[Fink-devel] Re: 10.2-gcc3 issues

2003-10-17 Thread Jack Howarth
Martin, I see the same error building g77 on my Powermac dual G5. I have Darwin 6.8.5 installed (still waiting on my copy of Panther). This is with the 10.2-gcc3 fink rsync and using the Aug 2003 gcc-3.3 updater from connect.apple.com. One other question. Does anyone with g77 3.4 compiled

Re: [Fink-devel] 10.2-gcc3 issues

2003-10-17 Thread Jack Howarth
Blair, It appears that the failures of building g77 are only happening on G5 powermacs. I looked over the gcc testsuite mailing list but it doesn't look as if any builds are being done with G5's yet. Jack --- This SF.net

[Fink-devel] How to rebuild all fink packages installed in 10.2-gcc3.3 rsync?

2003-10-22 Thread Jack Howarth
I have determined (as mentioned in my message on fink-users) that the build failures under Darwin 6.8.5 on my G5 of the most current g77 3.4 package is due entirely to fink itself. If I disable fink and build manually there are no problems and after sourcing fink, a make check-g77 of that

[Fink-devel] favoring static libs???

2003-11-22 Thread Jack Howarth
I may be dim here but I can't figure out how to do the following under the Darwin linker. I have some code that be linked against the static versions of a library and on linux can easily do this by passing the compiler... -Xlinker -Bstatic $(PYTHON_LDFLAGS) -Xlinker -Bdynamic which causes

[Fink-devel] newer snapshot for -minsert-sched-nops

2003-11-23 Thread Jack Howarth
Jeff, You may want to grab a newer snapshot of gcc 3.4 and release another g77 release to get the new -minsert-sched-nops support that IBM added... http://gcc.gnu.org/ml/gcc/2003-11/msg01233.html From reading Apple's G5 performance tech note (TN2086) it could prevent some significant

[Fink-devel] problem with newer g77 snapshots

2003-11-28 Thread Jack Howarth
Jeffrey, Have you tried updating the g77 package to a more recent snapshot. I seem to be see a huge number of new failures when I try the 20031126 snapshot... === g77 tests === Schedule of variations: unix Running target unix Using /sw/share/dejagnu/baseboards/unix.exp

Re: [Fink-devel] updates for packages that I don't maintain

2004-03-06 Thread Jack Howarth
David, Have you had any luck yet with the pymol-0.93 package that Scott posted? Did you try moving aside your current /sw and reinstalling fink 10.3? Also have you tried another machine? Jack ps If anyone else has had problems using Scott's posted pymol info/patch files could

[Fink-devel] lammpi 7.0.6-10 in 10.3/unstable build is broken

2004-08-10 Thread Jack Howarth
The current build of lammpi 7.0.6-10 in unstable is flawed in that it creates a hybrid mix of shared and static libs rather than a complete set of one or the other. I fixed this locally by appending --enable-shared to the ConfigureParams. This change allowed me to build a shared lib version

[Fink-devel] shlibs vs Type variants

2004-08-11 Thread Jack Howarth
I am trying to create a -mpi variant of the fftw package using the Type field. I have managed to create a fftw.info that will build either fftw/fftw-shlibs or fftw-mpi/fftw-mpi-shlibs depending on what (fftw or fftw-mpi) is passed to 'fink install'. However am baffled on what options I have to

[Fink-devel] new fink breaks fftw to fftw-mpi upgrade

2004-08-23 Thread Jack Howarth
Daniel, I have only tested this on one machine but it seems the current fink in 10.3 (0.21.2-1) breaks upgrading fftw/fftw-shlibs to fink-mpi/ fink-mpi-shlibs with the following comands... fink install fftw fink install fftw-mpi Now the installation of fftw-mpi fails with... /usr/bin/sudo

[Fink-devel] fink and conditional provides

2004-08-24 Thread Jack Howarth
Daniel, You might want to take a look at how fink currently handles Provides. As I mentioned before, I had to create a new revision of fftw (2.1.5-6) because the addition of Provides: fftw to both the fftw and fftw-mpi as well as Provides: fftw-shlibs to both the fftw-shlibs and

Re: [Fink-devel] fink and conditional provides

2004-08-24 Thread Jack Howarth
Dave, Could you look at the current fftw.info and grace.info in unstable and make some suggestions? The problem that the Provides was meant to solve was the following. If one does fink install grace it will automatically install fftw. However without the Provides: fftw-shlibs added to

Re: [Fink-devel] fink and conditional provides

2004-08-25 Thread Jack Howarth
Dave, Can you clarify this a little more? I don't quite see where the breakage will occur if I use Provides: fftw-shlibs in the main fftw package which contains the headers. For example, I did... fink install gromacs (picking fftw) fink install gromacs-mpi (which installed fftw-mpi) Then

Re: [Fink-devel] fink gcc?

