[Fink-users] ARB for FINK: help please
The current fink version of ARB (a phylogenetics package used by biologists around the world) is now obsolete. Ben Hines has been instrumental in getting ARB onto the Mac but is unable to continue this task. Matt Cottrell has been able to get the latest version of ARB, running in 64 bit, and with all the 64-bit dependencies, up on MacPorts at: http://trac.macports.org/browser/trunk/dports/science/arb/Portfile My request is for someone to help get a similar version available from Fink. Matt tells me the code is now very clean, and needs little or no patching. However, he had to work up the 64-bit dependencies. So it would need to be someone who can package, and who knows about the 64-bit upgrades to existing packages in fink. The listed dependencies are: glew glw gsed imake lynx mesa openmotif sablotron tiff My role in the past has been to test out the program to see that it functions, and to provide written instructions to help people to install it. The advantage of having ARB updated on Fink is the availability of so many other programs, and the large pool of helpful members of the Fink community. ARB is a very important scientific tool and is used widely, so I'm hoping to hear from someone soon. Mike Dyall-Smith PS: details about ARB in Fink are at: http://pdb.finkproject.org/pdb/package.php/arb?rel_id=10.6-x86_64-current-unstable -- _ Mike Dyall-Smith, Ph.D., Visiting Professor, Max Planck Institute for Biochemistry, Am Klopferspitz 18a, Martinsried D82152, Germany email: mike.dyallsm...@gmail.com web: www.haloarchaea.com skype: mike.dyallsmith _ On measuring microbial diversity: This is like randomly sampling a bus load of people and then trying to infer the diversity of all people in the world. You would not expect to find many Lithuanians. - Curtis and Sloan, 2005 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] mplayer
Has anyone got mplayer to compile on OS X 10.5.4? I am using an intel macbook. Fink was self-updated and update-all'ed. The last part of the output before execution fails is below. - Mike Dyall-Smith cc -I. -I.. -Wdeclaration-after-statement -fno-PIC -O4 -march=pentium-m -mtune=pentium-m -pipe -ffast-mat -fomit-frame-pointer -mdynamic-no-pic -falign-loops=16 -DSYS_DARWIN -DCONFIG_DARWIN -shared-libgcc -arch i386 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/sw/include/libcdparanoia -I/sw/lib/freetype219/include -I/sw/lib/fontconfig2/include -I/sw/include -I/usr/X11/include -I/sw/include/SDL -D_GNU_SOURCE=1 -D_THREA _SAFE -I/sw/include/artsc -I/sw/include/glib-2.0 -I/sw/lib/glib-2.0/include -I/sw/include -I/sw/lib/free ype219/include/freetype2 -I/sw/lib/freetype219/include -I/sw/include/gtk-1.2 -I/sw/include/glib-1.2 -I/sw lib/glib/include -I/usr/X11R6/include -U_FILE_OFFSET_BITS -fno-omit-frame-pointer -mno-omit-leaf-frame-p inter -DMPLAYER -D__WINE__ -c pe_image.c In file included from wine/winnt.h:1043, from wine/winbase.h:5, from pe_image.c:56: wine/poppack.h:5: error: too many #pragma options align=reset In file included from wine/winnt.h:1494, from wine/winbase.h:5, from pe_image.c:56: wine/poppack.h:5: error: too many #pragma options align=reset In file included from wine/winnt.h:2170, from wine/winbase.h:5, from pe_image.c:56: wine/poppack.h:5: error: too many #pragma options align=reset In file included from wine/winnt.h:2667, from wine/winbase.h:5, from pe_image.c:56: wine/poppack.h:5: error: too many #pragma options align=reset In file included from wine/winbase.h:1083, from pe_image.c:56: wine/poppack.h:5: error: too many #pragma options align=reset In file included from wine/module.h:76, from pe_image.c:60: wine/poppack.h:5: error: too many #pragma options align=reset In file included from pe_image.c:61: wine/debugtools.h:67: warning: useless type name in empty declaration pe_image.c: In function 'fixup_imports': pe_image.c:315: warning: pointer targets in passing argument 2 of 'LookupExternalByName' differ in signed ess pe_image.c:336: warning: pointer targets in passing argument 2 of 'LookupExternalByName' differ in signed ess make[1]: *** [pe_image.o] Error 1 make: *** [loader/libloader.a] Error 2 ### execution of make failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-mplayer-1.0.0rc1-1021 (Reading database ... 