Re: [Fink-devel] A few 10.11 glitches and possible workarounds

[William G. Scott]

> On Oct 1, 2015, at 8:01 AM, Alexander Hansen <alexanderk.han...@gmail.com> 
> wrote:
> 
> 
>> On Oct 1, 2015, at 07:59, Hanspeter Niederstrasser <f...@snaggledworks.com> 
>> wrote:
>> 
>> On Thu, October 1, 2015 9:17 am, William G. Scott wrote:
>>> 
>>>> On Oct 1, 2015, at 4:16 AM, Hanspeter Niederstrasser
>>>> <f...@snaggledworks.com> wrote:
>>>> 
>>>> What happens if you run
>>>> 
>>>> . /sw/sbin/fink-buildenv-helper.sh
>>>> 
>>>> from a new terminal window?  If it immediately exits (say with a
>>>> MACOSX_DEPLOYMENT_TARGET failure), set MACOSX_DEPLOYMENT_TARGET to 10.11
>>>> in your shell, and try running fink-buildenv-helper.sh again.
>>>> 
>>>> Hanspeter
>>> 
>>> OK, that was the problem, and manually setting $MACOSX_DEPLOYMENT_TARGET
>>> worked.  (I didn’t explicitly check to see if that solved the problem
>>> within the package I was having trouble with, but the output suggests that
>>> it would).  To my knowledge, I never explicitly set
>>> $MACOSX_DEPLOYMENT_TARGET in previous OS X versions (i.e., the same
>>> package compiles without incident on 10.10, 10.9, 10.6).  This happens
>>> with bash, tcsh and zsh.
>> 
>> There are two mismatch checks in fink-buildenv-helper.sh.  One checks that
>> your OS version matches the MACOSX_DEPLOYMENT_TARGET that Fink sets during
>> a build. The other check is to make sure that the available SDK and
>> MACOSX_DEPLOYMENT_TARGET match.  But 10.11 now also uses the 10.10 SDK, so
>> I need to release a new helper script that says 10 equals 11.
>> 
>> Hanspeter
>> 
>> -- 
>> More agile than a turtle, stronger than a mouse, nobler than a lettuce
>> 
>> 
> 
> Isn’t it the other way around?  I thought the case was that 10.10 uses the 
> 10.11 SDK for Xcode 7.
> 


May I suggest changing all instances of “exit 1” to “return 1”  in  
/sw/lib/fink-buildenv-modules/base.sh so that the shell itself doesn’t exit 
when the file is sourced rather than executed?



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Re: [Fink-devel] A few 10.11 glitches and possible workarounds

[William G. Scott]

> On Oct 1, 2015, at 4:16 AM, Hanspeter Niederstrasser  
> wrote:
> 
> What happens if you run
> 
> . /sw/sbin/fink-buildenv-helper.sh
> 
> from a new terminal window?  If it immediately exits (say with a 
> MACOSX_DEPLOYMENT_TARGET failure), set MACOSX_DEPLOYMENT_TARGET to 10.11 in 
> your shell, and try running fink-buildenv-helper.sh again.
> 
> Hanspeter

OK, that was the problem, and manually setting $MACOSX_DEPLOYMENT_TARGET 
worked.  (I didn’t explicitly check to see if that solved the problem within 
the package I was having trouble with, but the output suggests that it would).  
To my knowledge, I never explicitly set $MACOSX_DEPLOYMENT_TARGET in previous 
OS X versions (i.e., the same package compiles without incident on 10.10, 10.9, 
10.6).  This happens with bash, tcsh and zsh.

[BTW, running  /sw/sbin/fink-buildenv-helper.sh  as an executable gives me a 
meaningful error.  Sourcing it   .  /sw/sbin/fink-buildenv-helper.sh  just 
exits the shell. ]
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Re: [Fink-devel] command-line tools for 10.10-beta ?

[William G. Scott]

 On Oct 5, 2014, at 5:58 PM, Alexander Hansen alexanderk.han...@gmail.com 
 wrote:
 
 On 10/5/14, 4:05 PM, William G. Scott wrote:
 
 
 On Oct 5, 2014, at 3:14 PM, Alexander Hansen alexanderk.han...@gmail.com 
 wrote:
 
 Are you using our Yosemite developer branch ('HalfDome')?
 
 Yes.  (Sorry, I should have specified this.)
 
 
 Hmm...Maybe they changed the name of the receipt again.  I've got a developer 
 preview environment (but I haven't been looking at it in a while) so I'll see 
 what I get.
 
 -- 
 Alexander Hansen, Ph.D.
 Fink User Liaison
 My package updates: http://finkakh.wordpress.com/

I wound up hacking the bootstrap script to get it to work.

Along the way, I needed to make minor changes to the following packages that 
are indirect (or direct) dependencies on mine:

sci/fftw.info   (changed to gcc49; used Jack Howarth's exptl)
libs/perlmods/locale-gettext-pm.info
devel/help2man-perl.info
devel/intltool40-10.10.info
libs/perlmods/scalar-list-utils-pm
graphics/libvpx.info
ocaml
devel/po4a-10.10.info
libs/perlmods/term-readkey-pm.info

I never succeeded in gettinggraphvizto work on 10.10.
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[Fink-devel] command-line tools for 10.10-beta ?

[William G. Scott]

Hi folks:

I’m trying to do a fresh fink install using my 10.10-beta (public, not paid 
developer) distribution of OS X to make sure my packages
are in shape for the upcoming release of 10.10.  I’ve installed the Xcode 6.1 
release for 10.10 beta from Apple’s website.  I can’t find the corresponding 
command-line tools for 10.10b anywhere on the (non-paid) Apple developer tools 
webpage. (I could swear it had this a couple of months ago when I installed 
this on my laptop.) Is this now only available for paid developers?

On bootstrapping, I get this:


Distribution: 10.10
Architecture: x86_64
Checking cc... looks good.
Checking make... looks good.
Checking head... looks good.
Verifying that installed Xcode Command Line Tools version is supported...
ERROR: I couldn't find the correct receipt for the Command Line Tools
for your OS X version.  Tools from a prior OS X version won't work properly.
You can install them by running the command

xcode-select —install

Issuing that command fails silently.

Likewise,  issuing


open /System/Library/CoreServices/Install Command Line Developer Tools.app”  

also fails silently.

I’m stuck now. 

Any suggestions for what to do?

Thanks.

Bill



William G. Scott

http://scottlab.ucsc.edu/~wgscott


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Re: [Fink-devel] command-line tools for 10.10-beta ?

[William G. Scott]

 

 On Oct 5, 2014, at 3:14 PM, Alexander Hansen alexanderk.han...@gmail.com 
 wrote:
 
 Are you using our Yosemite developer branch ('HalfDome')?  

Yes.  (Sorry, I should have specified this.)   
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Re: [Fink-devel] Fink's blt-2.4z-161 fails - missing dependency?

[William G. Scott]

On Aug 29, 2014, at 4:11 AM, Kevin Horton khorto...@gmail.com wrote:

 I’m gradually building up my list of installed Fink packages in OS X 10.10 
 beta.  blt-2.4z-161 fails to build due to a missing tkint.h.  
 
….

 =
 I took a quick look at the available tk packages, but there are so many that 
 it wasn’t completely clear which one I’m missing.  My first guess would be 
 tklib.
 
 What package do I need to install to get tkint.h?
 
 Thanks,
 
 -- 
 Kevin Horton

Hi Kevin:

I’m just catching up with you.

Briefly, the problem is tcltk 8.5 rather than 8.6 is getting installed on 
10.10.  I haven’t had a chance to try to figure out why.  There is a 
conditional test in blt that, ironically, would have failed in such a way as to 
make this work, until I fixed the syntax for 10.10.

Ultimately, we are better off getting the right tcltk (8.6) installing on 10.10.

Bill



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Re: [Fink-devel] OS X version comparisons (was Re: zsh-templates with OS X 10.10)

[William G. Scott]

Hi Kevin:

I thought I fixed it (and tested it on 10.10 beta).

Sorry.  I am having troubles reproducing this.

Bill


On Aug 28, 2014, at 6:40 PM, Kevin Horton khorto...@rogers.com wrote:

 I see that zsh-templates 2.0.5-2 showed up, with a change log that suggests a 
 fix. But I still see the same issue after updating to this version :(.
 
 -- 
 Kevin Horton
 
 
 
 On August 27, 2014 at 10:40:00 PM, Daniel Macks (dma...@netspace.org) wrote:
 A quick grep for this construct found 43 of them in *.info, but there 
 are lots more similar cases not as easy to find with a one-liner. A 
 more portable way might be what sqlite3.info does: cut off the 
 major-version (just compare N not 10.N) and do numerical (not string) 
 comparison. 
 
 dan
 
 On Wed, 27 Aug 2014 19:02:14 -0700, William G. Scott 
 wgsc...@ucsc.edu wrote:
 Hi Kevin:
 
  It looks like all (or at least most) of the problems are due to 
  conditional tests of the form
 
  if [[ $(sw_vers -productVersion)  10.N ]]; then
 
  (where N is 4, 5, 6, 7, 8, 9. 10.10 is evaluated as 10.1.)
 