2004-08-26 Thread Jack Howarth
Martin, Has anyone documented a few of these g++ problems and brought them up on the darwin-development mailing list at Apple? I have found that the Apple devtool programmers that monitor that list can often be quite helpful. At the very least, it will bring these problems to their attention

Re: [Fink-devel] fink gcc?

2004-08-26 Thread Jack Howarth
Martin, Just a stab in the dark, but have you considered trying to rebuild octave with -fssa and -fssa-dce? Perhaps using the experimental dead code elimination will work around the missing symbols. Jack --- SF.Net

[Fink-devel] fink breakage?

2004-08-28 Thread Jack Howarth
Daniel, William Scott just pointed out that fftw now creates shared libs with dependencies into /sw/src. otool -L /sw/lib/libdfftw.2.dylib /sw/lib/libdfftw.2.dylib: /sw/src/root-fftw-mpi-2.1.5-6/sw/lib/libdfftw.2.dylib (compatibility version 3.0.0, current version 3.7.0)

Re: [Fink-devel] fink breakage?

2004-08-29 Thread Jack Howarth
Peter, I am using the libtool from Xcode 1.5. Unfortunately I don't see a way to tell what version that libtool is. Perhaps if a package needs to use ''make install prefix=%i', it should have an explicit BuildDepends on a specific libtool from fink devel? Jack

Re: [Fink-devel] problems compiling against fftw-2.1.5-6

2004-08-29 Thread Jack Howarth
Martin, I was able to fix this by moving the '--infodir=%p/share/info' into ConfigureParams and changing any occurances of... make install prefix=%i infodir=%i/share/info ...into... make install DESTDIR=%d With those changes, sent to the maintainer, I find that the linkage problem

Re: [Fink-devel] fink breakage?

2004-08-29 Thread Jack Howarth
Peter, Perhaps the fink packaging manual should be corrected to be more explicit about this problem. It should probably state clearly that make install DESTDIR=%d is the perferred form of installation (compared to using make install prefix=%i) whenever possible. Jack

[Fink-devel] freeglut

2004-08-31 Thread Jack Howarth
Daniel, I have updated the freeglut packaging for the proposed freeglut package. I have now verified that it is in fact a binary compatible drop-in replacement for glut. I am able to have glut/glut-shlibs/molmol/gopenmol installed and upgrade to freeglut/freeglut-shlibs without any binary

[Fink-devel] freeglut package

2004-09-21 Thread Jack Howarth
I have had my proposed freeglut packaging in tracker for awhile now and there has been no further comments even though it is still marked as undergoing evaluation. https://sourceforge.net/tracker/?func=detailatid=414256aid=1017330group_id=17203 Is there any particular problems with this

Re: [Fink-devel] freeglut package

2004-09-21 Thread Jack Howarth
Michal, I have been told that the compatibility version is rather arbitrary and that is a non-issue. All the major Linux distros have adopted freeglut since it is trully open source and, more importantly, actively maintained. As for rbogl, I would suggest you file a bug report with the form

[Fink-devel] Xcode 1.5 c++ fix released!

2004-11-19 Thread Jack Howarth
Apple has released the November 2004 gcc 3.3 update on connect.apple.com today. This updater fixes the c++ compiler issues that have been plaguing fink. Jack --- This SF.Net email is sponsored by: InterSystems CACHE FREE

[Fink-devel] g95 code

2005-04-15 Thread Jack Howarth
In testing some builds of the APBS Adpative Poisson-Boltzmann Solver package under fink, I noticed that the g95 compiler currently in 10.3 unstable builds a usable version of apbs. However I was shocked at how much of a performance regression there was from g77. APBS runs almost 60% slower

[Fink-devel] Re: glut-3.7-23

2005-04-16 Thread Jack Howarth
Dan, I noticed your messages about the freeglut packaging being broken. With the 10.4 branch being created, I think now is a good time to address this issue. Since glut and freeglut are not really binary replacements it should be decided whether freeglut should replace the glut package in the