73123 files and directories currently installed.) Removing fink-buildlock-mplayer-1.0.0rc1-1021 ... Failed: phase compiling: mplayer-1.0.0rc1-1021 failed - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] arb install fails compile error
Thanks for tracking this issue down. I found this file had been lost when I tried to run a compiled version of ARB. The main window starts up but you can't run the EDIT window. I thought I had done something myself, and had to grab libGLw.1.dylib from an old install and move it to its wanted position. Once I had done that, everything seems to work. Another ARB user had this advice: I figured out that xcode's installer didn't actually install /usr/X11/ lib/libGLw.dylib! I had to pkgutil --forget and re-install, as per http://www.uoregon.edu/~noeckel/LeopardIntelSetup.html Hope this helps. - Mike Dyall-Smith Date: Sun, 24 Feb 2008 16:22:37 +0100 From: Martin Costabel [EMAIL PROTECTED] Subject: Re: [Fink-users] arb install fails compile error To: Martin Costabel [EMAIL PROTECTED] Cc: fink-users@lists.sourceforge.net, Daniel Rogers [EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Martin Costabel wrote: Daniel Rogers wrote: I'm running Mac OS 10.5.2 and fink 0.28.0. Fink has installed fine and selfupdate-cvs works as well. However, installing arb with: fink install arb results in an error. I installed arb successfully on other 10.5 macs and I'm at a loss as to what the problem may be. The install ends as follows. Make everything in RNA3D g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DARB_OPENGL -DFAKE_VTAB_PTR=char -D_ARB_RNA3D -c -o RNA3D_Main.o RNA3D_Main.cxx -I. -I/sw/src/fink.build/arb-20071207-1005/./INCLUDE -I/usr/X11R6/include -I/sw/include/ In file included from RNA3D_Main.cxx:1: RNA3D_GlobalHeader.hxx:46:26: error: GL/GLwMDrawA.h: No such file or directory There is something strange going on with this file. It is installed (in /usr/X11/include) by the X11SDK package, and on both machines I looked at it, it was absent. One of the machines I have TimeMachine running, and I could see how the file was present on February 12 and absent the following day. On the same day, two SoftwareUpdate packages were installed, among them my main suspect, QuickTime741_Leopard.pkg. After re-reading my installer logs more carefully, I found that I had also updated OSX to 10.5.2 the same day, and this is indeed the culprit: The 10.5.2 updater. I don't know what the story behind this is, but the MacOSX-10.5.2 updater package runs a script named removeOldPreLeopardX11 which has the following lines: rm -rf $3/usr/X11/X11.app rm -rf $3/usr/X11/bin/dumpkeymap rm -rf $3/usr/X11/include/xorg rm -rf $3/usr/X11/lib/X11/man/man1 rm -rf $3/usr/X11/lib/libGLw.1.dylib rm -rf $3/usr/X11/lib/libGLw.dylib rm -rf $3/usr/X11/include/GL/GLwDrawA.h rm -rf $3/usr/X11/include/GL/GLwDrawAP.h rm -rf $3/usr/X11/include/GL/GLwMDrawA.h rm -rf $3/usr/X11/include/GL/GLwMDrawAP.h Now I know nothing about this GLw stuff, but the dynamic libGLw was observed to be new in Leopard, Tiger having only a static libGLw.a. This has caused problems for other packages like molmol. It seems that these packages cannot be built with Apple's X11 any more, unless there is some other source for libGLw. -- Martin Mike Dyall-Smith Dept. Microbiology and Immunology University of Melbourne Ph: +61 3 8344 5693 Fx: +61 3 9347 1540 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] fink website hijacked?