  I’ll try to come up with a reasonable fix. 
 
  Bill
 
 
 
 
  On Aug 27, 2014, at 1:51 PM, Kevin Horton khorto...@rogers.com wrote:
 
   I’m running the second public beta of OS X 10.10 on my secondary 
  computer. zsh-templates works mostly well, but something is awry 
  with dirstack, cd? and gdirs. All three emit three “-i used with 
  no filenames on the command line, reading from STDIN.” lines in the 
  terminal for each entry (i.e. 60 lines of this spurious output, for 
  the default 20 returned values). The functions do work, but their 
  usefulness is greatly reduced at the CLI, as you must scroll and 
  visually parse the output to find the directory stack lines. 
I’d be happy to help debug in any way - just tell me what 
  additional info you need. 
Thanks for zsh-templates. 
--  Kevin Horton
   Ottawa, Canada
 
 
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 dma...@netspace.org
 
 
 
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Re: [Fink-devel] zsh-templates with OS X 10.10

[William G. Scott]

Hi Kevin:

It looks like all (or at least most) of the problems are due to conditional 
tests of the form

if [[ $(sw_vers -productVersion)  10.N ]]; then

(where N is 4, 5, 6, 7, 8, 9.  10.10 is evaluated as 10.1.)

I’ll try to come up with a reasonable fix.

Bill




On Aug 27, 2014, at 1:51 PM, Kevin Horton khorto...@rogers.com wrote:

 I’m running the second public beta of OS X 10.10 on my secondary computer.  
 zsh-templates works mostly well, but something is awry with dirstack, cd? and 
 gdirs.  All three emit three “-i used with no filenames on the command line, 
 reading from STDIN.” lines in the terminal for each entry (i.e. 60 lines of 
 this spurious output, for the default 20 returned values).  The functions do 
 work, but their usefulness is greatly reduced at the CLI, as you must scroll 
 and visually parse the output to find the directory stack lines.
 
 I’d be happy to help debug in any way - just tell me what additional info you 
 need.
 
 Thanks for zsh-templates.
 
 -- 
 Kevin Horton
 Ottawa, Canada


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[Fink-devel] Cannot install fink on a 10.9

[William G. Scott]

I’m also getting Caux’s error (as reported from the Oct 19th email, which 
appears in today’s digest; I didn’t find anything more recent in the on-line 
archive):

gcc -I. -I. -I../test -DHAVE_CONFIG_H   -D_DARWIN_C_SOURCE -DNDEBUG -I. 
-I../include -I/sw/include -O2  -dynamic -c ../test/tclock.c -o 
../obj_s/tclock.o
gcc -O2  -o tclock ../obj_s/tclock.o -Wl,-search_paths_first -I. -I. -I../test 
-DHAVE_CONFIG_H   -D_DARWIN_C_SOURCE -DNDEBUG -I. -I../include -I/sw/include 
-O2  -dynamic  `echo -L../lib -lform -lmenu -lpanel -lncurses | sed -e 
's/-lform.*-lpanel[^ ]*//'` -lutil  
Undefined symbols for architecture x86_64:
  ___sincos_stret, referenced from:
  _main in tclock.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [tclock] Error 1
make: *** [all] Error 2
### execution of make failed, exit code 2
phase compiling: ncurses-5.9-20110507-1 failed

…

and the No recognized Xcode CLI installed”  even after I (re)installed them.

zsh-% which gcc
/usr/bin/gcc
zsh-% gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
--with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include/c++/4.2.1
Apple LLVM version 5.0 (clang-500.2.76) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin13.0.0
Thread model: posix
zsh-% 
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Re: [Fink-devel] Cannot install fink on a 10.9

[William G. Scott]

On Oct 23, 2013, at 1:27 PM, Alexander Hansen alexanderk.han...@gmail.com 
wrote:

 On 10/23/13 1:13 PM, William G. Scott wrote:
 I’m also getting Caux’s error (as reported from the Oct 19th email, which 
 appears in today’s digest; I didn’t find anything more recent in the on-line 
 archive):
 
 gcc -I. -I. -I../test -DHAVE_CONFIG_H   -D_DARWIN_C_SOURCE -DNDEBUG -I. 
 -I../include -I/sw/include -O2  -dynamic -c ../test/tclock.c -o 
 ../obj_s/tclock.o
 gcc -O2  -o tclock ../obj_s/tclock.o -Wl,-search_paths_first -I. -I. 
 -I../test -DHAVE_CONFIG_H   -D_DARWIN_C_SOURCE -DNDEBUG -I. -I../include 
 -I/sw/include -O2  -dynamic  `echo -L../lib -lform -lmenu -lpanel -lncurses 
 | sed -e 's/-lform.*-lpanel[^ ]*//'` -lutil
 Undefined symbols for architecture x86_64:
   ___sincos_stret, referenced from:
   _main in tclock.o
 ld: symbol(s) not found for architecture x86_64
 clang: error: linker command failed with exit code 1 (use -v to see 
 invocation)
 make[1]: *** [tclock] Error 1
 make: *** [all] Error 2
 ### execution of make failed, exit code 2
 phase compiling: ncurses-5.9-20110507-1 failed
 
 …
 
 and the No recognized Xcode CLI installed”  even after I (re)installed them.
 
 zsh-% which gcc
 /usr/bin/gcc
 zsh-% gcc --version
 Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr 
 --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include/c++/4.2.1
 Apple LLVM version 5.0 (clang-500.2.76) (based on LLVM 3.3svn)
 Target: x86_64-apple-darwin13.0.0
 Thread model: posix
 zsh-%
 
 
 That looks like you're using a set of 10.8 command-line tools instead of 
 those for 10.9.  From a fresh Mavericks command-line tools install I get:
 
 $ gcc --version
 Configured with: --prefix=/Library/Developer/CommandLineTools/usr 
 --with-gxx-include-dir=/usr/include/c++/4.2.1
 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
 Target: x86_64-apple-darwin13.0.0
 Thread model: posix
 
 The tools are listed as unrecognized because fink can't find 
 com.apple.pkg.CLTools_Executables in the receipts database.  This is the new 
 name under which the command-line tools are installed for 10.9.
 -- 
 Alexander Hansen, Ph.D.
 Fink User Liaison
 My package updates: http://finkakh.wordpress.com/

Thanks, this worked.

The problem is Xcode 5.0 released prior to the 10.9 release does not update to 
these command-line tools.  I installed the package “Command Line Tools (OS X 
Mavericks) for Xcode - Late October Oct 22, 2013) from the Developer website, 
and now the bootstrap works.




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[Fink-devel] Help with 10.9 g++ errors

[William G. Scott]

Dear learned ones:

I'm getting errors in two packages that I maintain on 10.9 with the Oct22 
command-line tools and Xcode installed:

The one appended below is an example of one of a set from coot; the other set 
is from rdkit.

I have absolutely no idea how to deal with this, and would be grateful for any 
help I might be able to get.

libtool: compile:  g++ -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ 
-DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ 
-DPACKAGE=\coot\ -DVERSION=\0.7.1\ -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 
-DHAVE_DLFCN_H=1 -DLT_OBJDIR=\.libs/\ -I. -I../coot-utils 
-DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/sw/include 
-I/sw/include/rdkit -I/sw/src/fink.build/coot-0.7.1.0-8/coot-0.7.1/lidia-core 
-I/sw/include/libglade-2.0/glade -I/sw/include/libglade-2.0 
-I/sw/include/python2.7 -I/sw/include/mmdb -I/sw/include/ssm -I/sw/include/ccp4 
-I/sw/include/clipper -I/sw/include -I/usr/X11R6/include -g -O2 -MT 
CXXFortranFile.lo -MD -MP -MF .deps/CXXFortranFile.Tpo -c CXXFortranFile.cpp  
-fno-common -DPIC -o .libs/CXXFortranFile.o
In file included from CXXTorusElement.cpp:10:
In file included from ./CXXTorusElement.h:17:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/list:781:5:
 error: 
  implicit instantiation of undefined template '__static_assert_testfalse'
static_assert((is_samevalue_type, typename 
allocator_type::value_type::value),
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config:411:35:
 note: 
  expanded from macro 'static_assert'
typedef __static_assert_checksizeof(__static_assert_test(__b)) \
  ^
CXXTorusElement.cpp:259:3: note: in instantiation of template class 
'std::__1::listCXXTriangle *,
  CXX::CXXAllocCXXTriangle ' requested here
listCXXTriangle *, CXX::CXXAllocCXXTriangle ::iterator 
matchingTriangle;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config:407:24:
 note: 
  template is declared here
template bool struct __static_assert_test;
   ^
CXXTorusElement.cpp:259:53: error: use of class template iterator requires 
template arguments
listCXXTriangle *, CXX::CXXAllocCXXTriangle ::iterator 
matchingTriangle;
  ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/iterator:415:25:
 note: 
  template is declared here
struct _LIBCPP_TYPE_VIS iterator


Thanks.

