[99842] trunk/dports/science/arb
ryandesign at macports.org
ryandesign at macports.org
Sun Nov 18 21:01:58 PST 2012
Revision: 99842
https://trac.macports.org/changeset/99842
Author: ryandesign at macports.org
Date: 2012-11-18 21:01:58 -0800 (Sun, 18 Nov 2012)
Log Message:
-----------
arb: maintainer update to 5.5 (#37043)
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-RNA3D_Textures.cxx.diff
trunk/dports/science/arb/files/patch-ARB-glpng.c.diff
trunk/dports/science/arb/files/patch-ARB-glpng.h.diff
Modified: trunk/dports/science/arb/Portfile
===================================================================
--- trunk/dports/science/arb/Portfile 2012-11-19 04:36:51 UTC (rev 99841)
+++ trunk/dports/science/arb/Portfile 2012-11-19 05:01:58 UTC (rev 99842)
@@ -5,10 +5,9 @@
name arb
epoch 1
-version 5.3
-revision 7
+version 5.5
categories science
-maintainers mac.com:matt.cottrell
+maintainers mac.com:matt.cottrell
platforms darwin
description ARB graphical DNA, RNA and amino acid sequence analysis tool
@@ -28,10 +27,10 @@
distname arbsrc
extract.suffix .tgz
dist_subdir ${name}/${version}
-worksrcdir arbsrc_8210
+worksrcdir arbsrc_9167
-checksums sha1 535b72bfbf99f498deee17824c1f167228ad2088 \
- rmd160 d4b240da693f903d0e8bd59f4b1f1043b6935508
+checksums rmd160 f8b7b12cd9259b1b0f7cbbc29aca4f85585e8b9f \
+ sha256 25246355ccaebff2e3350a553732636896f0f9f21eca3bb2bcf75cbeb7ac92a9
depends_build port:imake \
port:makedepend
@@ -44,22 +43,33 @@
port:glew \
port:xfig \
port:gv \
- port:xorg-libXaw
+ port:xorg-libXaw \
+ port:gtime
patchfiles patch-ARB-config.makefile.diff \
- patch-ARB-makefile.diff \
- patch-ARB-RNA3D_GlobalHeader.hxx.diff \
- patch-ARB-DARWIN.pl.diff \
patch-ARB-intro.fig.diff \
- patch-GDEHELP-Makefile.diff
-
+ patch-ARB-glpng.h.diff \
+ patch-ARB-glpng.c.diff \
+ patch-ARB-RNA3D_Textures.cxx.diff
+
configure {
+ if {${build_arch} == "ppc" || ${build_arch} == "i386"} {
+ set is64bit 0
+ } else {
+ set is64bit 1
+ }
+
+ 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/GDEmenus \
${worksrcpath}/GDEHELP/genhelp.sh \
${worksrcpath}/GDEHELP/genhelptree.sh \
${worksrcpath}/SOURCE_TOOLS/make_java_dependencies.sh \
@@ -67,50 +77,43 @@
${worksrcpath}/AISC_COM/AISC/Makefile \
${worksrcpath}/GDEHELP/Makefile \
${worksrcpath}/HELP_SOURCE/genhelp/Makefile \
- ${worksrcpath}/GDEHELP/Makefile.helpfiles
- file copy ${worksrcpath}/config.makefile.template ${worksrcpath}/config.makefile
- file copy ${filespath}/arb_macsetup ${worksrcpath}/bin
- reinplace "s|@@LIBPERLDIR@@|[exec ${prefix}/bin/perl -e "use Config; print \$Config{archlib};"]/CORE|g" ${worksrcpath}/PERL2ARB/DARWIN.PL
- reinplace "s|@@PREFIX@@|${prefix}|g" ${worksrcpath}/bin/arb_macsetup
-
- if {${build_arch} == "ppc" || ${build_arch} == "i386"} {
- set is64bit 0
- } else {
- set is64bit 1
- }
- reinplace "s|@@64BIT@@|${is64bit}|g" ${worksrcpath}/config.makefile
+ ${worksrcpath}/GDEHELP/Makefile.helpfiles \
}
build.env-append PREFIX=${prefix} \
ARBHOME=${worksrcpath} \
- PATH=${worksrcpath}/bin:$env(PATH)
+ PATH=${worksrcpath}/bin:${prefix}/libexec/gnubin:$env(PATH)
# https://trac.macports.org/ticket/33756
-if {${configure.compiler} == "clang"} {