Looks to me like the fink project website has been hijacked. At the usual fink URL of http://www.finkproject.org/, I now see some advertising page, courtesy of GoDaddy.com - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] touchpad and X11 on 10.5
Why doesn't the (intel) macbook touchpad work on an X11 window? Is there an easy way to get it working? I've also had variable success with the scroll wheel function using a mouse. I have tried looking through the archives and the web, but I can't see an answer. thanks, Mike D-S - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] touchpad and X11 on 10.5
Thanks Alex, I will expand and make my query more relevant to the fink list. Using an intel macbook, I normally use the touchpad at the base of the keyboard rather than attaching a mouse (I find I have less problems with RSI this way). When you port a linux application to run on OS X under X11, the touchpad control of the window is lost. I cannot do a two-finger scroll of the window using the touchpad on my macbook laptop. I have to click-drag on the side window bar. I am using X11 2.1.1, the latest version. I have found linux web pages that show how to edit an xorg.conf file to modify touchpad function (to do almost anything!), but I haven't seen how to do this under OS X. I would appreciate any advice here. - Mike D-S Mike Dyall-Smith wrote: Why doesn't the (intel) macbook touchpad work on an X11 window? Is there an easy way to get it working? I've also had variable success with the scroll wheel function using a mouse. I have tried looking through the archives and the web, but I can't see an answer. thanks, Mike D-S I'd think this was more a matter for Apple's lists than ours, but for interested people please define what you mean by the touchpad not working in an X11 window. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHappdB8UpO3rKjQ8RAuoFAJ9ApEDp+MJSPLyK7HSo7eGKbGq4igCdHJfi OAqu300FHBTbyEDu6y9HFa0= =dQYJ -END PGP SIGNATURE-- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] curl times out
I noticed the problem mentioned on the beginners list, and I seem to have hit the same one trying to download tarballs via fink curl. The always time out given the 30 second limit. If I manually issue the same command but increase it to 70 seconds, they can be downloaded. Is there anyway to change the script for curl to increase the timeout limit to 70 seconds? Otherwise, I am having to download them all individually. - Mike Dyall-Smith example: curl --connect-timeout 30 -f -L -A 'fink/0.27.9' -O http://distfiles.master.finkmirrors.net/glew-1.3.5-src.zip curl: (6) name lookup timed out ### execution of curl failed, exit code 6 Downloading the file glew-1.3.5-src.zip failed. - SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] arb fails to build; undefined symbols
Thanks Dan for your interest in this: Date: Sun, 25 Nov 2007 01:27:04 -0500 From: Daniel Macks [EMAIL PROTECTED] Subject: Re: [Fink-users] arb fails to build; undefined symbols On Sat, Nov 24, 2007 at 06:09:23PM +1100, Mike Dyall-Smith wrote: Trying to build arb (phylogeny package) on 10.4.11 with gcc-4.0.1, intel macbook. It fails with the following end output. What version-revision of the arb package? - The latest source, at: http://download.arb-home.de/latest_build/ /usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld: Undefined symbols: ___GLEW_ARB_point_sprite [...] Those undefined symbols are part of libglew on my machine...do you have fink's glew and glew-shlibs packages installed? If not, does installing them allow arb to compile successfully? - I had been switching things around and didn't have glew installed at this time. I did that and it eliminated the first few undefined symbols, then it got stuck on the last symbol on the list, _pngBind. I haven't figured out how to make it happy with this one. Any ideas what package this is looking for? I have been modifying .info and .patch files for the latest arb src, and would be very happy for any assistance. Regards, Mike Mike Dyall-Smith Dept. Microbiology and Immunology University of Melbourne - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] failure on compile of mjpegtools-1.6.2-1004