Bill






William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

 


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[Fink-devel] ccp4 package

[William G. Scott]

Hi folks:

I've been maintaining the ccp4 package for at least a decade.

However, it now compiles readily on OS X, and CCP4 prefers to distribute 
binaries and their own update system to users. Moreover, they no longer 
distribute patches to the source-code between releases, meaning that there is 
no reasonable way to correct problems in between releases.  This is true even 
with version 6.3.0, the latest in fink, but I persisted in maintaining it 
because it was the only 64-bit version available to OS X users.  That, 
fortunately, is no longer the case, so there is no compelling reason to 
continue the fink package, and several compelling reasons not to (not the least 
of which is that it is a major PITA to maintain).

What is the best way to handle this?  CCP4 distributes an installer (and update 
system) that installs into the user's /Applications directory.

Is there a way to make some sort of placeholder package, similar to the 
system packages, that would allow for checking if the user has installed the 
package in /Applications, and possibly make available a few extra items (like 
shell environment scripts)?

In anticipation of this transition, I have already created a few new 
stand-alone packages, such as libccp4 (providing the crucial GPL libraries 
other packages rely upon).

Thanks.

All the best,

Bill









William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

 


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Re: [Fink-devel] Fink's a2ps-4.14-2 fails deb validation

[William G. Scott]

Hi Hanspeter:

I have only the dimmest recollection of inheriting this package.  In any case, 
uncommenting the first line of the patch script solves this problem.  I have to 
confess I had no idea what an elc file even was (being a vi guy).

I did however find out it has a missing dependency on emacs or emacs-nox, so I 
need to put that in first before committing.

I just realized I never replied to your other email about boost/cmake/rdkit.  
Your changes work fine, so feel free to go ahead with it.

Bill


On Jun 23, 2013, at 3:51 AM, Hanspeter Niederstrasser f...@snaggledworks.com 
wrote:

 a2ps-4.14-2 on 10.7 fails validation with this error:
 
 Validating .deb dir /sw/build.build/root-a2ps-4.14-2...
 Error: Compiled .elc file installed. Package should install .el files, and 
 provide a /sw/lib/emacsen-common/packages/install/package script that byte 
 compiles them for each installed Emacs flavour.
   Offending file: /sw/share/emacs/site-lisp/a2ps-print.elc
   Offending file: /sw/share/emacs/site-lisp/a2ps.elc
 
 Hanspeter


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Re: [Fink-devel] ccp4 on 10.6/i386

[William G. Scott]

On Feb 9, 2013, at 4:17 AM, Hanspeter Niederstrasser f...@snaggledworks.com 
wrote:

 Our ccp4 package currently doesn't build on 10.6/i386 because both the .info 
 and the build process assume x86_64 in several places and this leads to files 
 being compiled for the wrong architecture and therefore unable to be linked 
 in i386 Fink.
 
 The attached .info and .patch allow the build to succeed on 10.6/i386. The 
 10.6/x86_64 also finishes. Please check that the resulting builds actually 
 work.
 
 Hanspeter
 ccp4.infoccp4.patch

Dear Hanspeter:

Thanks very much for this.. I really appreciate your efforts and apologize for 
how much of a mess this is.

A new revision will be available upstream within the next few days, so I will  
incorporate those changes.

Also, I have been communicating with the CCP4 organization about the future of 
CCP4 on OS X.  They are
moving toward having 32 and 64-bit binary packages with internal automatic 
update systems.  (Currently they have
a 32 bit package with an internal update system).  The consensus was that this 
would make the fink package and
its lack of their internal update system obsolete and and an additional 
maintenance burden for them (and me).

My plan was to have one final update when the revision appears in early [sic] 
February, but then to phase it out
with a system-ccp4 package or something like that.

Part of the CCP4 package includes libraries required for other packages (like 
coot) that are GPL and are in fink.  CCP4 releases the libraries under LGPL, 
but the binary executables themselves are covered under a more restrictive 
license -- scientists in industry are supposed to pay to use them via what is 
in essence an honors system.  So perhaps a libccp4 package (as a successor to 
the gpp4 package, which is a fork) would be the most appropriate future?

Thanks again for your help.

Bill



William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
 
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[Fink-devel] boost

[William G. Scott]

Hi folks (Martin et al.):

I'm trying to put together a fink package for rdkit, which is a new dependency 
for coot (which I maintain). rdkit requires a fairly recent version of boost.  
I can build it using version 1.53.   Fink has 1.35, which is a bit long in the 
tooth.  (I also tried using boost1.46.1.cmake.  I got nowhere, but this might 
be simply the vastness of my own ignorance.)

In any case, would it be possible to get a boost1.53 package ?  Right now I am 
building the required library within my nascent rdkit package, but this is a 
bandaid approach.

Many thanks.

Bill

 



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Re: [Fink-devel] boost

[William G. Scott]

On Feb 9, 2013, at 9:16 AM, Martin Costabel costa...@wanadoo.fr wrote:

 On 9/02/13 17:22, William G. Scott wrote:
 Hi folks (Martin et al.):
 
 I'm trying to put together a fink package for rdkit, which is a new 
 dependency for coot (which I maintain). rdkit requires a fairly recent 
 version of boost.  I can build it using version 1.53.   Fink has 1.35, which 
 is a bit long in the tooth.  (I also tried using boost1.46.1.cmake.  I got 
 nowhere, but this might be simply the vastness of my own ignorance.)
 
 In any case, would it be possible to get a boost1.53 package ?  Right now I 
 am building the required library within my nascent rdkit package, but this 
 is a bandaid approach.
 
 Hi,
 
 just yesterday, someone sent me a package description for 1.52. As usual, 
 there are problems with the boost-python libs and the build system has 
 slightly changed. But maybe this might be useful for 1.53, too.
 
 Since I haven't looked at this for a very long time (boost-cmake seemed to be 
 the wave of the future), I cannot tell how long it will take me to get 
 something acceptable, but I'll have a look. The users of the boost libraries 
 seem to fall into one of two classes: Those who don't care about python and 
 those who *only* want the libboost-python libs and don't care about the rest. 
 Maybe two separate package descriptions might simplify the update process.
 
 -- 
 Martin
 


I think I might be a member of both classes.  In any case, all I need is  
libboost_python.dylib, and it is easy enough to tell it to build just that 
library (so currently I am doing it within the other package and hiding it).

I'd be happy to make a minimal libboost_python package if someone would be 
willing to fix all of the idiot-mistakes I will likely introduce.

Bill

PS:  I couldn't get boost.cmake to work for compiling rdkit.




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[Fink-devel] Is it permissible to use hfsCompression in a post-install script?

[William G. Scott]

I would like to do this to reduce a 3.3 GB text file database to 1.1 GB:


PostInstScript: 
mv %p/share/xtal/ccp4-%v/share/BALBES/Package  
%p/share/xtal/ccp4-%v/share/BALBES/Package.tmp
/usr/bin/ditto --hfsCompress %p/share/xtal/ccp4-%v/share/BALBES/Package.tmp   
%p/share/xtal/ccp4-%v/share/BALBES/Package/bin/rm -rf 
%pshare/xtal/ccp4-%v/share/BALBES/Package.tmp 



Thanks.

Bill



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Re: [Fink-devel] Is it permissible to use hfsCompression in a post-install script?

[William G. Scott]

 

On Sep 13, 2012, at 2:00 PM, Alexander Hansen alexanderk.han...@gmail.com 
wrote:

 On 9/13/12 1:10 PM, William G. Scott wrote:
 I would like to do this to reduce a 3.3 GB text file database to 1.1 GB:
 
 
 PostInstScript: 
 mv %p/share/xtal/ccp4-%v/share/BALBES/Package  
 %p/share/xtal/ccp4-%v/share/BALBES/Package.tmp
 /usr/bin/ditto --hfsCompress %p/share/xtal/ccp4-%v/share/BALBES/Package.tmp  
  %p/share/xtal/ccp4-%v/share/BALBES/Package/bin/rm -rf 
 %pshare/xtal/ccp4-%v/share/BALBES/Package.tmp 
 
 
 
 Thanks.
 
 Bill
 
 
 
 
 I assume that whatever needs this datafile knows how to decompress it to
 read it?  Or at least there will be some user instructions?
 
 As long as -hfsCompress is supported by ditto on all platforms you're
 planning to update I can't think of a good reason why not to do that.
 