- configure.compiler llvm-gcc-4.2
-}
+compiler.blacklist clang
build.args GCC=${configure.cc} \
GPP=${configure.cxx}
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
eval xinstall -m 0755 [glob ${worksrcpath}/bin/*] ${destroot}${prefix}/bin
+
file mkdir ${destroot}${prefix}/share/arb/bin
+ file copy ${worksrcpath}/PERL_SCRIPTS ${destroot}${prefix}/share/arb/PERL_SCRIPTS
+ file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP
file copy ${worksrcpath}/lib ${destroot}${prefix}/share/arb/lib
- file copy ${worksrcpath}/GDEHELP ${destroot}${prefix}/share/arb/GDEHELP
+ file copy ${worksrcpath}/SH ${destroot}${prefix}/share/arb/SH
+ file copy ${worksrcpath}/demo.arb ${destroot}${prefix}/share/arb
+
file mkdir ${destroot}${prefix}/lib/help
file copy ${worksrcpath}/HELP_SOURCE/oldhelp ${destroot}${prefix}/lib/help
- 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
+
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
@@ -162,9 +165,13 @@
enter the following command:
source ~/.cshrc
-3)
-create a text file in your home folder called .xmodmap that contains the text below:
+C) to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup
+
+************************************************************************************************************************************
+You can set up keyboard shortcuts manually by creating a text file in your home folder called .xmodmap that contains the text below:
+************************************************************************************************************************************
+
clear Mod1
clear Mod2
keycode 63 = Mode_switch
@@ -173,14 +180,16 @@
add Mod1 = Meta_L Meta_R
add Mod2 = Mode_switch
-C)
-to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup
+*******************************************************************
+Use keys Control+Command Arrow Key to jump over bases
+Use Keys Option Arrow Key to pull in bases across alignment gaps
+Use the right Command Key plus a letter key to activate a menu item
+*******************************************************************
-D)
-type arb to start ARB
+*****************************
+Type 'arb' to start using 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,
@@ -195,10 +204,6 @@
${prefix}/share/arb/lib/macros.default/
${prefix}/share/arb/lib/arb_tcp.dat.default
-Use keys Control+Command Arrow Key to jump over bases
-Use Keys Option Arrow Key to pull in bases across alignment gaps
-Use the right Command Key plus a letter key to activate a menu item
-
These notes can be viewed at any time by typing 'port notes arb'
Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371
Added: trunk/dports/science/arb/files/patch-ARB-RNA3D_Textures.cxx.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-RNA3D_Textures.cxx.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-RNA3D_Textures.cxx.diff 2012-11-19 05:01:58 UTC (rev 99842)
@@ -0,0 +1,11 @@
+--- RNA3D/RNA3D_Textures.cxx.orig 2012-11-17 17:33:22.000000000 -0500
++++ RNA3D/RNA3D_Textures.cxx 2012-11-17 17:33:30.000000000 -0500
+@@ -61,7 +61,7 @@
+ pngInfo info;
+
+ // Using pngLoadAndBind to set texture parameters automatically.