I have stated this failure back on NOV 15, 2007. I am still getting a compile error. Here is compile error: gcc -fno-common -Wall -Wunused -o .libs/lavplay lavplay.o -Wl,- framework -Wl,Cocoa -L/sw/lib ../utils/libmjpegutils.a ./.libs/ liblavplay.dylib ./.libs/liblavjpeg.dylib ./.libs/liblavfile.dylib / sw/ lib/libjpeg.dylib /sw/lib/libdv.dylib -lm /sw/lib/libglib.dylib - lpthread -lSDLmain /sw/lib/libSDL.dylib -L/usr/X11/lib /usr/X11/lib/ libX11.6.2.0.dylib /usr/X11/lib/libXau.6.0.0.dylib /usr/X11/lib/ libXdmcp.6.0.0.dylib ld: cycle in dylib re-exports with /usr/X11/lib/libGL.dylib - Is there a reason /usr/X11 being used instead of /usr/X11R6 ? collect2: ld returned 1 exit status make[2]: *** [lavplay] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 ### execution of make failed, exit code 2 MDS - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] failure on compile of mjpegtools-1.6.2-100
On 26/11/2007, at 11:51 AM, [EMAIL PROTECTED] wrote: Message: 6 Date: Sun, 25 Nov 2007 19:50:47 -0500 From: Hans Kruse [EMAIL PROTECTED] Subject: Re: [Fink-users] failure on compile of mjpegtools-1.6.2-1004 I think you will find a softlink X11R6 - X11 in /usr, so it should in general not matter. My /usr directory (Tiger) does not have a soft link, just the X11R6 directory. Perhaps the link is elsewhere. I looked at the patch for mjpegtools and noticed: SetLDFLAGS: -dylib_file /System/Library/Frameworks/OpenGL.framework/ Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/ OpenGL.framework/Versions/A/Libraries/libGL.dylib Can someone tell me why this flag uses two identical paths for libGL.dylib (they look the same to me)? MDS - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] arb fails to build; undefined symbols
Trying to build arb (phylogeny package) on 10.4.11 with gcc-4.0.1, intel macbook. It fails with the following end output. Any ideas why? Thanks, Mike D-S Target 'bin/arb_edit4' not found - rebuilding bin/arb_edit4 (Thu Jan 1 09:59:59 1970) Link bin/arb_edit4 g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -L/sw2/lib -Wl,- stack_size -Wl,1000 -Wl,-stack_addr -Wl,c000 -lGLU -lGL -lGLw -lglut -lglui -dylib_file /System/Library/Frameworks/OpenGL.framework/ Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/ OpenGL.framework/Versions/A/Libraries/libGL.dylib -o bin/arb_edit4 -L/ sw2/src/fink.build/arb-2007-1003/./LIBLINK -L/sw2/lib RNA3D/RNA3D.a NAMES_COM/client.a AWTC/AWTC.a EDIT4/EDIT4.a SECEDIT/SECEDIT.a SERVERCNTRL/SERVERCNTRL.a STAT/STAT.a ARB_GDE/ARB_GDE.a ISLAND_HOPPING/ISLAND_HOPPING.a SL/HELIX/HELIX.a SL/AW_HELIX/ AW_HELIX.a SL/AW_NAME/AW_NAME.a SL/FILE_BUFFER/FILE_BUFFER.a XML/ XML.a -lARBDB -lstdc++ -lAW -lAWT -L/usr/X11R6/lib -L/sw2/lib -lXm - lXt -lX11 -lXext -lXp -lc /usr/libexec/gcc/i686-apple-darwin8/4.0.1/ld: Undefined symbols: ___GLEW_ARB_point_sprite ___GLEW_EXT_point_parameters ___GLEW_VERSION_1_2 ___glewPointParameterfEXT ___glewPointParameterfvEXT _glewGetErrorString _glewGetString _glewInit _pngBind collect2: ld returned 1 exit status make: *** [bin/arb_edit4] Error 1 ### execution of /var/tmp/tmp.2.v6tUjI failed, exit code 2 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] arb package not appearing in fink list
2. arb package not appearing in fink list (Matthew Cottrell)
3. Re: arb package not appearing in fink list (Daniel Macks)
Dear Matthew and Daniel, yes, arb has been mauled by the leopard
and is awaiting rescue. Recently, I posted the message below to the
fink developers list. I post it here for your information, and hopefully
to attract someone able to troubleshoot the code. I don't have a 10.5
box yet either.
__post to fink-devel list_
I am looking for some assistance compiling the phylogeny package,
ARB. Ben Hines will be looking at compiling ARB on Leopard but I
would like to get the latest source for ARB to compile on intel/
Tiger. So far, it compiles much of the way then stops with the
error: invalid conversion from 'int*' to 'GLint*'. I have seen
discussions of this kind of error but I would appreciate some expert
assistance on how to patch the ARB code.
