February 2011 - macports-changes - lists.macosforge.org

[76348] trunk/dports/science/pymol-devel/Portfile
by adfernandes＠macports.org 20 Feb '11

20 Feb '11

Revision: 76348 http://trac.macports.org/changeset/76348 Author: adfernandes(a)macports.org Date: 2011-02-20 08:12:01 -0800 (Sun, 20 Feb 2011) Log Message: ----------- science/pymol-devel ; trivial version bump to latest svn Modified Paths: -------------- trunk/dports/science/pymol-devel/Portfile Modified: trunk/dports/science/pymol-devel/Portfile =================================================================== --- trunk/dports/science/pymol-devel/Portfile 2011-02-20 13:53:24 UTC (rev 76347) +++ trunk/dports/science/pymol-devel/Portfile 2011-02-20 16:12:01 UTC (rev 76348) @@ -4,7 +4,7 @@ PortSystem 1.0 name pymol-devel -svn.revision 3928 +svn.revision 3937 version 1.3.${svn.revision} revision 1 conflicts pymol

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[76347] trunk/dports/math/atlas
by vince＠macports.org 20 Feb '11

20 Feb '11

Revision: 76347 http://trac.macports.org/changeset/76347 Author: vince(a)macports.org Date: 2011-02-20 05:53:24 -0800 (Sun, 20 Feb 2011) Log Message: ----------- Bump to 3.9.35. Modified Paths: -------------- trunk/dports/math/atlas/Portfile Added Paths: ----------- trunk/dports/math/atlas/files/patch-ATL_FreeAtomicCount_mut_c.diff Modified: trunk/dports/math/atlas/Portfile =================================================================== --- trunk/dports/math/atlas/Portfile 2011-02-20 12:34:39 UTC (rev 76346) +++ trunk/dports/math/atlas/Portfile 2011-02-20 13:53:24 UTC (rev 76347) @@ -5,7 +5,7 @@ categories math name atlas -version 3.9.33 +version 3.9.35 #revision 4 # additional versions @@ -30,12 +30,12 @@ distfiles ${atlasdist}:atlas \ ${lapackdist}:lapack -patchfiles patch-SpewMakeInc.c.diff +patchfiles patch-SpewMakeInc.c.diff \ + patch-ATL_FreeAtomicCount_mut_c.diff -checksums atlas3.9.33.tar.bz2 \ - md5 8f518f386b69bdfd1f5061704aa196f9 \ - sha1 8dbc6015318458ff7abd178964d90350a18ce9fa \ - rmd160 810033a9f81c11994a5221dc268e3da84e2367d7 \ +checksums atlas3.9.35.tar.bz2 \ + sha1 24fbcfb32fadd226f7c7ec262cbc979deeb9e883 \ + rmd160 59a5ff1a2065744db99111a43751b18cd411a423 \ lapack-3.3.0.tgz \ md5 84213fca70936cc5f1b59a7b1bf71697 \ sha1 4f0b103da52110e7f60d1d7676727103aca9785e \ Added: trunk/dports/math/atlas/files/patch-ATL_FreeAtomicCount_mut_c.diff =================================================================== --- trunk/dports/math/atlas/files/patch-ATL_FreeAtomicCount_mut_c.diff (rev 0) +++ trunk/dports/math/atlas/files/patch-ATL_FreeAtomicCount_mut_c.diff 2011-02-20 13:53:24 UTC (rev 76347) @@ -0,0 +1,9 @@ +--- src/threads/ATL_FreeAtomicCount_mut.c.orig 2011-02-09 05:04:03.000000000 +0100 ++++ src/threads/ATL_FreeAtomicCount_mut.c 2011-02-20 09:31:49.000000000 +0100 +@@ -1,5 +1,6 @@ + #include <stdlib.h> + #include <pthread.h> ++#include "atlas_misc.h" + void ATL_FreeAtomicCount(void *vp) + { + char *cp=vp;

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[76346] trunk/dports/science/smodels/Portfile
by snc＠macports.org 20 Feb '11

