[119367] trunk/dports/science/arb
mf2k at macports.org
mf2k at macports.org
Wed Apr 23 12:52:12 PDT 2014
Revision: 119367
https://trac.macports.org/changeset/119367
Author: mf2k at macports.org
Date: 2014-04-23 12:52:12 -0700 (Wed, 23 Apr 2014)
Log Message:
-----------
arb: Update to version 6.0-rc1. Mavericks build fix. (#43339)
Modified Paths:
--------------
trunk/dports/science/arb/Portfile
trunk/dports/science/arb/files/patch-ARB-config.makefile.diff
Added Paths:
-----------
trunk/dports/science/arb/files/patch-ARB-ARBDB.diff
trunk/dports/science/arb/files/patch-ARB-arb.diff
Modified: trunk/dports/science/arb/Portfile
===================================================================
--- 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)
@@ -5,8 +5,7 @@
name arb
epoch 1
-version 5.5
-revision 2
+version 6.0-rc1
categories science
maintainers mac.com:matt.cottrell
platforms darwin
@@ -24,14 +23,15 @@
(http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment \
for sequence data. Nucleic Acids Research. 32:1363-1371.
-master_sites http://download.arb-home.de/release/arb_${version}/
-distname arbsrc
+license Restrictive/Distributable
+
+master_sites http://download.arb-home.de/build/$name-${version}/
+distname arb-${version}-source-hotfix1
extract.suffix .tgz
-dist_subdir ${name}/${version}
-worksrcdir arbsrc_9167
+worksrcdir arbsrc_11977
-checksums rmd160 f8b7b12cd9259b1b0f7cbbc29aca4f85585e8b9f \
- sha256 25246355ccaebff2e3350a553732636896f0f9f21eca3bb2bcf75cbeb7ac92a9
+checksums rmd160 9ef6edf8e2e386794cfc204519bb00f4394549ee \
+ sha256 cb9bcbd999d6f8b3c06bde70a1d1e5a61ca564e80c16da4bb01bb7820f396e10
depends_build port:imake \
port:makedepend
@@ -45,14 +45,16 @@
port:xfig \
port:gv \
port:xorg-libXaw \
- port:gtime
+ port:gtime \
+ path:lib/pkgconfig/glib-2.0.pc:glib2 \
+ port:coreutils
+
+
patchfiles patch-ARB-config.makefile.diff \
patch-ARB-intro.fig.diff \
- patch-ARB-glpng.h.diff \
- patch-ARB-glpng.c.diff \
- patch-ARB-RNA3D_Textures.cxx.diff \
- patch-ARB-Makefile.diff
+ patch-ARB-arb.diff \
+ patch-ARB-ARBDB.diff
configure {
if {${build_arch} eq "ppc" || ${build_arch} eq "i386"} {
@@ -63,43 +65,15 @@
file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile
- 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 \
- ${worksrcpath}/GDEHELP/Makefile.helpfiles
+ reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/SH/arb_macsetup
}
build.env-append PREFIX=${prefix} \
ARBHOME=${worksrcpath} \
PATH=${worksrcpath}/bin:$env(PATH)
-# https://trac.macports.org/ticket/33756
-compiler.blacklist *clang*
-
-platform darwin {
- if {${os.major} >= 13} {
- depends_lib
- depends_run
- pre-fetch {
- ui_error "$name does not build on Mavericks or later."
- error "unsupported platform"
- }
- }
-}
-
+compiler.blacklist *llvm-gcc-4.2
+
build.args GCC=${configure.cc} \
GPP=${configure.cxx}
@@ -126,7 +100,6 @@
ln -s ${prefix}/bin/arb_name_server ${destroot}${prefix}/share/arb/bin/arb_name_server
xinstall -m 777 -d ${destroot}${prefix}/share/arb/lib/pts
-
}
# to be investigated later
@@ -223,5 +196,5 @@
"
livecheck.type regex
-livecheck.url http://download.arb-home.de/release/
-livecheck.regex ${name}_(\[0-9.\]+)/
+livecheck.url http://download.arb-home.de/build/
+livecheck.regex ${name}-(\[0-9.\]+)-rc1-source/${extract.suffix}
Added: trunk/dports/science/arb/files/patch-ARB-ARBDB.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-ARBDB.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-ARBDB.diff 2014-04-23 19:52:12 UTC (rev 119367)
@@ -0,0 +1,20 @@
+Index: ARBDB/arbdb.cxx
+===================================================================
+--- ARBDB/arbdb.cxx (revision 11958)
++++ ARBDB/arbdb.cxx (working copy)
+@@ -447,6 +447,7 @@
+ return inside_shell;
+ }
+
++#if 0
+ struct GB_test_shell_closed {
+ ~GB_test_shell_closed() {
+ if (GB_shell::in_shell()) { // leave that call
+@@ -455,6 +456,7 @@
+ }
+ };
+ static GB_test_shell_closed test;
++#endif
+
+ #if defined(UNIT_TESTS)
+ static bool closed_open_shell_for_unit_tests() {
Added: trunk/dports/science/arb/files/patch-ARB-arb.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-arb.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-arb.diff 2014-04-23 19:52:12 UTC (rev 119367)
@@ -0,0 +1,11 @@
+--- SH/arb.orig 2013-03-02 09:47:45.000000000 -0500
++++ SH/arb 2013-03-02 14:09:54.000000000 -0500
+@@ -62,7 +62,7 @@
+ esac
+
+ # use ARBHOME defined by location of script (comment out for old behavior)
+-ARBHOME=$ARBHOME_OF_SCRIPT
++#ARBHOME=$ARBHOME_OF_SCRIPT
+
+ echo "Using ARBHOME='$ARBHOME'"
+
Modified: trunk/dports/science/arb/files/patch-ARB-config.makefile.diff
===================================================================
--- 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)
@@ -1,15 +1,15 @@
---- 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
+--- 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
--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
+ # Include features using OPENGL?
+-OPENGL := 1
++OPENGL := 0
- # --------------------------------------------------------------------------------
-@@ -30,8 +30,8 @@
+ # 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 @@
# ------------
# Section: Linux
@@ -20,7 +20,7 @@
# DEBIAN := 1 # uncomment for DEBIAN systems
# REDHAT := 1 # uncomment for REDHAT systems
-@@ -39,7 +39,7 @@
+@@ -43,7 +43,7 @@
# ------------
# Section: Mac OSX
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