[Fink-devel] Re: Re: glut-3.7-23

2005-04-16 Thread Jack Howarth
Dan, I think we should follow Debian's lead here. They are in the process of depreciating out their libglut3 package in favor of freeglut. They have replaced their old libglut3 package, based on the old non-free version, with a dummy package that depends on freeglut as a transitional

[Fink-devel] Re: Re: glut-3.7-23

2005-04-16 Thread Jack Howarth
Dan, I believe the following versions of freeglut.info and glut.info are close to what we need for 10.4 Package: freeglut Version: 2.2.0 Revision: 2 GCC: 3.3 Maintainer: Jack Howarth [EMAIL PROTECTED] Source

[Fink-devel] Re: Re: glut-3.7-23

2005-04-16 Thread Jack Howarth
://freeglut.sourceforge.net/ - Package: glut Version: 3.7 Revision: 25 GCC: 3.3 Maintainer: Jack Howarth [EMAIL PROTECTED] Source: None Depends: freeglut BuildDepends: fink (= 0.9.9) BuildDependsOnly: True PatchScript: CompileScript

[Fink-devel] Re: Re: Re: glut-3.7-23

2005-04-17 Thread Jack Howarth
Dan, What if we patch the freeglut package to build with a different shared lib version number? I think this is the main source of the confusion out there. The developers of freeglut let it create a libglut.3.x.x.so/dylib when it should have been bumped up to libglut.4.x.x.so/dylib or such

Re: [Fink-devel] Re: Re: Re: glut-3.7-23

2005-04-17 Thread Jack Howarth
Chris, Well I did a quick test of changing the versioning and that doesn't help much under fink anyway. If I use... Package: freeglut Version: 2.2.0 Revision: 2 GCC: 3.3 Maintainer: Jack Howarth howarth at bromo.med.uc.edu Source: mirror:sourceforge:freeglut/%N-%v.tar.gz Source-MD5

Re: [Fink-devel] Re: Re: Re: glut-3.7-23

2005-04-17 Thread Jack Howarth
Chris, I've tried a test build of the current glut package where I have the following packaging... ...for the glut package... -rwxr-xr-x 1 root admin 744232 17 Apr 15:56 /sw/lib/glut/libglut.a lrwxr-xr-x 1 root admin 14 17 Apr 15:56 /sw/lib/libglut.a - glut/libglut.a lrwxr-xr-x 1 root

[Fink-devel] revised glut/freeglut again

2005-04-17 Thread Jack Howarth
and the debs they create all pass fink validate. -- Package: glut Version: 3.7 Revision: 24 GCC: 3.3 Maintainer: Jack Howarth [EMAIL PROTECTED] Source: http://www.opengl.org/developers/documentation/%N/%N-%v.tar.gz Source-MD5

[Fink-devel] Re: Re: Re: Re: glut-3.7-23

2005-04-18 Thread Jack Howarth
Martin, I didn't try to add a BuildConflicts yesterday to either the glut or freeglut packaging. The proposed packaging I posted yesterday didn't cause glut to be removed automatically when freeglut was built and freeglut to be removed when glut was built. Since the freeglut examples seem to

[Fink-devel] glut and freeglut one last time

2005-04-18 Thread Jack Howarth
that need glut. Jack Package: freeglut Version: 2.2.0 Revision: 2 GCC: 3.3 Maintainer: Jack Howarth [EMAIL PROTECTED] Source: mirror:sourceforge:freeglut/%N-%v.tar.gz Source-MD5: 9439b8745f443131c2dad00bc93dc0ef

[Fink-devel] glut/freeglut/pymol/molmol on tracking server

2005-04-19 Thread Jack Howarth
Dan, I believe I finally have the revised glut and freeglut packaging done. I have submitted their info files onto the tracking server as well as revised info files for molmol and pymol so they can be built against either. Let me know if there are any problems but everything is passing

[Fink-devel] packages in tracking

2005-04-20 Thread Jack Howarth
Is there anything I can do to accelerate the movement of the revised packaging I have submitted for glut, freeglut, pymol and molmol through the tracking system and into unstable fink 10.3? These submissions are...