+- texture[i] = pngBind(ImageFile, PNG_NOMIPMAP, PNG_ALPHA, &info, GL_CLAMP, GL_NEAREST, GL_NEAREST);
++ texture[i] = pngBind(ImageFile, GLPNG_NOMIPMAP, GLPNG_ALPHA, &info, GL_CLAMP, GL_NEAREST, GL_NEAREST);
+
+ if (texture[i] == 0) {
+ throw string(GBS_global_string("Error loading %s", ImageFile));
Modified: trunk/dports/science/arb/files/patch-ARB-config.makefile.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-config.makefile.diff 2012-11-19 04:36:51 UTC (rev 99841)
+++ trunk/dports/science/arb/files/patch-ARB-config.makefile.diff 2012-11-19 05:01:58 UTC (rev 99842)
@@ -1,14 +1,6 @@
---- config.makefile 2012-09-20 07:33:17.000000000 -0400
-+++ config.makefile.template 2012-09-20 07:34:36.000000000 -0400
-@@ -13,14 +13,14 @@
- TRACESYM := 1# insert symbols for meaningful backtraces into executables
-
- # Include features using OPENGL?
--OPENGL := 1
-+OPENGL := 0
-
- # 0 = use old PTSERVER (recommended)
- # 1 = use the new PTPan implementation as pt-server (Not tested very well, do NOT use!)
+--- 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
Added: trunk/dports/science/arb/files/patch-ARB-glpng.c.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-glpng.c.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-glpng.c.diff 2012-11-19 05:01:58 UTC (rev 99842)
@@ -0,0 +1,169 @@
+--- GL/glpng/glpng.c.orig 2012-11-17 16:28:36.000000000 -0500
++++ GL/glpng/glpng.c 2012-11-17 17:26:13.000000000 -0500
+@@ -38,9 +38,9 @@
+ #include <png.h>
+
+ #if 0
+-#define PNG_CHECK_SIG(header,size) png_check_sig(header,size) // old libpng
++#define GLPNG_CHECK_SIG(header,size) png_check_sig(header,size) // old libpng
+ #else
+-#define PNG_CHECK_SIG(header,size) (png_sig_cmp(header,0,size)==0)
++#define GLPNG_CHECK_SIG(header,size) (png_sig_cmp(header,0,size)==0)
+ #endif
+
+ /* Used to decide if GL/gl.h supports the paletted extension */
+@@ -284,14 +284,14 @@
+ if (pinfo == NULL) return 0;
+
+ fread(header, 1, 8, fp);
+- if (!PNG_CHECK_SIG(header, 8)) return 0;
++ if (!GLPNG_CHECK_SIG(header, 8)) return 0;
+
+ png = png_create_read_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL);
+ info = png_create_info_struct(png);
+ endinfo = png_create_info_struct(png);
+
+ // DH: added following lines
+- if (setjmp(png->jmpbuf))
++ if (setjmp(png_jmpbuf(png)))
+ {
+ png_destroy_read_struct(&png, &info, &endinfo);
+ return 0;
+@@ -389,7 +389,7 @@
+ png_uint_32 i;
+
+ fread(header, 1, 8, fp);
+- if (!PNG_CHECK_SIG(header, 8)) return 0;
++ if (!GLPNG_CHECK_SIG(header, 8)) return 0;
+
+ png = png_create_read_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL);
+ info = png_create_info_struct(png);
+@@ -437,12 +437,12 @@
+ if (color == PNG_COLOR_TYPE_GRAY || color == PNG_COLOR_TYPE_GRAY_ALPHA)
+ png_set_gray_to_rgb(png);
+
+- if (color&PNG_COLOR_MASK_ALPHA && trans != PNG_ALPHA) {
