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

[76563] trunk/dports/science/arb
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76563 http://trac.macports.org/changeset/76563 Author: ryandesign(a)macports.org Date: 2011-02-28 03:09:01 -0800 (Mon, 28 Feb 2011) Log Message: ----------- arb: find the path to libperl at compile time instead of hardcoding it; see #28276 Modified Paths: -------------- trunk/dports/science/arb/Portfile trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff Modified: trunk/dports/science/arb/Portfile =================================================================== --- trunk/dports/science/arb/Portfile 2011-02-28 09:47:06 UTC (rev 76562) +++ trunk/dports/science/arb/Portfile 2011-02-28 11:09:01 UTC (rev 76563) @@ -72,8 +72,8 @@ ${worksrcpath}/GDEHELP/Makefile.helpfiles file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile file copy ${filespath}/arb_macsetup ${worksrcpath}/bin - reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/PERL2ARB/DARWIN.PL \ - ${worksrcpath}/bin/arb_macsetup + reinplace "s|@@LIBPERLDIR@@|[exec ${prefix}/bin/perl -e "use Config; print \$Config{archlib};"]/CORE|g" ${worksrcpath}/PERL2ARB/DARWIN.PL + reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/bin/arb_macsetup reinplace "s|OSX_SDK:=/Developer/SDKs/MacOSX10.5.sdk|OSX_SDK:=${configure.sdkroot}|g" ${worksrcpath}/Makefile Modified: trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff =================================================================== --- trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff 2011-02-28 09:47:06 UTC (rev 76562) +++ trunk/dports/science/arb/files/patch-ARB-DARWIN.pl.diff 2011-02-28 11:09:01 UTC (rev 76563) @@ -6,7 +6,7 @@ 'VERSION_FROM' => 'ARB.pm', # finds $VERSION - #'LIBS' => '-L../ARBDB2 -lARBDB -L/usr/local/lib/perl5/5.10.0/darwin-2level/CORE/ -lperl', # e.g., '-lm' - 'LIBS' => '-L../ARBDB2 -lARBDB -L/System/Library/Perl/lib/5.10/ -lperl', #System provides 64-bit Perl with Snow Leopard -+ 'LIBS' => '-L../ARBDB2 -lARBDB -L@@PREFIX@@/lib/perl5/5.8.9/darwin-2level/CORE/ -lperl', #MacPorts installs 64-bit perl5.8.9 ++ 'LIBS' => '-L../ARBDB2 -lARBDB -L@@LIBPERLDIR@@ -lperl', 'DEFINE' => '', # e.g., '-DHAVE_SOMETHING' 'INC' => '-I../INCLUDE', # e.g., '-I/usr/include/other' 'CCFLAGS' => '-arch x86_64',

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[76562] trunk/dports/science/arb/Portfile
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76562 http://trac.macports.org/changeset/76562 Author: ryandesign(a)macports.org Date: 2011-02-28 01:47:06 -0800 (Mon, 28 Feb 2011) Log Message: ----------- arb: don't clobber the config file or macros the user might have edited; see #28276 Modified Paths: -------------- trunk/dports/science/arb/Portfile Modified: trunk/dports/science/arb/Portfile =================================================================== --- trunk/dports/science/arb/Portfile 2011-02-28 09:34:43 UTC (rev 76561) +++ trunk/dports/science/arb/Portfile 2011-02-28 09:47:06 UTC (rev 76562) @@ -6,7 +6,7 @@ name arb version 5.1 epoch 1 -revision 1 +revision 2 categories science maintainers me.com:matt.cottrell platforms darwin @@ -94,8 +94,11 @@ CPPreal=${configure.cpp} destroot.keepdirs ${destroot}${prefix}/share/arb/lib/pts +destroot { + # Give the default settings a recognizable name ending in .default + file rename ${worksrcpath}/lib/arb_tcp.dat ${worksrcpath}/lib/arb_tcp.dat.default + file rename ${worksrcpath}/lib/macros ${worksrcpath}/lib/macros.default -destroot { eval xinstall -m 0755 [glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin file mkdir ${destroot}${prefix}/share/arb/bin file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib @@ -105,11 +108,9 @@ file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb - file attributes ${destroot}${prefix}/share/arb/lib/arb_tcp.dat -permissions a+w - file attributes ${destroot}${prefix}/share/arb/lib/pts -permissions a+w - file attributes ${destroot}${prefix}/share/arb/lib/macros -permissions a+w ln -s ${prefix}/bin/arb_pt_server ${destroot}${prefix}/share/arb/bin/arb_pt_server 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 @@ -117,6 +118,20 @@ post-activate { system "rm -rf `find ${prefix}/share/arb -type d -name .svn`" + + # Provide users with copies of the default configuration and macros + # if the user doesn't already have them. + if {![file exists ${prefix}/share/arb/lib/arb_tcp.dat]} { + xinstall -m 777 ${prefix}/share/arb/lib/arb_tcp.dat.default \ + ${prefix}/share/arb/lib/arb_tcp.dat + } + if {![file exists ${prefix}/share/arb/lib/macros]} { + file copy ${prefix}/share/arb/lib/macros.default \ + ${prefix}/share/arb/lib/macros + fs-traverse item ${prefix}/share/arb/lib/macros { + file attributes ${item} -permissions a+w + } + } } notes " @@ -132,7 +147,7 @@ B) Follow the steps below: -1a) +1) bash users add the following lines to your ~/.profile or to your ~/.bashrc ARBHOME=${prefix}/share/arb;export ARBHOME @@ -141,17 +156,31 @@ enter the following command: . ~/.profile -1b) +2) tcsh users add the following lines to your ~/.cshrc + setenv ARBHOME ${prefix}/share/arb setenv PATH ${prefix}/share/arb\:\$PATH enter the following command: source ~/.cshrc -2) +C) type arb to start ARB A demo data base is located at ${prefix}/share/arb/demo.arb +************************************************************************ +User generated macros, arb_tcp.dat and pt_servers have been preserved, +but you should keep backups of these just in case. They are located at: + +${prefix}/share/arb/lib/macros/ +${prefix}/share/arb/lib/arb_tcp.dat +${prefix}/share/arb/lib/pts/ + +Default settings are maintained at: + +${prefix}/share/arb/lib/macros.default/ +${prefix}/share/arb/lib/arb_tcp.dat.default + Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371 "