[Fink-devel] pymol 0.98-1

2005-05-05 Thread Jack Howarth
Daniel, Can you give me some guidance on what approach I should take with the freeglut/glut dependency? I assume you are using the freeglut/glut packages from 10.3 unstable that I recently submitted which should have resolved the conflicts between the two. However the absence of true

[Fink-devel] pymol-py 0.98-1

2005-05-16 Thread Jack Howarth
Dan, What else do I need to do to get the new variant version of the pymol package (now pymol-py) into fink unstable? Jack ps The pymol-py.info and pymol-py.patch files are both uploaded into the fink package tracker. Note that these would both replace the current pymol.info

[Fink-devel] pymol-py

2005-05-20 Thread Jack Howarth
Dan, I have uploaded a new revision of the pymol-py.info file which limits the package to building against freeglut. This should eliminate your last remaining complaint. Can we please proceed with depreciating the pymol package from fink 10.3 and 10.4-transitional unstable and replacing it

[Fink-devel] fink in unstable is unstable

2005-05-20 Thread Jack Howarth
Dan, I have noticed that the recent changes to fink in 10.4-transitional unstable make builds very fragile. For example, if one has glut and glut-shlibs installed and with the new proposed packaging for pymol-py (which limits the build to against freeglut) installed in

[Fink-devel] Re: fink in unstable is unstable

2005-05-23 Thread Jack Howarth
Martin, I don't think it is wise to remove the BuildConflicts for freeglut and glut. The current freeglut and glut packaging has freeglut built as libfreeglut rather than libglut to avoid the binary incompatibility of the libraries. However to avoid requiring any package that wants to use

[Fink-devel] revised freeglut/glut submitted

2005-05-23 Thread Jack Howarth
I have submitted revised version of the glut (3.7-25) and the freeglut (2.2.0-3) packages for fink unstable into the tracking system. The only changes made were the removal of the Build-Conflicts line which currently isn't handled properly under fink. This change will prevent fink from

[Fink-devel] new pymol-py package

2005-05-23 Thread Jack Howarth
I have resubmitted the pymol-py package as new package on the tracker since I was having no luck whatsoever in getting this into unstable. Once again, this pymol-py package replaces the current pymol package and allows builds against python2.2, python2.3 or python2.4 with the resulting

Re: [Fink-devel] new pymol-py package

2005-05-23 Thread Jack Howarth
Koen, The pymol-py package should go in both the 10.3 and 10.4-transitional trees (unstable). Thanks in advance. Jack --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space?

Re: [Fink-devel] new pymol-py package

2005-05-24 Thread Jack Howarth
Koen, Thanks for getting the modified freeglut and glut packages in 10.3 and 10.4-transitional unstable. I have one last request. I have uploaded a new molmol.info file (2k.2.0-19) for the unstable branch of 10.4-transitional. This version builds against gcc-4.0 and freeglut. It passes fink

Re: [Fink-devel] new pymol-py package

2005-05-24 Thread Jack Howarth
Koen, As requested by Daniel, I have reverted the molmol 2k.2.0-19 package to build with gcc-3.3 once again rather than gcc-4.0. This version will be okay for both 10.3 and 10.4-transitional unstable. It is uploaded into the tracker...

Re: [Fink-devel] new pymol-py package

2005-05-24 Thread Jack Howarth
Koen, Well in the case of glut and freeglut, I have verified that the builds aren't leaky. The glut build never looks in /sw/lib or /sw/include for headers or libraries. The freeglut build is safe with glut installed since it uses the freeglut basename for its headers and libraries and thus

Re: [Fink-devel] gcc-4.0 and g++-3.3

2005-05-27 Thread Jack Howarth
Peter, I had read the posts before about the ABI changes for c++ and knew that g++-3.3 was going to be retained as the default compiler for fink 10.4. However, I hadn't seen any explicit mention of gcc-4.0 being the c compiler. Jack

[Fink-devel] Re: gcc-4.0 and g++-3.3

2005-05-27 Thread Jack Howarth
Peter, I checked on the gcc mailing list and Mike Stump at Apple Computer replied... http://gcc.gnu.org/ml/gcc/2005-05/msg01515.html As I suspected, there will be cases of breakage when g++-3.3 is used to link programs containing gcc-4.0 generated object code. So we will have to be on the

[Fink-devel] gfortran package

2005-07-25 Thread Jack Howarth
Jeffrey, Could you possibly add a gfortran package to fink unstable based off of the main trunk or 4.1 branch? Since g95 and gfortran have heavily forked, any bugs I find and report against g95 aren't easily checked against the current gfortran code to see it the problem exists there. It

Re: [Fink-devel] gfortran package

2005-07-25 Thread Jack Howarth
Peter, For the features I need from gfortran, I'll need to be on the 4.1 branch. We should be testing that anyway since it is slated for release in Sept. In any case, I am trying the following gfortran.info at the moment...