 -- 
 Alexander Hansen, Ph.D.
 Fink User Liaison
 My package updates: http://finkakh.wordpress.com/

Hi Alexander:

HFS compression just stuffs data into the resource fork.  From what I 
understand, many of the ascii system files are HFS-compressed since 10.6.  It 
is completely transparent to whatever program reads the files.  The only way I 
can detect it is to use du on the directory of HFS-compessed files.  With 
textiles like these that have lots of white space (protein data bank files), it 
gives about a factor of 3 compression.


Bill




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Re: [Fink-devel] Is it permissible to use hfsCompression in a post-install script?

[William G. Scott]

On Sep 13, 2012, at 2:36 PM, Hanspeter Niederstrasser f...@snaggledworks.com 
wrote:

 On 9/13/2012 5:31 PM, William G. Scott wrote:
 
 
 
 On Sep 13, 2012, at 2:00 PM, Alexander Hansen alexanderk.han...@gmail.com 
 wrote:
 
 On 9/13/12 1:10 PM, William G. Scott wrote:
 I would like to do this to reduce a 3.3 GB text file database to 1.1 GB:
 
 
 PostInstScript: 
 mv %p/share/xtal/ccp4-%v/share/BALBES/Package  
 %p/share/xtal/ccp4-%v/share/BALBES/Package.tmp
 /usr/bin/ditto --hfsCompress 
 %p/share/xtal/ccp4-%v/share/BALBES/Package.tmp   
 %p/share/xtal/ccp4-%v/share/BALBES/Package/bin/rm -rf 
 %pshare/xtal/ccp4-%v/share/BALBES/Package.tmp
 
 
 
 Thanks.
 
 Bill
 
 
 
 
 I assume that whatever needs this datafile knows how to decompress it to
 read it?  Or at least there will be some user instructions?
 
 As long as -hfsCompress is supported by ditto on all platforms you're
 planning to update I can't think of a good reason why not to do that.
 
 --
 Alexander Hansen, Ph.D.
 Fink User Liaison
 My package updates: http://finkakh.wordpress.com/
 
 Hi Alexander:
 
 HFS compression just stuffs data into the resource fork.  From what I 
 understand, many of the ascii system files are HFS-compressed since 10.6.  
 It is completely transparent to whatever program reads the files.  The only 
 way I can detect it is to use du on the directory of HFS-compessed files.  
 With textiles like these that have lots of white space (protein data bank 
 files), it gives about a factor of 3 compression.
 
 Why PostInstScript and not CompileScript or InstallScript?  In 
 PostInstScript, the deb gets stuck having to deal with the 3.3GB file.
 
 Hanspeter

I tried.  It didn't work.  I wound up with a the original 3.3 GB directory 
size.  When I do it in the post-install script (it didn't get stuck), I wind up 
with a 1.1 GB directory size.

I assume that is because of how the debian utilities handle the copying from 
the deb file to the disk, but I really don't know.


 
 


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[Fink-devel] avoiding linking system's python

[William G. Scott]

Hi folks:

Despite my best attempts, I cannot seem to persuade the coot package I am 
maintaining from linking to

/System/Library/Frameworks/Python.framework/Versions/2.7/Python 

Is there a way to keep it out of there?

I have in the package

NoSetCPPFLAGS: true
NoSetLDFLAGS: true

and

alias python=%p/bin/python2.7
export PYTHON=%p/bin/python2.7
export python=%p/bin/python2.7

CPPFLAGS=-I%p/include/python2.7
LDFLAGS=-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib

but I still get the binary linking to the framework python.

Any advice?

Thanks.

Bill




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[Fink-devel] zsh update?

[William G. Scott]

Hi folks:

I would like to update zsh (the Z shell) packages to the recent 5.0.0 release.

Also, a few years ago, when multibyte support was offered, I created a second 
package.  At this point 
enabling the multibyte feature isn't experimental, and Apple's own zsh 4.3.11 
has this enabled by default,
so it is kind of silly not to do this with Fink's 5.0.0 package.

So I would like to merge the two packages and remove zsh-multibyte.info.

Any objections?

Just to be certain, I also checked on the zsh mailing list, and got the 
following reply:

 }Currently we have two packages,
 } differing only in being compiled with or without multibyte support. Is
 } there any valid reason to do this, or is there any potential harm done
 } or lack of functionality with always having it on?
 
 As of 5.0.0 there really isn't any reason to disable multibyte support
 at compile time.  The remaining bugs with it are all in very obscure
 cases, and it should suffice to 'unsetopt multibyte' if there is some
 backwards-compatibility reason why it isn't wanted.



Thanks.

Bill Scott
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[Fink-devel] Fwd: problem with sudo apt-get dist-upgrade

[William G. Scott]

Hi folks:

I've been serving some compiled fink packages from a 10.7 machine at work, 
mainly for my lab and colleagues who do similar work.

I just got an email from someone in Scotland who is having trouble with the new 
sensible-utils.

 package architecture (darwin-x86_64) does not match system (x86_64-darwin)

The full context is appended below.  I can't reproduce this.  Everything else 
he got from my machine (in the US) I think works.

My server has:

psbmini-% uname -mv
Darwin Kernel Version 11.4.0: Mon Apr  9 19:32:15 PDT 2012; 
root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64

Any idea what to fix?

Thanks.

Bill




Begin forwarded message:

 80 packages upgraded, 9 newly installed, 0 to remove and 0  not upgraded.
 Need to get 0B/841MB of archives. After unpacking 234MB will be used.
 Do you want to continue? [Y/n] 
 /sw/bin/dpkg: error processing 
 /sw/var/cache/apt/archives/sensible-utils_0.0.7-4_darwin-x86%5f64.deb 
 (--unpack):
 package architecture (darwin-x86_64) does not match system (x86_64-darwin)
 Errors were encountered while processing:
 /sw/var/cache/apt/archives/sensible-utils_0.0.7-4_darwin-x86%5f64.deb
 E: Sub-process /sw/bin/dpkg returned an error code (1)



William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

 


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Re: [Fink-devel] [Fink-announce] fink-0.32.4.1 released

[William G. Scott]

On Mar 27, 2012, at 10:44 PM, Alexander Hansen wrote:

 On 3/27/2012 10:14 PM, William G. Scott wrote:
 On Mar 27, 2012, at 9:39 PM, Alexander Hansen wrote:
 
 fink-0.32.4.1 supports Xcode 4.3.x in whatever
 location it is installed.
 Hi Alexander:
 
 Is there any reason a user needs to have Xcode installed, since the 
 command-line stuff and headers, etc, are all available via I separate 
 stand-alone download?
 
 Bill
 
 
 
 Good question.  I haven't actually checked to see what the ramifications of 
 that would be.  Any package which builds using xcodebuild wouldn't function, 
 and such packages would need to have an explicitly declared BuildDepends: 
 xcode.  The bootstrap script would need to be modified as well, since it now 
 checks for Xcode.
 
 Beyond that, I'm not sure.  I'll cc the developer list with my reply for any 
 thoughts.

FWIW, 

% which xcodebuild  
/usr/bin/xcodebuild

It seems to get installed with the command-line tools.  This is on a laptop 
with no Xcode installed (due to space).

The download is here:  https://developer.apple.com/downloads  and is entitled 
Command Line Tools for Xcode, late March

I've been hoping for this for about 10 years.

Bill


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Re: [Fink-devel] does fink-0.32.4.1 require Xcode? (was fink-0.32.4.1)

[William G. Scott]

On Mar 27, 2012, at 10:44 PM, Alexander Hansen wrote:

 On 3/27/2012 10:14 PM, William G. Scott wrote:
 On Mar 27, 2012, at 9:39 PM, Alexander Hansen wrote:
 
 fink-0.32.4.1 supports Xcode 4.3.x in whatever
 location it is installed.
 Hi Alexander:
 
 Is there any reason a user needs to have Xcode installed, since the 
 command-line stuff and headers, etc, are all available via I separate 
 stand-alone download?
 
 Bill
 
 
 
 Good question.  I haven't actually checked to see what the ramifications of 
 that would be.  Any package which builds using xcodebuild wouldn't function, 
 and such packages would need to have an explicitly declared BuildDepends: 
 xcode.  The bootstrap script would need to be modified as well, since it now 
 checks for Xcode.
 
 Beyond that, I'm not sure.  I'll cc the developer list with my reply for any 
 thoughts.

FWIW, 

% which xcodebuild  
/usr/bin/xcodebuild

It seems to get installed with the command-line tools.  This is on a laptop 
with no Xcode installed (due to space).

The download is here:  https://developer.apple.com/downloads  and is entitled 
Command Line Tools for Xcode, late March

I've been hoping for this for about 10 years.