Thanks, Mike Dyall-Smith, mlds (AT) unimelb (DOT) edu.au
Make everything in RNA3D
g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -
DARB_OPENGL -DFAKE_VTAB_PTR=char -D_ARB_RNA3D -c -o RNA3D_Main.o
RNA3D_Main.cxx -I. -I/sw2/src/fink.build/arb-20071029ogl-2007/./
INCLUDE -I/usr/X11R6/include -I/sw2/include/
g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -
DARB_OPENGL -DFAKE_VTAB_PTR=char -D_ARB_RNA3D -c -o RNA3D_Interface.o
RNA3D_Interface.cxx -I. -I/sw2/src/fink.build/arb-20071029ogl-2007/./
INCLUDE -I/usr/X11R6/include -I/sw2/include/
g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -
DARB_OPENGL -DFAKE_VTAB_PTR=char -D_ARB_RNA3D -c -o RNA3D_Graphics.o
RNA3D_Graphics.cxx -I. -I/sw2/src/fink.build/arb-20071029ogl-2007/./
INCLUDE -I/usr/X11R6/include -I/sw2/include/
g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -
DARB_OPENGL -DFAKE_VTAB_PTR=char -D_ARB_RNA3D -c -o
RNA3D_OpenGLEngine.o RNA3D_OpenGLEngine.cxx -I. -I/sw2/src/
fink.build/arb-20071029ogl-2007/./INCLUDE -I/usr/X11R6/include -I/sw2/
include/
g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -
DARB_OPENGL -DFAKE_VTAB_PTR=char -D_ARB_RNA3D -c -o
RNA3D_OpenGLGraphics.o RNA3D_OpenGLGraphics.cxx -I. -I/sw2/src/
fink.build/arb-20071029ogl-2007/./INCLUDE -I/usr/X11R6/include -I/sw2/
include/
RNA3D_OpenGLGraphics.cxx: In member function 'void
OpenGLGraphics::WinToScreenCoordinates(int, int, GLdouble*)':
RNA3D_OpenGLGraphics.cxx:110: error: invalid conversion from 'int*'
to 'GLint*'
RNA3D_OpenGLGraphics.cxx:110: error: initializing argument 2 of
'void glGetIntegerv(GLenum, GLint*)'
RNA3D_OpenGLGraphics.cxx:117: error: invalid conversion from 'int*'
to 'const GLint*'
RNA3D_OpenGLGraphics.cxx:117: error: initializing argument 6 of
'GLint gluUnProject(GLdouble, GLdouble, GLdouble, const GLdouble*,
const GLdouble*, const GLint*, GLdouble*, GLdouble*, GLdouble*)'
make[1]: *** [RNA3D_OpenGLGraphics.o] Error 1
make: *** [RNA3D/RNA3D.dummy] Error 2
### execution of /var/tmp/tmp.2.AmmNm4 failed, exit code 2
_for reference, lines 102-118 of
RNA3D_OpenGLGraphics.cxx: _
void OpenGLGraphics::WinToScreenCoordinates(int x, int y, GLdouble
*screenPos) {
//project window coords to gl coord
glLoadIdentity();
GLdouble modelMatrix[16];
glGetDoublev(GL_MODELVIEW_MATRIX,modelMatrix);
GLdouble projMatrix[16];
glGetDoublev(GL_PROJECTION_MATRIX,projMatrix);
int viewport[4];
glGetIntegerv(GL_VIEWPORT,viewport);
gluUnProject(x, y, 0,
modelMatrix,
projMatrix,
viewport,
//the next 3 parameters are the pointers to the
final object coordinates.(double)
screenPos[0], screenPos[1], screenPos[2]
);
}
__
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[Fink-users] wwwblast fails
I'm trying to install wwwblast on OS X 10.4.6, PPC. I get the following error (see below). I have selfupdated fink. [snip] ncbi/asnstat/asntseq.h ncbi/lib/ ncbi/include/ ncbi/build/ ncbi/bin/ patch -p1 /sw/fink/dists/unstable/main/finkinfo/sci/wwwblast.patch patching file Src/Makefile patching file index.html cp -p Src/Makefile Src/Makefile.old echo NCBI = /sw/share/ncbitools Src/Makefile echo NCBI_INCDIR = /sw/include/ncbitools Src/Makefile echo NCBI_ALTLIB = Src/Makefile echo NCBI_LIBDIR = /sw/lib Src/Makefile cat Src/Makefile.old Src/Makefile cd Src; make cc -c -O2 -g -I. -I/sw/include/ncbitools -no-cpp-precomp -Wno-long- double psiblast.c cc -O2 -g -I. -I/sw/include/ncbitools -framework CoreServices psiblast.o wwwbutl.c /sw/lib/ncbithr.o \ -L/sw/lib -lncbidesk -lvibgif -lncbitool -lncbiobj -lncbi -lc -o ./ psiblast.REAL /usr/bin/ld: Undefined symbols: _PrintDefLinesFromSeqAlignWithPath collect2: ld returned 1 exit status make: *** [psiblast.REAL] Error 1 ### execution of cd failed, exit code 2 Removing build lock... /sw/bin/dpkg-lockwait -r fink-buildlock-wwwblast-2.2.9-1 (Reading database ... 20022 files and directories currently installed.) Removing fink-buildlock-wwwblast-2.2.9-1 ... Failed: phase compiling: wwwblast-2.2.9-1 failed Mike Dyall-Smith ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] PHASE phylogenetics package