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[76561] trunk/dports/aqua/osxvnc/
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76561 http://trac.macports.org/changeset/76561 Author: ryandesign(a)macports.org Date: 2011-02-28 01:34:43 -0800 (Mon, 28 Feb 2011) Log Message: ----------- osxvnc: delete; was replaced_by vineserver over a year ago Removed Paths: ------------- trunk/dports/aqua/osxvnc/

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[76560] trunk/dports/audio/libofa
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76560 http://trac.macports.org/changeset/76560 Author: ryandesign(a)macports.org Date: 2011-02-28 01:06:22 -0800 (Mon, 28 Feb 2011) Log Message: ----------- libofa: fix incorrect runtime results; see #28201 Modified Paths: -------------- trunk/dports/audio/libofa/Portfile trunk/dports/audio/libofa/files/patch-mathutils Modified: trunk/dports/audio/libofa/Portfile =================================================================== --- trunk/dports/audio/libofa/Portfile 2011-02-28 06:51:40 UTC (rev 76559) +++ trunk/dports/audio/libofa/Portfile 2011-02-28 09:06:22 UTC (rev 76560) @@ -4,6 +4,7 @@ name libofa version 0.9.3 +revision 1 categories audio platforms darwin maintainers nomaintainer Modified: trunk/dports/audio/libofa/files/patch-mathutils =================================================================== --- trunk/dports/audio/libofa/files/patch-mathutils 2011-02-28 06:51:40 UTC (rev 76559) +++ trunk/dports/audio/libofa/files/patch-mathutils 2011-02-28 09:06:22 UTC (rev 76560) @@ -1,13 +1,10 @@ ---- lib/JAMA/tnt_math_utils.h~ 2010-01-05 20:41:48.000000000 -0800 -+++ lib/JAMA/tnt_math_utils.h 2010-01-05 19:47:22.000000000 -0800 -@@ -30,7 +30,10 @@ +--- lib/JAMA/tnt_math_utils.h~ 2006-05-10 13:58:50.000000000 -0400 ++++ lib/JAMA/tnt_math_utils.h 2011-01-29 22:34:16.000000000 -0500 +@@ -19,6 +19,7 @@ + + namespace TNT { - - if (a== 0) -+ { -+ using __gnu_cxx::abs; - return abs(b); -+ } - else - { - Real c = b/a; ++template <class Real> Real abs(const Real &a); + /** + @returns hypotenuse of real (non-complex) scalars a and b by + avoiding underflow/overflow