Re: [Fink-devel] gfortran package

2005-07-25 Thread Jack Howarth
Peter, I think one can hardly call the g95 compilers we currently put out as 'released compilers'. These are daily snapshot builds of g95 which are broken and fixed at regular intervals. As for the gcc-4.0.1 package...what is its real purpose? The compilers other than c and c++ are likely

Re: [Fink-devel] gfortran package

2005-07-25 Thread Jack Howarth
Peter, You may have point regarding the 4.1 branch, but I would say that the 4.0.2 branch is highly unlikely to be much less stable for gfortran than the 4.0.1 release is. Again the question really is what is the purpose of the gcc4 package? If it is primarily a release mechanism for gfortran,

Re: [Fink-devel] gfortran package

2005-07-28 Thread Jack Howarth
Still one has to ask exactly which compilers in the gcc4 package we should be focusing on? The gfortran compiler specifically is making really good progress. With patches to be added today, it should pass almost all of the NIST Fortran validation testsuite. I think we would be far better off

[Fink-devel] why is fink svn so slow?

2005-10-31 Thread Jack Howarth
Now that the gcc developers have switched over to svn and stopped keeping their cvs tree as current, I decided to fink install the svn-client under MacOS X 10.4.3. However I found that 'svn -q checkout svn://gcc.gnu.org/svn/gcc/trunk gcc' appears to take more than a order of magnitude longer

[Fink-devel] proper fix for g77 package?

2005-11-16 Thread Jack Howarth
Since a new gromacs, version 3.3 has been released, I will be updating the fink gromacs package soon. However, we will need to address the breakage in g77 from Xcode 2.2 for the required lammpi support to work. The last time I asked any of the Darwin programmers about the buried path to

Re: [Fink-devel] proper fix for g77 package?

2005-11-17 Thread Jack Howarth
Jeffrey, FYI, I have finished a revised fftw3.info script which allows -mpi versions of fftw3 to be built as we currently do for fftw. I will need the mpi support in fftw3 when I upgrade the gromacs-mpi package to version 3.3 which was just released. Currently I am stuck on some new shared

[Fink-devel] lammpi 7.1.1 build problems

2005-11-18 Thread Jack Howarth
Has anyone tried updating lammpi from fink 10.4-transitional unstable to the newer 7.1.1 release source code? I am seeing the same thing that William Scott was. The fink packaging produces a lammpi for 7.1.1 which appears to compile and install fine but is unable to execute lamboot properly. I

[Fink-devel] RE: lammpi 7.1.1 build problems

2005-11-18 Thread Jack Howarth
I don't understand why this build problem happens under fink but I believe I have identified the offending file. It appears that the breakage in the fink build of lam 7.1.1 originates in the liblam.0.0.0.dylib shared library. Oddly the fink built version shows... otool -L liblam.0.0.0.dylib

[Fink-devel] RE: lammpi 7.1.1 build problems

2005-11-18 Thread Jack Howarth
Oddly I see to see that when fink links liblam.0.0.0.dylib with gcc called as gcc-4.0, I have... gcc-4.0 -dynamiclib ${wl}-undefined ${wl}dynamic_lookup -o .libs/liblam.0.0.0.dylib ...etc whereas when I build lam 7.1.1 manually I end up with... gcc -dynamiclib ${wl}-flat_namespace

Re: [Fink-devel] RE: lammpi 7.1.1 build problems

2005-11-19 Thread Jack Howarth
Peter, Actually 'NoSetMACOSX_DEPLOYMENT_TARGET: true' is insufficient. I had to resort to 'SetMACOSX_DEPLOYMENT_TARGET: 10.2' in order to force libtool to use -undefined suppress. I'll post the packaging I have into the fink tracking system later today. There also was a patch I added to force

[Fink-devel] new gromacs/gromacs-mpi/fftw3/lammpi

2005-11-19 Thread Jack Howarth
I have posted new gromacs and gromacs-mpi 3.3-1 packages on the fink tracking system. While upgrading gromacs, I noticed that the lammpi build for 7.1.1 needed fixing for fink packaging and have posted 7.1.1-1 packaging which produces a working lamboot. Lastly I have updated the fftw3 packages

[Fink-devel] -force_flat_namespace not allowed with -dynamiclib

2005-11-19 Thread Jack Howarth
I have posted three updated packages on the fink tracking system for lammpi 7.1.1-1, fftw3-3.0.1-1 and gromacs/gromacs-mpi 3.3-1. However I discovered afterwards that while the lam-7.1.1-1 package has a working lamboot it seems to have broken the linking of gromacs-mpi. I am now seeing errors