Bill



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[Fink-devel] numpy in 10.6/5/4 stable needs a nose-py27

[William G. Scott]

The stable version of nose-py in the 10.4/10.5/10/6 tree of fink doesn't offer 
nose-py27, but numpy-py27 depends on this.  Maybe the easiest fix is to put 
what is in the 10.7 stable tree into the earlier stable tree?



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Re: [Fink-devel] pymol in 10.7

[William G. Scott]

Well, I am getting so senile I didn't even remember that something other than 
the plug-ins depended on gfortran until I tried to make a lite one.  I still 
might, because it would be kind of cool to have one that uses the aqua-tk 
interface…


On Jul 31, 2011, at 4:27 PM, Koen van der Drift wrote:

 Bill,
 
 Thanks for this explanation - with this excellent info it only seems logical 
 to include scipy and gcc to the package, no need to make a lite version, as 
 far as I am concerned. Sorry for the noise :)
 
 - Koen.
 
 
 On Jul 31, 2011, at 7:21 PM, William G. Scott wrote:
 
 Dear Koen et al:
 
 The reason for the inclusion of scipy it to support two pymol plugins:  APBS 
 (an electrostatics program that is quite popular amongst structural 
 molecular biologists) and a py-nmr plugin (of use to NMR spectroscopists).  
 There may be other reasons as well that I am not aware of.
 
 Please note, even if the plugins that I and other maintainers in this 
 package's history were removed, and the dependency upon scipy, there would 
 STILL be a required dependency on gcc46 (or some form of gfortran) because 
 of the python gui, i.e., the tkinter python megawidgets has a dependency 
 upon BLT (a tcltk widget), and BLT has a dependency upon a fortran 
 component.  Omitting the fortran components from BLT still allows it to 
 compile, but it is not the fully-enabled BLT required by some other packages.
 
 So we are doomed, unless we want to create a separate set of dependencies 
 for a slimmed-down pymol.  I am willing to do this, but this does come with 
 some overhead.
 
 Bill
 
 
 


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[Fink-devel] These packages work in 10.7, and I really need them ...

[William G. Scott]

The following all work on 10.7, and are dependencies for one or more packages I 
maintain.  Any chance they might be added?

Many thanks in advance.

fftw
gsl
gtk2-engines
gtkglarea2
pygobject2-py
pygtk2-gtk-py

I've Bcc-ed maintainers for those packages that have them.

-- Bill





William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA




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Re: [Fink-devel] pymol in 10.7

[William G. Scott]

Dear Koen et al:

The reason for the inclusion of scipy it to support two pymol plugins:  APBS 
(an electrostatics program that is quite popular amongst structural molecular 
biologists) and a py-nmr plugin (of use to NMR spectroscopists).  There may be 
other reasons as well that I am not aware of.

Please note, even if the plugins that I and other maintainers in this package's 
history were removed, and the dependency upon scipy, there would STILL be a 
required dependency on gcc46 (or some form of gfortran) because of the python 
gui, i.e., the tkinter python megawidgets has a dependency upon BLT (a tcltk 
widget), and BLT has a dependency upon a fortran component.  Omitting the 
fortran components from BLT still allows it to compile, but it is not the 
fully-enabled BLT required by some other packages.

So we are doomed, unless we want to create a separate set of dependencies for a 
slimmed-down pymol.  I am willing to do this, but this does come with some 
overhead.

Bill



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[Fink-devel] fftw (ver 2) in 10.7 please?

[William G. Scott]

Can we (or I) put the fftw package in stable/sci for 10.7 please?  It appears 
to work fine for all of the packages I maintain that require it as a dependency.

Thanks.

Bill Scott

PS:  sorry if this appears twice.  I think I sent it from an unregistered user 
address the first time.
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[Fink-devel] Pymol

[William G. Scott]

May I suggest we make Jack Howarth the official maintainer of pymol, which is 
simply recognizing the reality of his hard work on this?

Also, as Koen suggested, it might be nice to have a minimal version with no 
plug-ins, etc.  I would be happy to put together and maintain that.  

There is good reason for this, in that subsequent to the untimely death of the 
original author, the importance of keeping a free, open-source accessible 
version for students and others with a minimal number of impediments is 
imperative.  Most such users in my experiment use pymol mainly for viewing 
molecules and for making pretty ray-traced figures (including many of those you 
have seen on the covers of Nature and Science in the last decade).

Also, I would lobby heavily for having a stable release of the gcc46 package 
available as a binary distribution, to save users the burden of compiling it.

All the best,

Bill



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Re: [Fink-devel] [Fink-users] mmdb can't find c++ on 10.4

[William G. Scott]

On Dec 15, 2010, at 10:48 PM, David Lowe wrote:

   I don't speak config well enough to understand specifically what it is 
 checking for, but is it supposed to be looking for g++ in sw/lib/ rather than 
 /usr/bin/ ?

There was one point where I thought I needed to do this to get something to 
play right with some fortran in a different dependency package, but the short 
answer is that it isn't needed, and I am guilty of having something obsolete in 
stable.

-- Bill



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[Fink-devel] pmw-py.info

[William G. Scott]

Dear Fink Dev Core:

Does anyone mind if I change the line #7 in pmw-py.info from

7 Type: python (2.3 2.4 2.5 2.6)

to

7 Type: python (2.3 2.4 2.5 2.6 2.7)

It works fine, at least in the context of pymol.

Thanks.

Bill




William G. Scott
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and The Center for the Molecular Biology of RNA
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  +1-831-459-5292 (lab)
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[Fink-devel] gcc45 build fails on two 10.6 64-bit machines

[William G. Scott]

This is happening on two different up-to-date 10.6 64-bit fink installations...

rm -f stage_current
Comparing stages 2 and 3
warning: gcc/cc1-checksum.o differs
warning: gcc/cc1obj-checksum.o differs
warning: gcc/cc1objplus-checksum.o differs
warning: gcc/cc1plus-checksum.o differs
Bootstrap comparison failure!
x86_64-apple-darwin10.3.0/libgomp/.libs/bar.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/barrier.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/env.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/iter.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/iter_ull.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/lock.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/loop.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/loop_ull.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/ordered.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/parallel.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/proc.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/sections.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/single.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/task.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/team.o differs
x86_64-apple-darwin10.3.0/libgomp/.libs/work.o differs
x86_64-apple-darwin10.3.0/libgomp/bar.o differs
x86_64-apple-darwin10.3.0/libgomp/barrier.o differs
x86_64-apple-darwin10.3.0/libgomp/env.o differs
x86_64-apple-darwin10.3.0/libgomp/iter.o differs
x86_64-apple-darwin10.3.0/libgomp/iter_ull.o differs
x86_64-apple-darwin10.3.0/libgomp/lock.o differs
x86_64-apple-darwin10.3.0/libgomp/loop.o differs
x86_64-apple-darwin10.3.0/libgomp/loop_ull.o differs
x86_64-apple-darwin10.3.0/libgomp/ordered.o differs
x86_64-apple-darwin10.3.0/libgomp/parallel.o differs
x86_64-apple-darwin10.3.0/libgomp/proc.o differs
x86_64-apple-darwin10.3.0/libgomp/sections.o differs
x86_64-apple-darwin10.3.0/libgomp/single.o differs
x86_64-apple-darwin10.3.0/libgomp/task.o differs
x86_64-apple-darwin10.3.0/libgomp/team.o differs
x86_64-apple-darwin10.3.0/libgomp/work.o differs
make[2]: *** [compare] Error 1
make[1]: *** [stage3-bubble] Error 2
make: *** [all] Error 2
### execution of /var/tmp/tmp.2.zeHDDP failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-gcc45-4.5.0-1000
(Reading database ... 235337 files and directories currently installed.)
Removing fink-buildlock-gcc45-4.5.0-1000 ...
Updating the list of locally available binary packages.
Scanning dists/unstable/main/binary-darwin-x86_64
New package: 
dists/unstable/main/binary-darwin-x86_64/libs/libmpc2-shlibs_0.8.1-1_darwin-x86_64.deb
New package: 
dists/unstable/main/binary-darwin-x86_64/libs/libmpc2_0.8.1-1_darwin-x86_64.deb
Failed: phase compiling: gcc45-4.5.0-1000 failed

Before reporting any errors, please run fink selfupdate and
try again.  If you continue to have issues, please check to see if the
FAQ on fink's website solves the problem.  If not, ask on the fink-users
or fink-beginners mailing lists, with a carbon copy to the maintainer:

Jack Howarth howa...@bromo.med.uc.edu

Note that this is preferable to emailing the maintainer directly, since
most fink package maintainers do not have access to all possible
hardware and software configurations.
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Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines

[William G. Scott]

Ok, if this build fails, I will give that a try...