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[76559] trunk/dports/www/apache20
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76559 http://trac.macports.org/changeset/76559 Author: ryandesign(a)macports.org Date: 2011-02-27 22:51:40 -0800 (Sun, 27 Feb 2011) Log Message: ----------- apache20: fix build with openssl 1.0.0; see #25621 Modified Paths: -------------- trunk/dports/www/apache20/Portfile Added Paths: ----------- trunk/dports/www/apache20/files/patch-openssl-1.0.0.diff Modified: trunk/dports/www/apache20/Portfile =================================================================== --- trunk/dports/www/apache20/Portfile 2011-02-28 06:46:30 UTC (rev 76558) +++ trunk/dports/www/apache20/Portfile 2011-02-28 06:51:40 UTC (rev 76559) @@ -68,7 +68,8 @@ port:openssl \ port:pcre -patchfiles patch-httpd-std.conf.in +patchfiles patch-httpd-std.conf.in \ + patch-openssl-1.0.0.diff platform darwin { post-patch { Added: trunk/dports/www/apache20/files/patch-openssl-1.0.0.diff =================================================================== --- trunk/dports/www/apache20/files/patch-openssl-1.0.0.diff (rev 0) +++ trunk/dports/www/apache20/files/patch-openssl-1.0.0.diff 2011-02-28 06:51:40 UTC (rev 76559) @@ -0,0 +1,40 @@ +--- modules/ssl/ssl_engine_init.c.orig 2007-12-29 00:07:53.000000000 +0900 ++++ modules/ssl/ssl_engine_init.c 2010-05-01 22:17:22.000000000 +0900 +@@ -531,7 +531,7 @@ + ssl_die(); + } + +- SSL_CTX_set_client_CA_list(ctx, (STACK *)ca_list); ++ SSL_CTX_set_client_CA_list(ctx, ca_list); + } + + /* +--- modules/ssl/ssl_util_ssl.c.orig 2006-07-12 16:40:55.000000000 +0900 ++++ modules/ssl/ssl_util_ssl.c 2010-05-01 22:20:18.000000000 +0900 +@@ -291,7 +291,7 @@ + #ifdef HAVE_SSL_X509V3_EXT_d2i + X509_EXTENSION *ext; + int ext_nid; +- STACK *sk; ++ STACK_OF(SSL_CIPHER) *sk; + BOOL is_sgc; + int idx; + int i; +@@ -300,7 +300,7 @@ + idx = X509_get_ext_by_NID(cert, NID_ext_key_usage, -1); + if (idx >= 0) { + ext = X509_get_ext(cert, idx); +- if ((sk = (STACK *)X509V3_EXT_d2i(ext)) != NULL) { ++ if ((sk = X509V3_EXT_d2i(ext)) != NULL) { + for (i = 0; i < sk_num(sk); i++) { + ext_nid = OBJ_obj2nid((ASN1_OBJECT *)sk_value(sk, i)); + if (ext_nid == NID_ms_sgc || ext_nid == NID_ns_sgc) { +@@ -466,7 +466,7 @@ + X509 *x509; + unsigned long err; + int n; +- STACK *extra_certs; ++ STACK_OF(X509) *extra_certs; + + if ((bio = BIO_new(BIO_s_file_internal())) == NULL) + return -1;

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[76558] trunk/dports/gnome/gnome-common/Portfile
by jmr＠macports.org 28 Feb '11

28 Feb '11

Revision: 76558 http://trac.macports.org/changeset/76558 Author: jmr(a)macports.org Date: 2011-02-27 22:46:30 -0800 (Sun, 27 Feb 2011) Log Message: ----------- gnome-common: license Modified Paths: -------------- trunk/dports/gnome/gnome-common/Portfile Modified: trunk/dports/gnome/gnome-common/Portfile =================================================================== --- trunk/dports/gnome/gnome-common/Portfile 2011-02-28 06:34:19 UTC (rev 76557) +++ trunk/dports/gnome/gnome-common/Portfile 2011-02-28 06:46:30 UTC (rev 76558) @@ -9,6 +9,7 @@ maintainers nomaintainer categories gnome platforms darwin +license GPL-3 supported_archs noarch description Files that should be in pretty much every GNOME application.

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[76557] trunk/dports/textproc/docbook-xml-5.0/Portfile
by jmr＠macports.org 28 Feb '11

28 Feb '11

Revision: 76557 http://trac.macports.org/changeset/76557 Author: jmr(a)macports.org Date: 2011-02-27 22:34:19 -0800 (Sun, 27 Feb 2011) Log Message: ----------- docbook-xml-5.0: license Modified Paths: -------------- trunk/dports/textproc/docbook-xml-5.0/Portfile Modified: trunk/dports/textproc/docbook-xml-5.0/Portfile =================================================================== --- trunk/dports/textproc/docbook-xml-5.0/Portfile 2011-02-28 05:40:35 UTC (rev 76556) +++ trunk/dports/textproc/docbook-xml-5.0/Portfile 2011-02-28 06:34:19 UTC (rev 76557) @@ -7,6 +7,7 @@ version [lindex [split $name -] 2] categories textproc platforms darwin +license MIT maintainers nomaintainer supported_archs noarch description Version $version of the DocBook XML DTDs

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[76556] trunk/dports/textproc/docbook-xml/Portfile
by jmr＠macports.org 28 Feb '11