Has anyone successfully compiled the phylogenetics package PHASE (Ben Hines, Maintainer) recently? I have scanned the fink archives but see nothing apart from minor updates to the .patch and .info files last year. Below is the output (edited) I get when I try to install it. I am on OS X 10.4.6, PPC. It looks to me like the files are not found because they are not being sought in the right directory, but I'm not sure how to correct this. The files it complains are absent are present in the right folder, and can be seen in the unpacking stages (shown below). For example, the first 'absent' file, has a path: /sw/src/fink.build/phase-1.1-1/phase-1.1/include/Models/DnaModel.h Any help would be appreciated. Mike Dyall-Smith ---From the 'fink install phase' command, it downloads OK: The following package will be installed or updated: phase curl -f -L -O http://distfiles.bne.qld.au.finkmirrors.net/phase-1.1.tgz ---Then it unpacks the downloaded package Unpacking fink-buildlock-phase-1.1-1 (from .../fink-buildlock- phase-1.1-1_2006.06.12-21.57.39_darwin-powerpc.deb) ... Setting up fink-buildlock-phase-1.1-1 (2006.06.12-21.57.39) ... gzip -dc /sw/src/phase-1.1.tgz | /sw/bin/tar -xvf - --no-same-owner --no-same-permissions phase-1.1/ phase-1.1/blas/ phase-1.1/blas/Makefile . . . phase-1.1/include/Models/DnaModel.h . phase-1.1/include/Models/MixedPerturbator.h . . . ---Then it patches the makefile OK . phase-1.1/LICENSING phase-1.1/README patch -p1 /sw/fink/dists/unstable/main/finkinfo/sci/phase.patch patching file include/Models/Model.h patching file makefile /var/tmp/tmp.1.y4WwdA + make g++ -funroll-all-loops -O4 -fstrength-reduce -fexpensive- optimizations -I./include -I./include/Models -I./include/Tree -I./ include/Util -I./include/Sequence -o obj/MCMCphase.o -c src/MCMCphase.cc g++ -funroll-all-loops -O4 -fstrength-reduce -fexpensive- optimizations -I./include -I./include/Models -I./include/Tree -I./ include/Util -I./include/Sequence -o obj/Phase.o -c src/Phase.cc g++-3.3 -I/sw/include -c -o src/Models/DnaModel.o src/Models/ DnaModel.cc src/Models/DnaModel.cc:1:29: Models/DnaModel.h: No such file or directory src/Models/DnaModel.cc:7:36: Sequence/SequenceTable.h: No such file or directory src/Models/DnaModel.cc:9:32: Models/Perturbator.h: No such file or directory src/Models/DnaModel.cc:10:31: Util/ModelFactory.h: No such file or directory src/Models/DnaModel.cc:12:37: PatternDesign/Singleton.h: No such file or directory src/Models/DnaModel.cc:13:26: Util/statlib.h: No such file or directory [snip - lots of similar errors] src/Models/DnaModel.cc:599: error: syntax error before `' token src/Models/DnaModel.cc:601: error: syntax error before `' token src/Models/DnaModel.cc:602: error: syntax error before `.' token make: *** [src/Models/DnaModel.o] Error 1 ### execution of /var/tmp/tmp.1.y4WwdA failed, exit code 2 Removing build lock... /sw/bin/dpkg-lockwait -r fink-buildlock-phase-1.1-1 (Reading database ... 19431 files and directories currently installed.) Removing fink-buildlock-phase-1.1-1 ... Failed: phase compiling: phase-1.1-1 failed ___ ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] ET and FAKtory