20 Feb '11

Revision: 76346 http://trac.macports.org/changeset/76346 Author: snc(a)macports.org Date: 2011-02-20 04:34:39 -0800 (Sun, 20 Feb 2011) Log Message: ----------- smodels: * check configurepipe * check build_arch Modified Paths: -------------- trunk/dports/science/smodels/Portfile Modified: trunk/dports/science/smodels/Portfile =================================================================== --- trunk/dports/science/smodels/Portfile 2011-02-20 11:47:46 UTC (rev 76345) +++ trunk/dports/science/smodels/Portfile 2011-02-20 12:34:39 UTC (rev 76346) @@ -25,6 +25,10 @@ rmd160 032b9063635a1025dbe3528a7a803a7f2ccef9e0 configure.optflags -O3 +if {[string match ${configurepipe} yes]} { + configure.cxxflags-append -pipes +} +configure.cxxflags-append -arch ${build_arch} patch { reinplace s|/usr/bin|${prefix}/bin|g ${worksrcpath}/Makefile reinplace s|/usr/local/lib|${prefix}/lib|g ${worksrcpath}/Makefile

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[76345] trunk/dports/science/smodels/Portfile
by snc＠macports.org 20 Feb '11

20 Feb '11

Revision: 76345 http://trac.macports.org/changeset/76345 Author: snc(a)macports.org Date: 2011-02-20 03:47:46 -0800 (Sun, 20 Feb 2011) Log Message: ----------- smodels: remove unintentional override of CXX Modified Paths: -------------- trunk/dports/science/smodels/Portfile Modified: trunk/dports/science/smodels/Portfile =================================================================== --- trunk/dports/science/smodels/Portfile 2011-02-20 11:29:44 UTC (rev 76344) +++ trunk/dports/science/smodels/Portfile 2011-02-20 11:47:46 UTC (rev 76345) @@ -24,7 +24,6 @@ checksums sha1 cf3dd5a517afabaa858ccd63ff3e8b38e322f5eb \ rmd160 032b9063635a1025dbe3528a7a803a7f2ccef9e0 -configure.cxx /usr/bin/g++-4.2 configure.optflags -O3 patch { reinplace s|/usr/bin|${prefix}/bin|g ${worksrcpath}/Makefile

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[76344] trunk/dports/archivers/pbzip2/Portfile
by ram＠macports.org 20 Feb '11

20 Feb '11

Revision: 76344 http://trac.macports.org/changeset/76344 Author: ram(a)macports.org Date: 2011-02-20 03:29:44 -0800 (Sun, 20 Feb 2011) Log Message: ----------- archivers/pbzip2: update to 1.1.2 Modified Paths: -------------- trunk/dports/archivers/pbzip2/Portfile Modified: trunk/dports/archivers/pbzip2/Portfile =================================================================== --- trunk/dports/archivers/pbzip2/Portfile 2011-02-20 11:28:05 UTC (rev 76343) +++ trunk/dports/archivers/pbzip2/Portfile 2011-02-20 11:29:44 UTC (rev 76344) @@ -3,7 +3,7 @@ PortSystem 1.0 name pbzip2 -version 1.1.1 +version 1.1.2 categories archivers platforms darwin maintainers ram openmaintainer @@ -18,9 +18,9 @@ depends_lib port:bzip2 -checksums md5 b354422759da7113da366aad1876ed5d \ - sha1 605e2cc1596b540358d650bf3ab647ad9152f233 \ - rmd160 ad1755174cdaa7b172f1e0da674f93256d5acaf6 +checksums md5 1661d49b4aa37729ef5dde088fcf7bea \ + sha1 14322cddb34ba093bcb93b8052e48e7bef35bc9a \ + rmd160 7a6518cd4bc7a974ad381336505e22ac9771b850 set CFLAGS "${configure.ldflags} ${configure.cppflags}"

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[76343] trunk/dports/science/arb/Portfile
by ryandesign＠macports.org 20 Feb '11

20 Feb '11

Revision: 76343 http://trac.macports.org/changeset/76343 Author: ryandesign(a)macports.org Date: 2011-02-20 03:28:05 -0800 (Sun, 20 Feb 2011) Log Message: ----------- arb: fix typo in notes Modified Paths: -------------- trunk/dports/science/arb/Portfile Modified: trunk/dports/science/arb/Portfile =================================================================== --- trunk/dports/science/arb/Portfile 2011-02-20 11:27:21 UTC (rev 76342) +++ trunk/dports/science/arb/Portfile 2011-02-20 11:28:05 UTC (rev 76343) @@ -148,7 +148,7 @@ 2) type arb to start ARB -A demo data base is located at ${prefix}/share/arb.demo.arb +A demo data base is located at ${prefix}/share/arb/demo.arb Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371 "