++ if (color&PNG_COLOR_MASK_ALPHA && trans != GLPNG_ALPHA) {
+ png_set_strip_alpha(png);
+ color &= ~PNG_COLOR_MASK_ALPHA;
+ }
+
+- if (!(PalettedTextures && mipmap >= 0 && trans == PNG_SOLID))
++ if (!(PalettedTextures && mipmap >= 0 && trans == GLPNG_SOLID))
+ if (color == PNG_COLOR_TYPE_PALETTE)
+ png_set_expand(png);
+
+@@ -493,7 +493,7 @@
+ glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
+
+ #ifdef SUPPORTS_PALETTE_EXT
+- if (PalettedTextures && mipmap >= 0 && trans == PNG_SOLID && color == PNG_COLOR_TYPE_PALETTE) {
++ if (PalettedTextures && mipmap >= 0 && trans == GLPNG_SOLID && color == PNG_COLOR_TYPE_PALETTE) {
+ png_colorp pal;
+ int cols;
+ GLint intf;
+@@ -517,7 +517,7 @@
+ }
+ else
+ #endif
+- if (trans == PNG_SOLID || trans == PNG_ALPHA || color == PNG_COLOR_TYPE_RGB_ALPHA || color == PNG_COLOR_TYPE_GRAY_ALPHA) {
++ if (trans == GLPNG_SOLID || trans == GLPNG_ALPHA || color == PNG_COLOR_TYPE_RGB_ALPHA || color == PNG_COLOR_TYPE_GRAY_ALPHA) {
+ GLenum glformat;
+ GLint glcomponent;
+
+@@ -542,9 +542,9 @@
+ return 0;
+ }
+
+- if (mipmap == PNG_BUILDMIPMAPS)
++ if (mipmap == GLPNG_BUILDMIPMAPS)
+ Build2DMipmaps(glcomponent, width, height, glformat, data, 1);
+- else if (mipmap == PNG_SIMPLEMIPMAPS)
++ else if (mipmap == GLPNG_SIMPLEMIPMAPS)
+ Build2DMipmaps(glcomponent, width, height, glformat, data, 0);
+ else
+ glTexImage2D(GL_TEXTURE_2D, mipmap, glcomponent, width, height, 0, glformat, GL_UNSIGNED_BYTE, data);
+@@ -574,13 +574,13 @@
+ #define ALPHA *q
+
+ switch (trans) {
+- case PNG_CALLBACK:
++ case GLPNG_CALLBACK:
+ FORSTART
+ ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b);
+ FOREND
+ break;
+
+- case PNG_STENCIL:
++ case GLPNG_STENCIL:
+ FORSTART
+ if (r == StencilRed && g == StencilGreen && b == StencilBlue)
+ ALPHA = 0;
+@@ -589,48 +589,48 @@
+ FOREND
+ break;
+
+- case PNG_BLEND1:
++ case GLPNG_BLEND1:
+ FORSTART
+ a = r+g+b;
+ if (a > 255) ALPHA = 255; else ALPHA = a;
+ FOREND
+ break;
+
+- case PNG_BLEND2:
++ case GLPNG_BLEND2:
+ FORSTART
+ a = r+g+b;
+ if (a > 255*2) ALPHA = 255; else ALPHA = a/2;
+ FOREND
+ break;
+
+- case PNG_BLEND3:
++ case GLPNG_BLEND3:
+ FORSTART
+ ALPHA = (r+g+b)/3;
+ FOREND
+ break;
+
+- case PNG_BLEND4:
++ case GLPNG_BLEND4:
+ FORSTART
+ a = r*r+g*g+b*b;
+ if (a > 255) ALPHA = 255; else ALPHA = a;
+ FOREND
+ break;
+
+- case PNG_BLEND5:
++ case GLPNG_BLEND5:
+ FORSTART
+ a = r*r+g*g+b*b;
+ if (a > 255*2) ALPHA = 255; else ALPHA = a/2;
+ FOREND
+ break;
+
+- case PNG_BLEND6:
++ case GLPNG_BLEND6:
+ FORSTART
+ a = r*r+g*g+b*b;
+ if (a > 255*3) ALPHA = 255; else ALPHA = a/3;
+ FOREND
+ break;
+
+- case PNG_BLEND7:
++ case GLPNG_BLEND7:
+ FORSTART
+ a = r*r+g*g+b*b;
+ if (a > 255*255) ALPHA = 255; else ALPHA = (int) sqrt(a);
+@@ -642,9 +642,9 @@
+ #undef FOREND
+ #undef ALPHA
+
+- if (mipmap == PNG_BUILDMIPMAPS)
++ if (mipmap == GLPNG_BUILDMIPMAPS)