On Jun 2, 2010, at 4:55 PM, Jack Howarth wrote:

  One possible workaround might be to change gcc45.info
 to reduce the number of parallel builds so that the
 load sensitivity is reduced. So instead of using...
 
 num_cpu=$(echo `sysctl -n hw.ncpu`)
 make -j $num_cpu
 
 we would reduce num_cpu by one if greater
 than one so that the build is either serial
 or leaves a free core whenever building in parallel.
 This won't 'fix' the problem but it might make
 it less likely.
Jack


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Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines

[William G. Scott]

On Jun 2, 2010, at 5:04 PM, Benjamin Reed wrote:

 So if GCC's build is not repeatably compatible with -jN, then it
 should probably not be doing it by default.  :P

Anything to speed this build up is delightful.

Perhaps the best compromise is a conditional test, i.e.,

if [[  $(sysctl -n hw.ncpu) -gt 2 ]];then

 make -j   $(( $(sysctl -n hw.ncpu) - 1 ))

else

make

fi



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Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines

[William G. Scott]

On Jun 2, 2010, at 5:13 PM, Benjamin Reed wrote:

 On 6/2/10 8:10 PM, William G. Scott wrote:
 Anything to speed this build up is delightful.
 
 Well sure, but not knowing if it's going to fail 10 hours into it is
 not so delightful.  ;)


Which is why it would be ever-so-cool if fink were to make binaries available, 
with priority based on some soft of coefficient of build odiousness.
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Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines

[William G. Scott]

On Jun 2, 2010, at 5:37 PM, Jack Howarth wrote:

 Bill,
   What happens if you change...
 
 make -j $num_cpu
 
 ...to...
 
 nice -n -20 make -j $num_cpu

Previous re-build is still re-building...



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[Fink-devel] info and patch files encapsulated in deb archive

[William G. Scott]

Dear Fink group:

Whomever decided it would be a good idea to encapsulate the info and patch 
files in the debian archive just saved me about six hours of reconstructive 
surgery. I cannot thank you enough.

Bill
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Re: [Fink-devel] [Fink-users] Please remove screen from fink

[William G. Scott]

On Jan 14, 2010, at 11:08 PM, Michal Suchanek wrote:

 2010/1/15 William G. Scott wgsc...@chemistry.ucsc.edu:
 In my case, fink's screen works flawlessly (including sudo), and Apple's is 
 problematic (hangs).  I am not using bash.  Maybe bash is not playing well 
 with fink's screen...
 
 I don't think the shell could affect how sudo works but it could hang
 the screen. Perhaps your shell does no play well with it?

Quite possibly.

 
 What version of OS X do you have?

10.6.2

 
 Thanks
 
 Michal


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Re: [Fink-devel] [Fink-users] Please remove screen from fink

[William G. Scott]

In my case, fink's screen works flawlessly (including sudo), and Apple's is 
problematic (hangs).  I am not using bash.  Maybe bash is not playing well with 
fink's screen...
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Re: [Fink-devel] pymol-py abps_tools.py fix

[William G. Scott]

I seem to remember pmw opportunistically links to blt if it is present, but 
builds without complaint if it is not.  fink policy (as far as I understand it) 
is to have everyone's pwm (or any package) build the same way, so at some point 
I suggested making blt a dependency for pwm.
 
As for the fix on OS X, it is a one line change, so we can just make it on the 
fly if you don't want to mess with the code.


On Dec 9, 2009, at 12:14 PM, Michael Lerner wrote:

 I don't call blt directly from my plugin. In fact, I don't plot anything in
 the plugin, so unless Pmw automatically makes some blt calls for me, the
 plugin is probably blt-free.
 
 I haven't used pynmr before but it looks like you have to either compile
 something or get a precompiled binary from the web. I'd rather stick with
 pure python for the APBS Tools plugin.
 
 It looks to me like the plugin is closing PyMOL rather than crashing it when
 I make the suggested changes under Ubuntu.
 
 -michael
 
 On Wed, Dec 9, 2009 at 12:05 PM, Jack Howarth howa...@bromo.med.uc.eduwrote:
 
 Michael,
  Do you know if the APBS Tools plugin uses blt? I have working under
 the assumption that these problems are a manifestation of breakage in
 the existing blt 2.4z. Have you consider changing ABPS Tools to
 function more like pynmr (ie open its own window instead of a dialog)?
 I don't think I've ever seen pynmr crash pymol.
Jack
 
 On Wed, Dec 09, 2009 at 11:14:08AM -0500, Michael Lerner wrote:
 Hi,
 
 When I try that on my Ubuntu image, it makes it so that quitting the
 plugin
 causes PyMOL to quit.
 
 I don't really know much about tk. If there's a standard way to open /
 destroy the plugin, I'd be glad to change things around. As far as I
 know,
 the relevant bits are
 
def __init__(self,app):
self.parent = app.root
 
# Create the dialog.
self.dialog = Pmw.Dialog(self.parent,
 buttons = ('Register APBS Use',
 'Register
 PDB2PQR Use', 'Set grid', 'Run APBS', 'Exit APBS tools'),
 title = 'PyMOL APBS Tools',
 command = self.execute)
self.dialog.protocol('WM_DELETE_WINDOW',self.quit)
self.dialog.withdraw()
Pmw.setbusycursorattributes(self.dialog.component('hull'))
...
self.showAppModal()
 
def showAppModal(self):
#self.dialog.activate(geometry = 'centerscreenfirst', globalMode
 =
 'nograb')
#self.dialog.activate(geometry = 'centerscreenalways', globalMode
 =
 'nograb')
#self.dialog.activate(geometry = 'centerscreenfirst')
self.dialog.show()
 
def execute(self, result, refocus=True):
if result == 'Register APBS Use':
...
else:
#
# Doing it this way takes care of clicking on the x in the
 top
 of the
# window, which as result set to None.
#
if __name__ == '__main__':
#
# dies with traceback, but who cares
#
self.parent.destroy()
else:
#self.dialog.deactivate(result)
global APBS_BINARY_LOCATION, APBS_PSIZE_LOCATION
APBS_BINARY_LOCATION = self.binary.getvalue()
APBS_PSIZE_LOCATION = self.psize.getvalue()
#self.dialog.withdraw()
#self.dialog.destroy() # stops CPU hogging, perhaps fixes
 Ubuntu bug MGL
self.quit()
def quit(self):
self.dialog.quit()
self.parent.quit()
#self.dialog.withdraw()
#self.dialog.destroy()
 
 
 by the way, we've started a google wave about the plugin. I can add any
 of
 you that want to be on it.
 
 -michael
 
 On Sat, Dec 5, 2009 at 12:02 AM, William G. Scott 
 wgsc...@chemistry.ucsc.edu wrote:
 
 Hi Jack:
 
 Again, many thanks.  It has been a busy day so I didn't get a chance to
 try
 this until just now, but it fixed this highly annoying problem
 immediately.
 
 I'll pass it along upstream.
 
 All the best,
 
 Bill
 
 
 On Dec 4, 2009, at 8:25 AM, Jack Howarth wrote:
 
 Bill,
  Looking through the changes in the abps_tools.py script from
 pymol 1.r1 to the current 1.2r2, I believe I've found the offending
 code. If I revert the change...
 
 --- modules/pmg_tk/startup/apbs_tools.py.broken   2009-12-04
 11:11:03.0 -0500
 +++ modules/pmg_tk/startup/apbs_tools.py  2009-12-04
 11:18:08.0 -0500
 @@ -1124,7 +1124,7 @@
self.showAppModal()
 
def showAppModal(self):
 -self.dialog.activate(geometry = 'centerscreenfirst',
 globalMode
 = 'nograb')
 +#self.dialog.activate(geometry = 'centerscreenfirst',
 globalMode
 = 'nograb')
self.dialog.show()
#self.dialog.activate(geometry = 'centerscreenalways')
 
 I find that the use of the ABPS tools window no longer nukes the use
 of
 the main tk
 interface menus afterwards. You may want to update the current
 pymol-py
 package

Re: [Fink-devel] pymol-py abps_tools.py fix

[William G. Scott]

Hi Jack:

Again, many thanks.  It has been a busy day so I didn't get a chance to try 
this until just now, but it fixed this highly annoying problem immediately.

I'll pass it along upstream.

All the best,

Bill


On Dec 4, 2009, at 8:25 AM, Jack Howarth wrote:

 Bill,
   Looking through the changes in the abps_tools.py script from
 pymol 1.r1 to the current 1.2r2, I believe I've found the offending
 code. If I revert the change...
 