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[76342] trunk/dports/science/smodels/Portfile
by snc＠macports.org 20 Feb '11

20 Feb '11

Revision: 76342 http://trac.macports.org/changeset/76342 Author: snc(a)macports.org Date: 2011-02-20 03:27:21 -0800 (Sun, 20 Feb 2011) Log Message: ----------- smodels: UsingTheRightCompiler Modified Paths: -------------- trunk/dports/science/smodels/Portfile Modified: trunk/dports/science/smodels/Portfile =================================================================== --- trunk/dports/science/smodels/Portfile 2011-02-20 11:23:53 UTC (rev 76341) +++ trunk/dports/science/smodels/Portfile 2011-02-20 11:27:21 UTC (rev 76342) @@ -24,11 +24,13 @@ checksums sha1 cf3dd5a517afabaa858ccd63ff3e8b38e322f5eb \ rmd160 032b9063635a1025dbe3528a7a803a7f2ccef9e0 +configure.cxx /usr/bin/g++-4.2 configure.optflags -O3 patch { reinplace s|/usr/bin|${prefix}/bin|g ${worksrcpath}/Makefile reinplace s|/usr/local/lib|${prefix}/lib|g ${worksrcpath}/Makefile reinplace "s|-O3 -Wall -W|${configure.cxxflags}|g" ${worksrcpath}/Makefile + reinplace s|g\+\+|${configure.cxx}|g ${worksrcpath}/Makefile } use_configure no

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[76341] trunk/dports/lang/php5-devel/Portfile
by jwa＠macports.org 20 Feb '11

20 Feb '11

Revision: 76341 http://trac.macports.org/changeset/76341 Author: jwa(a)macports.org Date: 2011-02-20 03:23:53 -0800 (Sun, 20 Feb 2011) Log Message: ----------- added license PHP 3.01 Modified Paths: -------------- trunk/dports/lang/php5-devel/Portfile Modified: trunk/dports/lang/php5-devel/Portfile =================================================================== --- trunk/dports/lang/php5-devel/Portfile 2011-02-20 11:18:35 UTC (rev 76340) +++ trunk/dports/lang/php5-devel/Portfile 2011-02-20 11:23:53 UTC (rev 76341) @@ -16,6 +16,7 @@ distname php-${version} use_bzip2 yes platforms darwin freebsd +license PHP-3.01 use_parallel_build yes description \

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[76340] trunk/dports/science/arb
by ryandesign＠macports.org 20 Feb '11