Re: [Fink-devel] -force_flat_namespace not allowed with -dynamiclib

2005-11-19 Thread Jack Howarth
Peter, I have verified that the current gromacs-mpi packaging for 3.3-1 in fink tracking builds fine against the lam-7.0.6-11 currently in unstable. The problem seems to be specific to lam-7.1.1. With the lam-7.1.1-1 package installed (which was built with MACOSX_DEPLOYMENT_TARGET 10.2), I

Re: [Fink-devel] -force_flat_namespace not allowed with -dynamiclib

2005-11-20 Thread Jack Howarth
Peter, Actually I think the problem with lam 7.1.1 originates more from the massive changes they have made to its aclocal.m4 file. The libtool that is generated from configure during the build shows the following diffs from that generated by lam 7.0.6... # How to create reloadable object

Re: [Fink-devel] -force_flat_namespace not allowed with -dynamiclib

2005-11-21 Thread Jack Howarth
Peter, Are you certain it is the need for -fPIC is limited at all with regard to static code in shared libs. In his article, Drepper says... The most important recommendation is to always use -fpic or -fPIC when generating code which ends up in DSOs. This applies to data as well as code. Code

Re: [Fink-devel] -force_flat_namespace not allowed with -dynamiclib

2005-11-21 Thread Jack Howarth
Peter, Hmmm. Is -fPIC and -fno-common equivalent? I specifically recall that I had to add -fno-common to the compilation of the static lib liblammpio.a to eliminate the common symbols in it and thus eliminate the need for the -W1,-single-module hack to build gromacs-mpi's shared libs. I would

Re: [Fink-devel] -force_flat_namespace not allowed with -dynamiclib

2005-11-21 Thread Jack Howarth
Peter, FYI, James Gibbs just emailed me to say he should no longer be considered an active developer and not to wait on him to submit the new packaging for lammpi 7.1.1-1. He said that I could adopt maintaining lammpi or it could be considered unowned. I'll be happy to maintain lammpi and

[Fink-devel] pymol-py bus errors

2005-12-19 Thread Jack Howarth
Is anyone having problems with the pymol-py package. I got a report today about undefined symbols for _XF86VidModeGetViewPort referenced from libfreeglut.3.dylib in _cmd.so. I don't see this under Xcode 2.2 but on our G4s I am finding that pymol has a bus error when it gets to the point of

[Fink-devel] how to make patch script fail if patch missing

2005-12-19 Thread Jack Howarth
If a package uses a patchscript rather than the automatic patch application by fink, is there a recommended approach to aborting the build if the patch is missing. I just noticed that 'fink install pymol-py24' will build against the python 2.3 headers if the pymol-py.patch file is missing. Are

[Fink-devel] RE: pymol-py bus errors

2005-12-19 Thread Jack Howarth
I've puzzled out the general cause of the bus errors on the G4 here at work with pymol. Since I had two equal sized drives in the machine and the system drive was getting full, I had archived the /sw directory and moved it over to /Volumes/Data with a symlink in the root partition of the

[Fink-devel] what is fink policy on system python?

2005-12-22 Thread Jack Howarth
While testing the apbs and pdb2pqr packages (which run their python scripts using /usr/bin/python), I discovered some potential breakage. The current info scripts for these packages have a Depends on python. However since these packages (at least pdb2pqr for sure) build extensions against the

[Fink-devel] Re: what is fink policy on system python?

2005-12-23 Thread Jack Howarth
Daniel, I figured out last night that passing configure 'py_path=/usr/bin/python' seems allow the system python to be properly located even if the fink python package is installed. I'll take a look at some of the other fink packages still using python as a depends to try to identify which ones

[Fink-devel] Re: why doesn't curl work for molmol

2005-12-25 Thread Jack Howarth
Martin, Here I get... ftp ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip Connected to imb-sv-30.ethz.ch. 220 Welcome to Molecular Biology FTP service. 331 Please specify the password. 230- 230- Welcome to the ftp-Server of the Biophysics Group 230-

[Fink-devel] freeglut in stable

2005-12-25 Thread Jack Howarth
Daniel, Can we move freeglut into stable so that we can have pymol-py in stable as well? I don't believe there is anything left broken in freeglut now. It builds its libs as libfreeglut and none of the existing packages should still have glut|freeglut (i.e. they all pick one or the other for