 --- modules/pmg_tk/startup/apbs_tools.py.broken   2009-12-04 
 11:11:03.0 -0500
 +++ modules/pmg_tk/startup/apbs_tools.py  2009-12-04 11:18:08.0 
 -0500
 @@ -1124,7 +1124,7 @@
 self.showAppModal()
 
 def showAppModal(self):
 -self.dialog.activate(geometry = 'centerscreenfirst', globalMode = 
 'nograb')
 +#self.dialog.activate(geometry = 'centerscreenfirst', globalMode = 
 'nograb')
 self.dialog.show()
 #self.dialog.activate(geometry = 'centerscreenalways')
 
 I find that the use of the ABPS tools window no longer nukes the use of the 
 main tk
 interface menus afterwards. You may want to update the current pymol-py 
 package with
 that change. I haven't tested it yet but this might also solve the same issue 
 with
 pymol-py and the current x86_64 blt package.
   Jack


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Re: [Fink-devel] pmw-py, blt, and 64-bit fink

[William G. Scott]

Begin forwarded message:

 I suspect the problem, ultimately, is blt.  blt officially doesn't work with 
 tcltk 8.5.X, but I incorporated some fixes a couple of months ago to get it 
 working.  I now suspect what I did was at the very least incomplete, and it 
 has come back to bite me.
 
 I would be extremely grateful for any help fixing this.

With considerable help, I've managed to fix blt-x86_64 to get this to work with 
Pmw.  I think it was 2002 or so I badgered Matt Stephenson into creating this 
package, so I feel indirectly responsible.  It is currently unmaintained, so 
I'll take it on if there are no objections (I will happily defer to someone 
more competent).

Bill Scott



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[Fink-devel] pmw-py, blt, and 64-bit fink

[William G. Scott]

Hi folks:

I'm having trouble with pmw-py26, specifically the blt module.

The pwm-py package (python megawidgets) does not depend upon blt, but if it 
finds blt, it builds extra functionality automatically.

(This means the package does not build identically on all systems, which is 
probably out of compliance with fink policy).

Unfortunately, when pmw builds in the presence of blt on 64-bit fink (which 
uses tcltk 8.5.7), it results in a blt package that under some conditions will 
segfault.  I discovered this in the context of pymol, which uses pmw for its tk 
GUI.

One can reproduce this problem by installing blt and then (re)building 
pmw-py26, followed by issuing

 cd /sw/lib/python2.6/site-packages/Pmw/Pmw_1_3/tests
 /sw/bin/python2.6 -v All.py 

I suspect the problem, ultimately, is blt.  blt officially doesn't work with 
tcltk 8.5.X, but I incorporated some fixes a couple of months ago to get it 
working.  I now suspect what I did was at the very least incomplete, and it has 
come back to bite me.

I would be extremely grateful for any help fixing this.  The most obvious way 
to do this (apart from fixing blt, which might be impossible) I think would be 
to force pmw not to use the blt module, but I don't know how, and the package 
(like blt) has no official maintainer.

All the best,

Bill



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Re: [Fink-devel] libgegl0.0.0-shlibs-0.0.22-1 fail: 10.6.1 64-bit

[William G. Scott]

On Oct 30, 2009, at 11:32 PM, Martin Costabel wrote:

 William G. Scott wrote:
 Hi Folks:
 The only thing left standing between me and gimp2 on 10.6 is   
 libgegl0.0.0-shlibs-0.0.22-1.  It fails thusly:
 libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../gegl/ 
 buffer - I../gegl/property-types -I../gegl/operation -I/sw/include/ 
 glib-2.0 -I/ sw/lib/glib-2.0/include -I/sw/include/babl-0.0 - 
 DLIBDIR=\/sw/lib\ - DGEGL_LOCALEDIR=\/sw/share/locale\ -I/sw/ 
 lib/fontconfig2/include -I/ sw/include -Os -Wall -Wdeclaration- 
 after-statement -Wmissing- prototypes -Wmissing-declarations -Winit- 
 self -Wpointer-arith -Wold- style-definition -mmmx -msse -c gegl- 
 cpuaccel.c  -fno-common -DPIC - o .libs/gegl-cpuaccel.o
 /var/tmp//ccIVYf6E.s:76:suffix or operands invalid for `pushf'
 /var/tmp//ccIVYf6E.s:77:suffix or operands invalid for `pushf'
 /var/tmp//ccIVYf6E.s:78:suffix or operands invalid for `pop'
 /var/tmp//ccIVYf6E.s:81:suffix or operands invalid for `push'
 /var/tmp//ccIVYf6E.s:82:suffix or operands invalid for `popf'
 /var/tmp//ccIVYf6E.s:83:suffix or operands invalid for `pushf'
 /var/tmp//ccIVYf6E.s:84:suffix or operands invalid for `pop'
 /var/tmp//ccIVYf6E.s:85:suffix or operands invalid for `popf'
 make[3]: *** [gegl-cpuaccel.lo] Error 1
 Anyone know of a fix?

 From a message 2 weeks ago on the same subject, on the fink- 
 beginners list:
 Apparently the build system still thinks it's building for i386.
 (Maintainer CCed).
 The standard autotools-made configure scripts guess the build host  
 system wrong when building for x86_64. Anything cpu-specific will  
 then fail.

 -- 
 Martin

Thanks, Martin. (I tried the usual things like -m64 and even forcing  
use of the fink 64-bit compilers, but no joy.)

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Re: [Fink-devel] libgegl0.0.0-shlibs-0.0.22-1 fail: 10.6.1 64-bit

[William G. Scott]

On Oct 31, 2009, at 9:41 AM, Martin Costabel wrote:

 --build=%m-apple-darwin`uname -r|cut -f1 -d.` --host=%m-apple- 
 darwin`uname -r|cut -f1 -d.`

Thanks.  That is what is needed, both for this and gimp2 itself.



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[Fink-devel] libgegl0.0.0-shlibs-0.0.22-1 fail: 10.6.1 64-bit

[William G. Scott]

Hi Folks:

The only thing left standing between me and gimp2 on 10.6 is  
libgegl0.0.0-shlibs-0.0.22-1.  It fails thusly:


libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I../gegl/buffer - 
I../gegl/property-types -I../gegl/operation -I/sw/include/glib-2.0 -I/ 
sw/lib/glib-2.0/include -I/sw/include/babl-0.0 -DLIBDIR=\/sw/lib\ - 
DGEGL_LOCALEDIR=\/sw/share/locale\ -I/sw/lib/fontconfig2/include -I/ 
sw/include -Os -Wall -Wdeclaration-after-statement -Wmissing- 
prototypes -Wmissing-declarations -Winit-self -Wpointer-arith -Wold- 
style-definition -mmmx -msse -c gegl-cpuaccel.c  -fno-common -DPIC - 
o .libs/gegl-cpuaccel.o
/var/tmp//ccIVYf6E.s:76:suffix or operands invalid for `pushf'
/var/tmp//ccIVYf6E.s:77:suffix or operands invalid for `pushf'
/var/tmp//ccIVYf6E.s:78:suffix or operands invalid for `pop'
/var/tmp//ccIVYf6E.s:81:suffix or operands invalid for `push'
/var/tmp//ccIVYf6E.s:82:suffix or operands invalid for `popf'
/var/tmp//ccIVYf6E.s:83:suffix or operands invalid for `pushf'
/var/tmp//ccIVYf6E.s:84:suffix or operands invalid for `pop'
/var/tmp//ccIVYf6E.s:85:suffix or operands invalid for `popf'
make[3]: *** [gegl-cpuaccel.lo] Error 1

Anyone know of a fix?

Thanks.

Bill



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Re: [Fink-devel] Problem compiling a2ps

[William G. Scott]

I'm getting the same problem and don't know how to fix it, so I am cc- 
ing fink-dev with the hope someone smarter than me will help...

Bill


On Oct 13, 2009, at 4:46 PM, Etienne M. Gagnon wrote:

 Hi all,

 I've just installed fink on OSX 10.6 and updated to unstable. Now, I  
 needed the a2ps package, so I tried installing it and got the  
 following error. I tried selfupdate and update-all, yet the error  
 remains.

 Thanks for any help you can provide.