20 Feb '11

Revision: 76340 http://trac.macports.org/changeset/76340 Author: ryandesign(a)macports.org Date: 2011-02-20 03:18:35 -0800 (Sun, 20 Feb 2011) Log Message: ----------- arb: fix runtime failure with libpng 1.4, and ensure we always use X11 parts from ${prefix}; see #28276 Modified Paths: -------------- trunk/dports/science/arb/Portfile trunk/dports/science/arb/files/patch-ARB-makefile.diff Modified: trunk/dports/science/arb/Portfile =================================================================== --- trunk/dports/science/arb/Portfile 2011-02-20 11:08:49 UTC (rev 76339) +++ trunk/dports/science/arb/Portfile 2011-02-20 11:18:35 UTC (rev 76340) @@ -6,6 +6,7 @@ name arb version 5.1 epoch 1 +revision 1 categories science maintainers me.com:matt.cottrell platforms darwin Modified: trunk/dports/science/arb/files/patch-ARB-makefile.diff =================================================================== --- trunk/dports/science/arb/files/patch-ARB-makefile.diff 2011-02-20 11:08:49 UTC (rev 76339) +++ trunk/dports/science/arb/files/patch-ARB-makefile.diff 2011-02-20 11:18:35 UTC (rev 76340) @@ -1,20 +1,41 @@ ---- Makefile (revision 6192) +Index: Makefile +=================================================================== +--- Makefile (revision 6215) +++ Makefile (working copy) -@@ -202,11 +202,11 @@ +@@ -31,11 +31,12 @@ + # configurable in config.makefile + # + # ----------------------------------------------------- ++ + # Read configuration + include config.makefile + + ifeq ($(LD_LIBRARY_PATH),'') +-LD_LIBRARY_PATH:=${ARBHOME}/lib ++ LD_LIBRARY_PATH:=${ARBHOME}/lib + endif + + FORCEMASK = umask 002 +@@ -198,15 +197,15 @@ + + #---------------------- X11 location + +-XHOME:=/usr/X11R6 ++XHOME:=$(PREFIX) XINCLUDES:=-I$(XHOME)/include ifdef DARWIN - XINCLUDES := -I/sw/include -I$(OSX_SDK)/usr/X11/include -I$(OSX_SDK)/usr/include/krb5 -I/usr/OpenMotif/include #Snow Leopard couldn't find OpenMotif -+ XINCLUDES := -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/X11/include -I$(OSX_SDK)/usr/include/krb5 -I$(OSX_FW)/GLUT.framework/Headers -I$(PREFIX)/include ++ XINCLUDES += -I$(OSX_FW)/OpenGL.framework/Headers -I$(OSX_SDK)/usr/include/krb5 -I$(OSX_FW)/GLUT.framework/Headers endif ifdef DARWIN - XLIBS := -L/usr/OpenMotif/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi -+ XLIBS := -L$(PREFIX)/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi ++ XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi XLIBS += -lGLU -lGL -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib else XLIBS:=-L$(XHOME)/$(CROSS_LIB) -lXm -lXpm -lXp -lXt -lXext -lX11 -@@ -225,14 +225,9 @@ +@@ -225,14 +224,9 @@ GL_PNGLIBS := -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng @@ -32,7 +53,7 @@ GL_LIBS := $(GL_LIB) $(GLEWLIB) $(GLUTLIB) $(GL_PNGLIBS) #XLIBS += $(GL_LIB) -@@ -247,11 +242,7 @@ +@@ -247,11 +241,7 @@ #---------------------- tiff lib: @@ -45,12 +66,16 @@ #---------------------- basic libs: -@@ -318,7 +309,7 @@ +@@ -317,11 +307,7 @@ + # other used tools CTAGS := etags - ifdef DARWIN +-ifdef DARWIN - XMKMF := /usr/X11/bin/xmkmf -+ XMKMF := $(PREFIX)/bin/xmkmf - else - XMKMF := /usr/bin/X11/xmkmf - endif \ No newline at end of file +-else +- XMKMF := /usr/bin/X11/xmkmf +-endif ++XMKMF := $(PREFIX)/bin/xmkmf + MAKEDEPEND_PLAIN = makedepend + + MAKEDEPEND = $(FORCEMASK);$(MAKEDEPEND_PLAIN)

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[76339] trunk/dports/science/smodels/Portfile
by snc＠macports.org 20 Feb '11

20 Feb '11

Revision: 76339 http://trac.macports.org/changeset/76339 Author: snc(a)macports.org Date: 2011-02-20 03:08:49 -0800 (Sun, 20 Feb 2011) Log Message: ----------- smodels: * don't hardcode /opt/local * add livecheck Modified Paths: -------------- trunk/dports/science/smodels/Portfile Modified: trunk/dports/science/smodels/Portfile =================================================================== --- trunk/dports/science/smodels/Portfile 2011-02-20 11:05:32 UTC (rev 76338) +++ trunk/dports/science/smodels/Portfile 2011-02-20 11:08:49 UTC (rev 76339) @@ -26,11 +26,15 @@ configure.optflags -O3 patch { - reinplace s|/usr/bin|/opt/local/bin|g ${worksrcpath}/Makefile - reinplace s|/usr/local/lib|/opt/local/lib|g ${worksrcpath}/Makefile + reinplace s|/usr/bin|${prefix}/bin|g ${worksrcpath}/Makefile + reinplace s|/usr/local/lib|${prefix}/lib|g ${worksrcpath}/Makefile reinplace "s|-O3 -Wall -W|${configure.cxxflags}|g" ${worksrcpath}/Makefile } use_configure no notes "lparse is recommended for piping to smodels: `lparse | smodels`" + +livecheck.type regex +livecheck.url ${homepage} +livecheck.regex ${name}-(\\d+(\\.\\d+)+)

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