+ Build2DMipmaps(4, width, height, GL_RGBA, data2, 1);
+- else if (mipmap == PNG_SIMPLEMIPMAPS)
++ else if (mipmap == GLPNG_SIMPLEMIPMAPS)
+ Build2DMipmaps(4, width, height, GL_RGBA, data2, 0);
+ else
+ glTexImage2D(GL_TEXTURE_2D, mipmap, 4, width, height, 0, GL_RGBA, GL_UNSIGNED_BYTE, data2);
Added: trunk/dports/science/arb/files/patch-ARB-glpng.h.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-glpng.h.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-glpng.h.diff 2012-11-19 05:01:58 UTC (rev 99842)
@@ -0,0 +1,49 @@
+--- GL/glpng/glpng.h.orig 2012-11-17 16:18:10.000000000 -0500
++++ GL/glpng/glpng.h 2012-11-17 16:20:13.000000000 -0500
+@@ -47,28 +47,28 @@
+ #endif
+
+ /* Mipmapping parameters */
+-#define PNG_NOMIPMAPS 0 /* No mipmapping */
+-#define PNG_BUILDMIPMAPS -1 /* Calls a clone of gluBuild2DMipmaps() */
+-#define PNG_SIMPLEMIPMAPS -2 /* Generates mipmaps without filtering */
++#define GLPNG_NOMIPMAPS 0 /* No mipmapping */
++#define GLPNG_BUILDMIPMAPS -1 /* Calls a clone of gluBuild2DMipmaps() */
++#define GLPNG_SIMPLEMIPMAPS -2 /* Generates mipmaps without filtering */
+
+ /* Who needs an "S" anyway? */
+-#define PNG_NOMIPMAP PNG_NOMIPMAPS
+-#define PNG_BUILDMIPMAP PNG_BUILDMIPMAPS
+-#define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS
++#define GLPNG_NOMIPMAP GLPNG_NOMIPMAPS
++#define GLPNG_BUILDMIPMAP GLPNG_BUILDMIPMAPS
++#define GLPNG_SIMPLEMIPMAP GLPNG_SIMPLEMIPMAPS
+
+ /* Transparency parameters */
+-#define PNG_CALLBACK -3 /* Call the callback function to generate alpha */
+-#define PNG_ALPHA -2 /* Use alpha channel in PNG file, if there is one */
+-#define PNG_SOLID -1 /* No transparency */
+-#define PNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */
+-#define PNG_BLEND1 1 /* a = r+g+b */
+-#define PNG_BLEND2 2 /* a = (r+g+b)/2 */
+-#define PNG_BLEND3 3 /* a = (r+g+b)/3 */
+-#define PNG_BLEND4 4 /* a = r*r+g*g+b*b */
+-#define PNG_BLEND5 5 /* a = (r*r+g*g+b*b)/2 */
+-#define PNG_BLEND6 6 /* a = (r*r+g*g+b*b)/3 */
+-#define PNG_BLEND7 7 /* a = (r*r+g*g+b*b)/4 */
+-#define PNG_BLEND8 8 /* a = sqrt(r*r+g*g+b*b) */
++#define GLPNG_CALLBACK -3 /* Call the callback function to generate alpha */
++#define GLPNG_ALPHA -2 /* Use alpha channel in GLPNG file, if there is one */
++#define GLPNG_SOLID -1 /* No transparency */
++#define GLPNG_STENCIL 0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise */
++#define GLPNG_BLEND1 1 /* a = r+g+b */
++#define GLPNG_BLEND2 2 /* a = (r+g+b)/2 */
++#define GLPNG_BLEND3 3 /* a = (r+g+b)/3 */
++#define GLPNG_BLEND4 4 /* a = r*r+g*g+b*b */
++#define GLPNG_BLEND5 5 /* a = (r*r+g*g+b*b)/2 */
++#define GLPNG_BLEND6 6 /* a = (r*r+g*g+b*b)/3 */
++#define GLPNG_BLEND7 7 /* a = (r*r+g*g+b*b)/4 */
++#define GLPNG_BLEND8 8 /* a = sqrt(r*r+g*g+b*b) */
+
+ typedef struct {
+ unsigned int Width;
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