0500
-@@ -20,7 +20,7 @@
- # 2 = compile both, use old (recommended for development only)
- PTPAN := 0
</del><ins>+--- config.makefile.template.orig 2013-10-28 07:53:03.000000000 -0400
++++ config.makefile.template 2013-10-28 15:06:59.000000000 -0400
+@@ -13,7 +13,7 @@
+ TRACESYM := 1# insert symbols for meaningful backtraces into executables
</ins><span class="cx">
</span><del>--ARB_64 := 0# compile 64bit ARB version
-+ARB_64 := @@64BIT@@# compile 64bit ARB version
- #BUILDHOST_64 := 1# whether build host is 64bit (value defaults to ARB_64). Needed for cross-compile
</del><ins>+ # Include features using OPENGL?
+-OPENGL := 1
++OPENGL := 0
</ins><span class="cx">
</span><del>- # --------------------------------------------------------------------------------
-@@ -30,8 +30,8 @@
</del><ins>+ # 0 = use old PTSERVER (recommended)
+ # 1 = use the new PTPan implementation as pt-server (Not tested very well, do NOT use!)
+@@ -34,8 +34,8 @@
</ins><span class="cx"> # ------------
</span><span class="cx"> # Section: Linux
</span><span class="cx">
</span><span class="lines">@@ -20,7 +20,7 @@
</span><span class="cx">
</span><span class="cx"> # DEBIAN := 1 # uncomment for DEBIAN systems
</span><span class="cx"> # REDHAT := 1 # uncomment for REDHAT systems
</span><del>-@@ -39,7 +39,7 @@
</del><ins>+@@ -43,7 +43,7 @@
</ins><span class="cx"> # ------------
</span><span class="cx"> # Section: Mac OSX
</span><span class="cx">
</span></span></pre>
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