Dear Fink members, There is a DNA sequencing package called FAKtory http://www.cs.arizona.edu/faktory/FAKtory/over.html files at: http://bcf.arl.arizona.edu/resources/software/faktory/ doctutorials.html It is available as source, and as binaries for linux and solaris but not OS X. I contacted them and they emailed back the following statement: Sorry, but FAKtory only runs under Linux and Solaris. You are welcome to download the source code and try to compile on MacOS but I don't think that will work because it requires an old package called ET that only works with Tcl/Tk8.0. Does the package ET mean anything to anyone, and if so, do you know of a compiled version of ET for OS X. In the source folder I can see a libarary file et.o but it is already compiled by the look of it. Thanks, Mike Dyall-Smith --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Re: ET and FAKtory
Thanks for all the comments on this. I have some more information from the Faktory maintainer, Susan Miller: ET stands for Embedded Tk and this was written by Richard Hipp and supported up through Tk8.0. After that the package was replaced by mktclapp, but FAKtory already had thousands of lines of ET code and there was no automatable way to convert these calls to mktclapp. Hence FAKtory is stuck with ET/TclTk8.0 and will not work with more recent versions. Cheers, Mike --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] compiling ARB on 10.4.1
Dear Alexander Hansen, I have these files, but they have many more lines of text compared to the small file in /usr/include/stdarg.h Regards ,Mike Check and see if you have these, too: /System/Library/Frameworks/Kernel.framework/Versions/A/Headers/ stdarg.h /usr/include/gcc/darwin/3.3/stdarg.h /usr/lib/gcc/powerpc-apple-darwin8/4.0.0/include/stdarg.h /usr/lib/gcc/powerpc-apple-darwin8/4.0.0/install-tools/include/ stdarg.h (at least they're on my system. --AH --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] compiling ARB on 10.4.1
I have tried both g++2 and g++. With g++ it starts producing errors at about the same place, but continues (with errors) for longer. The output using g++ is below. The 'missing' aisc.h file is in GENH directory (which is in the NAMES_COM directory - where it is making at the time). The aisc.h file is produced by a script, but seems to be in the right places. I guess this might be difficult to pin down - there are a lot of files doing different things. Thanks anyway for your comments. - Mike D-Sits-dialin4asy23:~/arb_build mikeds$ sudo make arbmake arbbasic2 Make everything in AISC_MKPTPSgcc -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC_MKPTPS -c mkptypes.cgcc -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC_MKPTPS -o aisc_mkpt mkptypes.o Make everything in AISCg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC -c aisc.c -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC -c aisc_commands.c -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC -c aisc_var_ref.c -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC -c aisc_mix.c -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_AISC -o aisc aisc.o aisc_commands.o aisc_var_ref.o aisc_mix.o Make everything in NAMES_COMmake -r -f AISC/Makefile \ "MAIN_SOURCE=names.aisc" \ "PRIVATE_SERVER_OBJECTS = names_extern.o" \ "AISC_SAVE = YES" "COMPILER = g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_NAMES_COM" \ "CLIENTCOMPILER = g++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_NAMES_COM" "AR = ld -r -o"makedepend C/*.c GENC/*.c -I GENH -I C -f- -w1 | grep -v ' /usr' | sed -e 's/^C/O/g' .depends_newmakedepend: warning: C/aisc_extern.c, line 3: cannot find include file "aisc.h" not in GENH/aisc.h not in C/aisc.h not in /usr/local/lib/gcc-include/aisc.h not in /usr/include/aisc.hmakedepend: warning: C/client.c (reading /usr/include/stdarg.h, line 4): cannot find include file "stdarg.h"makedepend: warning: C/debug.c, line 6: cannot find include file "aisc_com.h"[snip]2 - LD_LIBRARY_PATH=../MAKEBIN/aisc AISC/aisc_server.pa