Re: [Fink-devel] freeglut in stable

2005-12-26 Thread Jack Howarth
Michal, No, freeglut and glut are not interchangable. However, freeglut now builds with -disable-replace-glut so that it remains named as libfreeglut rather than libglut. I do have the freeglut package symlink... ln -s libfreeglut.3.dylib %i/lib/libglut.dylib as well as the headers, so that

Re: [Fink-devel] -mtune/-mcpu and macintel

2006-04-10 Thread Jack Howarth
Dave, For the sparky-py fink packages, I have a sparky-py.patch which patches the Makefile to have ... -CXX= g++ -CXXFLAGS = +CXX= g++-3.3 +CXXFLAGS = -O3 -ffast-math -mtune=970 -fPIC -fno-common -Wno-long-double CC = gcc -CFLAGS =

[Fink-devel] what is macintel mtune/march defaults?

2006-04-11 Thread Jack Howarth
I am wondering if anyone with a MacIntel box can tell me what the default settings for the Apple gcc 4.0 compiler are on that architecture for -mtune and -march? Several web sites recommend the use of -mtune=prescott -march=pentium-m for FSF gcc. Are these the automatic defaults in Apple's

Re: [Fink-devel] what is macintel mtune/march defaults?

2006-04-11 Thread Jack Howarth
Martin, That doesn't quite make sense. How can MacIntel use nocona if the Core Duo's don't have the EMT64 extensions? Jack --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends

[Fink-devel] 10.4 unstable static?

2006-04-20 Thread Jack Howarth
Has work on the 10.4 branch stalled? I have noticed for the past several weeks that 'fink selfupdate' from the cvs doesn't seem to pull down any new updates. Only the messages about... cvs update: -m wrapper option is not supported remotely; ignored I starting to wonder if the cvs part of

[Fink-devel] non-PIC in shared lib detect in fink validate

2006-04-26 Thread Jack Howarth
I discovered that the gmp developers have been incorrectly building non-PIC code into their shared libraries. They have been using -fast which sets -mdynamic-no-pic without adding an explicit -fPIC. I recall some discussion on the debian mailing lists of checking for non-PIC code in linux

[Fink-devel] gcc4 needs patch

2006-04-29 Thread Jack Howarth
Jeff, Now that gmp 4.2 is in unstable we will need to patch gcc4 to build against it. This issue is discussed in the thread... http://gcc.gnu.org/ml/fortran/2006-04/msg00183.html and the proposed patch is in... http://gcc.gnu.org/ml/fortran/2006-04/msg00190.html which changes the dependency

[Fink-devel] why depend on g95?

2006-05-05 Thread Jack Howarth
I am wondering why packages like fftw3 are depending on g95 rather than gfortran? While this may be useful in the short term I think we would be far better off with gfortran in the long run. As far as I know the g95 source still is devoid of a decent test suite so there is no good way to

Re: [Fink-devel] why depend on g95?

2006-05-08 Thread Jack Howarth
Martin, Have you tried the current gcc 4.1 branch from snapshot or svn? I would avoid gcc 4.2 for now since it is so far from release. However there are a huge number of fixes in the 4.1 branch for gfortran since the 4.1.0 release. They might have backported the MacIntel changes into that

[Fink-devel] gcc 4.1.1 and gmp 4.2.1

2006-05-16 Thread Jack Howarth
Jeff, The gcc developers are still hashing over how to introduce the required patches for gmp 4.2.x since it no longer builds gmp against mpfr and must gfortran must link mpfr in explicitly. The patch I sent you a few weeks ago is still valid and can should be used for the gcc 4.1.1 package in

[Fink-devel] gcc4 and cctools

2006-06-05 Thread Jack Howarth
The cctoools installed by Xcode 2.3 apparently resolves the ld64 bugs in that were forcing gcc4 to be built with --disable-multilib... http://gcc.gnu.org/ml/gcc/2006-06/msg00160.html I'l try to get Geoffrey Keating to release a new cctool release in infrastructure of the gcc.gnu.org ftp

[Fink-devel] new odcctools needed

2006-06-06 Thread Jack Howarth
Jeff, According to Geoffrey Keating at Apple, the cctools from Xcode 2.3 eliminates the problem with ld64 which was forcing us to build gcc4 for 4.2 with --disable-multlib. While there isn't a new odcctools tarball yet, you can roll your own for a odcctools based on the same cctools 590.42.1

[Fink-devel] gcc4 4.2 without patches

2006-06-06 Thread Jack Howarth
Having noticed an odd c++ regression in gcc 4.2 built with the gcc4.info file from 10.4 unstable fink, I have been building gcc trunk for the last couple of weeks on a G5. I noticed if I build without the gcc4.patch applied that I end up with a slew of new g++ testsuite regressions. However,

Re: [Fink-devel] new odcctools needed

2006-06-06 Thread Jack Howarth
Peter, The problem is that almost no one is testing gcc trunk on darwin except for Apple. However they don't build things like gfortran so that breakage there can go unreported for quite a while. Most worrisome is the testsuite results like...