28 Feb '11

Revision: 76556 http://trac.macports.org/changeset/76556 Author: jmr(a)macports.org Date: 2011-02-27 21:40:35 -0800 (Sun, 27 Feb 2011) Log Message: ----------- docbook-xml: license Modified Paths: -------------- trunk/dports/textproc/docbook-xml/Portfile Modified: trunk/dports/textproc/docbook-xml/Portfile =================================================================== --- trunk/dports/textproc/docbook-xml/Portfile 2011-02-28 05:37:44 UTC (rev 76555) +++ trunk/dports/textproc/docbook-xml/Portfile 2011-02-28 05:40:35 UTC (rev 76556) @@ -8,6 +8,7 @@ version 5.0 categories textproc platforms darwin +license BSD maintainers nomaintainer supported_archs noarch description Install all of the versioned docbook-xml-* ports

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[76555] trunk/dports/devel/physfs
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76555 http://trac.macports.org/changeset/76555 Author: ryandesign(a)macports.org Date: 2011-02-27 21:37:44 -0800 (Sun, 27 Feb 2011) Log Message: ----------- physfs: update to 2.0.2; add readline dependency; new maintainer (#28566) Modified Paths: -------------- trunk/dports/devel/physfs/Portfile Removed Paths: ------------- trunk/dports/devel/physfs/files/ Modified: trunk/dports/devel/physfs/Portfile =================================================================== --- trunk/dports/devel/physfs/Portfile 2011-02-28 05:34:01 UTC (rev 76554) +++ trunk/dports/devel/physfs/Portfile 2011-02-28 05:37:44 UTC (rev 76555) @@ -5,9 +5,9 @@ PortGroup cmake 1.0 name physfs -version 2.0.1 +version 2.0.2 categories devel -maintainers nomaintainer +maintainers users.sourceforge.net:luiji platforms darwin description PhysicsFS is a library providing abstract archive access @@ -20,15 +20,11 @@ homepage http://icculus.org/physfs/ master_sites ${homepage}downloads/ -checksums md5 df00465fcfa80e87f718961c6dd6b928 \ - sha1 1e291e8717ce3bb921b74416ec7cbcf212efcaa1 \ - rmd160 b6f9b839e2d6fa8b01077daae2386a44f541df99 +checksums sha1 2d3d3cc819ad26542d34451f44050b85635344d0 \ + rmd160 9e45775c353e7b6fe0510d55063af9ddf1b7f678 -depends_lib port:zlib +depends_lib port:zlib port:readline -patch.pre_args -p2 -patchfiles f254870dd7dd.diff - configure.args-append -DPHYSFS_BUILD_WX_TEST=FALSE livecheck.type regex

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[76554] trunk/dports/www/apache2
by ryandesign＠macports.org 28 Feb '11

28 Feb '11

Revision: 76554 http://trac.macports.org/changeset/76554 Author: ryandesign(a)macports.org Date: 2011-02-27 21:34:01 -0800 (Sun, 27 Feb 2011) Log Message: ----------- apache2: add perl dependency, since apxs, dbmmanage and now printenv use it; see #28564 Modified Paths: -------------- trunk/dports/www/apache2/Portfile Added Paths: ----------- trunk/dports/www/apache2/files/patch-docs-cgi-examples-printenv.diff Modified: trunk/dports/www/apache2/Portfile =================================================================== --- trunk/dports/www/apache2/Portfile 2011-02-28 04:25:22 UTC (rev 76553) +++ trunk/dports/www/apache2/Portfile 2011-02-28 05:34:01 UTC (rev 76554) @@ -5,6 +5,7 @@ name apache2 version 2.2.17 +revision 1 categories www maintainers nomaintainer description The extremely popular second version of the Apache http server @@ -29,12 +30,16 @@ port:apr-util \ port:expat \ port:openssl \ - port:pcre + port:pcre \ + port:perl5 # Both apache and apache2 want to install dbmmanage.1 and other manpages. conflicts apache +patchfiles patch-docs-cgi-examples-printenv.diff + post-patch { + reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/docs/cgi-examples/printenv reinplace -E "s/(User|Group) daemon/\\1 www/" ${worksrcpath}/docs/conf/httpd.conf.in } Added: trunk/dports/www/apache2/files/patch-docs-cgi-examples-printenv.diff =================================================================== --- trunk/dports/www/apache2/files/patch-docs-cgi-examples-printenv.diff (rev 0) +++ trunk/dports/www/apache2/files/patch-docs-cgi-examples-printenv.diff 2011-02-28 05:34:01 UTC (rev 76554) @@ -0,0 +1,8 @@ +--- docs/cgi-examples/printenv.orig 2004-12-10 23:52:29.000000000 -0600 ++++ docs/cgi-examples/printenv 2011-02-27 23:12:32.000000000 -0600 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!@PREFIX@/bin/perl + ## + ## printenv -- demo CGI program which just prints its environment + ##

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