ors.aisc GENC/aisc_server.c GENH/aisc_server_extern.aisc GENH/import_proto.hg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_ORS_COM -Wno-unused -c -o GENC/aisc_debug_globals.o GENC/aisc_debug_globals.c -IGENH -I. -ICrm -f GENH/aisc_server_proto.h../MAKEBIN/aisc_mkpt -C GENC/aisc_server.c GENH/aisc_server_proto.hecho GENH/import_proto.hGENH/import_proto.hg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_ORS_COM -Wno-unused -c -o GENC/aisc_global.o GENC/aisc_global.c -IGENH -I. -IC -DAISC_SAVE_NOg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_ORS_COM -Wno-unused -c -o GENC/aisc_server.o GENC/aisc_server.c -IGENH -I. -IC -DAISC_SAVE_NOg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_ORS_COM -Wno-unused -c -o ors_extern.o ors_extern.c -IGENH -I. -IC -DAISC_SAVE_NOld -r -o client.a O/client.o O/debug.o GENC/aisc_debug_globals.old -r -o server.a O/server.o O/struct_man.o O/aisc_extern.o GENC/aisc_global.o GENC/aisc_server.o ors_extern.o(cd lib;make nameserver)(cd nas;make all)rm -f *% Make everything in SLg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_SL -D_ARB_HELIX -c BI_helix.cxx -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_SL -D_ARB_AW_HELIX -c AW_helix.cxx -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeg++ -DDARWIN -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL -O4 -DNDEBUG -DFAKE_VTAB_PTR=char -D_ARB_SL -D_ARB_AW_NAME -c AW_rename.cxx -I. -I/Users/mikeds/arb_build/INCLUDE -I/usr/X11R6/includeIn file included from BI_helix.cxx:6:/Users/mikeds/arb_build/INCLUDE/arbdb.h:5:2:
Re: [Fink-users] compiling ARB on 10.4.1
One possible problem is that the code is written for linux, and uses gnu sed statements, with flags that are not recognised by bsd sed (such as -i for ignore case). Is there somewhere that explains what to do to make gnu sed statements legal (and equivalent) for bsd sed? For example, is there some equivalent switch for 'ignore case' in bsd sed? Thanks, Mike Dyall-Smith --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477alloc_id=16492op=click ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Staden and Emboss
Has anyone been able to get the staden bioinformatics package to talk to the Emboss package in Fink? The staden interface is very nice, and emboss has many useful programs. The staden spin menu bar has an emboss entry that lists all the emboss programs but I can't seem to configure it correctly so that the fink installed emboss is recognised by the externally installed staden package. - Mike Dyall-Smith -- * Mike Dyall-Smith, Ph.D.. Senior Lecturer Department of Microbiology and Immunology, University of Melbourne, 3010 Australia Tel: +(613) 8344-5693 Fax: +(613) 9347-1540 e-m: [EMAIL PROTECTED] web: http://www.microbiol.unimelb.edu.au/micro/staff/mds/ * --- This SF.Net email is sponsored by: INetU Attention Web Developers Consultants: Become An INetU Hosting Partner. Refer Dedicated Servers. We Manage Them. You Get 10% Monthly Commission! INetU Dedicated Managed Hosting http://www.inetu.net/partner/index.php ___ Fink-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Xaw3d (for xfig) fails
I am trying to install xfig and it needs quite a few other applications. Among them is Xaw3d. I have the latest Fink and packages (updated today). I have already installed most of the supporting applications, but with Xaw3d I get stuck early on with: ___ rm -rf xaw3d-1.5-3 mkdir -p /sw/src/xaw3d-1.5-3 tar -xzf /sw/src/Xaw3d-1.5.tar.gz Failed: directory /sw/src/xaw3d-1.5-3/xc/lib/Xaw3d doesn't exist, check the package description ___ Sure enough, if you look in the decompressed directory xaw3d-1.5-3, it only has the directory Xaw3d-1.5, there is no xc directory. any ideas? Regards, Mike Dyall-Smith