Re: [Fink-devel] gcc4 4.2 without patches

2006-06-06 Thread Jack Howarth
In case anyone else is following gcc trunk with fink installed, I should clarify what I have found so far. If I have fink installed (but not odcctools), I can build gcc trunk from the gcc svn against Xcode 2.3. However, if fink is sourced I get the odd g++ regressions. If fink isn't sourced,

Re: [Fink-devel] gcc4 4.2 without patches

2006-06-06 Thread Jack Howarth
Matthew, I'll try a build tonight of gcc trunk with fink sourced but with the path reset to eliminate any directories in /sw. That should tell me if the problem is some binary in /sw/bin or /sw/sbin effecting the gcc trunk build. Jack

Re: [Fink-devel] gcc4 4.2 without patches

2006-06-06 Thread Jack Howarth
Matthew, I see the same g++ regressions (when I build gcc trunk under fink with odcctools deinstalled and Xcode 2.3 installed) as reported here... http://gcc.gnu.org/ml/gcc-testresults/2006-06/msg00221.html I am waiting to hear back from Bradley about the details of his build configuration.

Re: [Fink-devel] gcc4 4.2 without patches

2006-06-06 Thread Jack Howarth
Matthew, I believe I have pinpointed the component in fink 10.4 that was causing the c++ regressions in gcc trunk when built with fink sourced. After deinstalling bison 2.1 installed by fink, I find that gcc builds without c++ regressions. The regressions that previously occurred were those

[Fink-devel] bison needs updated to 2.3

2006-06-07 Thread Jack Howarth
I have confirmed that the c++ regressions I have been seeing in gcc trunk are specific to having the fink bison 2.1 package installed during the gcc build. If build with either the bison 2.1 package deinstalled or with a bison 2.3 package installed, the c++ regressions don't occur. I strongly

Re: [Fink-devel] bison needs updated to 2.3

2006-06-07 Thread Jack Howarth
Martin, Why would you think that a 2.x release series of bison wouldn't be backwardly compatible? Jack ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel

Re: [Fink-devel] fink build environment

2006-06-07 Thread Jack Howarth
JF, I checked it with some echo statements in the compile script. The only set in fink for the gcc4 build is SetMACOSX_DEPLOYMENT_TARGET. I've added... NoSetMACOSX_DEPLOYMENT_TARGET: True to gcc4.info and will try a build of tonight's gcc trunk. Hopefully this is the source of the g++

[Fink-devel] gcc 4.2 issues solved

2006-06-07 Thread Jack Howarth
Jeff, I figured out the g++ regressions I have been suffering with gcc trunk built as a fink package. The problem is in PR 26792... http://gcc.gnu.org/bugzilla/show_bug.cgi?id=26792 and can be solved simply by adding... NoSetMACOSX_DEPLOYMENT_TARGET: True ...to gcc4.info. You will also want

Re: [Fink-devel] gcc 4.2 issues solved

2006-06-08 Thread Jack Howarth
Martin, Well, from the comments in the PR, Geoff was protecting the 10.4 version of libgcc. I believe they are free to add that symbol to 10.5's libgcc however. FYI, what I have been doing is using gcc4 built with the current gcc trunk to build xplor-nih. In doing so I noticed a c++ regression

Re: [Fink-devel] bison needs updated to 2.3

2006-06-08 Thread Jack Howarth
Martin, Actually I thought of adding bison to the BuildConflicts for gcc4. However I still think upgrading to bison 2.3 can't be that bad of a move since it is a .X release. Anyway I try to be an optimist about the eventual progress in software development (however convoluted the path may be).

Re: [Fink-devel] gcc 4.2 issues solved

2006-06-09 Thread Jack Howarth
Peter, I'll test it. Hopefully we can get the odcctools update into fink soon and Jeff can create a new gcc4 from the next snapshot with '--disable-multlib' dropped and MACOSX_DEPLOYMENT_TARGET unset for that package. I would also not that Mike Stump has made a recent change that we really

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