 Here's the trace:

 fink install a2ps
 Information about 8326 packages read in 0 seconds.
 The following package will be installed or updated:
 a2ps
 Setting runtime build-lock...
 dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-a2ps-4.13-3 /sw/ 
 src/fink.build
 dpkg-deb : construction du paquet « fink-buildlock-a2ps-4.13-3 »  
 dans « /sw/src/fink.build/fink-buildlock- 
 a2ps-4.13-3_2009.10.13-19.35.32_darwin-i386.deb ».
 Installing build-lock package...
 /sw/bin/dpkg-lockwait -i /sw/src/fink.build/fink-buildlock- 
 a2ps-4.13-3_2009.10.13-19.35.32_darwin-i386.deb
 Sélection du paquet fink-buildlock-a2ps-4.13-3 précédemment  
 désélectionné.
 (Lecture de la base de données... 76149 fichiers et répertoires déjà  
 installés.)
 Dépaquetage de fink-buildlock-a2ps-4.13-3 (à partir de .../fink- 
 buildlock-a2ps-4.13-3_2009.10.13-19.35.32_darwin-i386.deb) ...
 Paramétrage de fink-buildlock-a2ps-4.13-3 (2009.10.13-19.35.32) ...
 gzip -dc /sw/src/a2ps-4.13.tar.gz | /sw/bin/tar -xf -  --no-same- 
 owner --no-same-permissions cp -f /sw/lib/fink/update/config.guess  
 auxdir
 cp -f /sw/lib/fink/update/config.sub auxdir
 cp -f /sw/lib/fink/update/ltconfig auxdir
 cp -f /sw/lib/fink/update/ltmain.sh auxdir
 perl -ni -e 'print unless /^ELCFILES =/' contrib/emacs/Makefile.in
 ./configure --prefix=/sw --mandir='${prefix}/share/man' --infodir='$ 
 {prefix}/share/info' ac_cv_exeext=''
 creating cache ./config.cache
 checking for a BSD compatible install... /sw/bin/ginstall -c
 checking whether build environment is sane... yes
 ...
 gcc -DHAVE_CONFIG_H -DLOCALEDIR=\/sw/share/locale\ -DSYSCONFFILE= 
 \/sw/etc/a2ps.cfg\ -I.. -I../intl -I. -I/sw/include -g -O2 -c  
 message.c -Wp,-MD,.deps/message.TPlo -o message.o
 echo timestamp  message.lo
 source='xstrrpl.c' object='xstrrpl.lo' libtool=yes \
   depfile='.deps/xstrrpl.Plo' tmpdepfile='.deps/xstrrpl.TPlo' \
   depmode=gcc /bin/sh ../auxdir/depcomp \
   /bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -DLOCALEDIR= 
 \/sw/share/locale\ -DSYSCONFFILE=\/sw/etc/a2ps.cfg\ -I.. -I../ 
 intl -I.  -I/sw/include  -g -O2  -c -o xstrrpl.lo xstrrpl.c
 gcc -DHAVE_CONFIG_H -DLOCALEDIR=\/sw/share/locale\ -DSYSCONFFILE= 
 \/sw/etc/a2ps.cfg\ -I.. -I../intl -I. -I/sw/include -g -O2 -c  
 xstrrpl.c -Wp,-MD,.deps/xstrrpl.TPlo -o xstrrpl.o
 xstrrpl.c:25:22: error: macro stpcpy requires 2 arguments, but  
 only 1 given
 xstrrpl.c:25: error: 'stpcpy' redeclared as different kind of symbol
 make[2]: *** [xstrrpl.lo] Error 1
 make[1]: *** [all-recursive] Error 1
 make: *** [all-recursive-am] Error 2
 ### execution of make failed, exit code 2
 Removing runtime build-lock...
 Removing build-lock package...
 ...

 -- 
 Etienne M. Gagnon, Ph.D.
 SableCC:http://sablecc.org



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Re: [Fink-devel] Problem compiling a2ps

[William G. Scott]

On Oct 13, 2009, at 6:47 PM, Peter O'Gorman wrote:

 On 10/13/2009 08:08 PM, William G. Scott wrote:

 xstrrpl.c:25:22: error: macro stpcpy requires 2 arguments, but
 only 1 given
 xstrrpl.c:25: error: 'stpcpy' redeclared as different kind of symbol


 http://trac.macports.org/browser/trunk/dports/print/a2ps/files/patch-lib__xstrrpl.c?rev=56498

 Does that patch fix it?

 Peter
 -- 
 Peter O'Gorman
 http://pogma.com

fixed now, thanks to Peter's suggestion.



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Re: [Fink-devel] x86_64 build of ffmpeg failing (still)

[William G. Scott]

This is a gimp2 dependency, so fairly important:

In file included from h264.h:32,
  from h264.c:31:
cabac.h: In function 'decode_significance_x86':
cabac.h:693: warning: cast from pointer to integer of different size
cabac.h:694: warning: cast from pointer to integer of different size
cabac.h: In function 'decode_significance_8x8_x86':
cabac.h:742: warning: cast from pointer to integer of different size
h264.c: In function 'hl_decode_mb_internal':
h264.c:2413: warning: suggest parentheses around arithmetic in operand  
of ^
h264.c:2419: warning: suggest parentheses around arithmetic in operand  
of ^
{standard input}:9509:suffix or operands invalid for `add'
{standard input}:9521:suffix or operands invalid for `add'
make[1]: *** [h264.o] Error 1
make: *** [lib] Error 2



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[Fink-devel] pymol-py26 in stable requires pmw-py26 which is in unstable only

[William G. Scott]

I've inherited pymol and just got email from a user who I surmise is  
trying to install the stable pymol-py26 and runs into an unmet  
dependency for pmw-py26.  (The problem doesn't arise for -py25  
variants, so I think what happened it a newer pymol got moved into  
stable without the upgrade needed for the dependency.)

What is the best course of action?

Thanks.

Bill



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Re: [Fink-devel] coot and gtkglext1

[William G. Scott]

On Sep 25, 2009, at 3:17 PM, Koen van der Drift wrote:

 Hi,

 When trying to install coot, I get the following warning:

 WARNING: The package coot Depends on gtkglext1,
but gtkglext1 only allows things to BuildDepend on it.

 Package manager version: 0.29.9
 Distribution version: selfupdate-cvs Fri Sep 25 18:09:20 2009, 10.5,  
 powerpc


 Thanks,

 - Koen.

Maybe I am wrong.  I am double-checking this now. 
  

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[Fink-devel] May I commit this fix for blt-x86_64.info ?

[William G. Scott]

Alternatively try using the attached patch
from the Fedora 12 blt srpm. It looks like
a true fix. Cheers.
Jack

--- src/bltInit.c.orig  2008-03-17 18:42:09.0 -0700
+++ src/bltInit.c   2008-03-17 18:43:05.0 -0700
@@ -415,7 +415,7 @@
  * Check that the versions of Tcl that have been loaded are
  * the same ones that BLT was compiled against.
  */
-   if (Tcl_PkgRequire(interp, Tcl, TCL_VERSION, EXACT) == NULL) {
+   if (Tcl_PkgRequire(interp, Tcl, TCL_VERSION, 0) == NULL) {
 return TCL_ERROR;
 }
 /* Set the blt_version, blt_patchLevel, and blt_libPath  
Tcl

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[Fink-devel] bltwish (blt) on 64-bit SL is messed up

[William G. Scott]

There is something wrong with blt on 64-bit:

cd /sw/lib/blt2.4/demos

% bltwish barchart1.tcl
Application initialization failed: version conflict for package Tcl:  
have 8.5.7, need exactly 8.5
Error in startup script: dlsym(0x1006d11f0, Blt_Unload): symbol not  
founddlsym(0x1006d11f0, Blt_SafeUnload): symbol not foundversion  
conflict for package Tcl: have 8.5.7, need exactly 8.5
 while executing
load $library BLT
 (procedure LoadBLT line 30)
 invoked from within
LoadBLT 2.4 /sw/lib/blt2.4
 (package ifneeded BLT 2.4 script)
 invoked from within
package require BLT
 (file barchart1.tcl line 3)


It isn't limited to the example.  I just reproduced an error that  
occurs with the ccp4i gui on my first try in the demo directory...

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[Fink-devel] xchemdraw

[William G. Scott]

I just tried to build xchemdraw on 64-bit SL.  It fails with this error:

../libtool: line 1800: cd: NONE: No such file or directory
libtool: link: cannot determine absolute directory name of `NONE'
make[2]: *** [xdrawchem] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Putting the following line in the PatchScript appears to result in a  
fully-functional xchemdraw:

   mkdir -p xdrawchem/NONE





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[Fink-devel] If everyone would just shut up and listen to me ...

[William G. Scott]

Dear Fink community:

Since my computer skills and diplomatic skills are both quite  
rudimentary (an assessment based on reality, not modesty),
I've been reluctant to say much (apart from accepting the blame for  
suggesting the latest scipy-core be updated, which
I based on some mistaken assumptions). Just as there are core members  
of fink, there are people like me who are very
peripheral in the sense that all of the packages I maintain are at  
most dependencies for other packages I maintain. So if
I mess something up, I am probably the only one who suffers the  
consequences (along with the end-users). This gives me
something of an outsider's perspective.  Hence I hope you might  
permit me a few observations from that perspective (with
my full advanced acknowledgment of its limitations).

1.  X11.app

Like many end-users, I have been updating to the latest X11.app from  
Xquartz, not because I crave the bleeding edge,
but simply because I understood this to be the best way to have as few  
bugs in X11 as possible, and also because I (wrongly)
assumed that the latest (2.4.0) would be what came out with OS X  
10.6.  I got burned, and got into a typically unpleasant
discussion on the X11 mailing list.  The net result is I learned I  
should have stopped at or before X11 2.3.3.2, but more
importantly, that the X11 in /etc/X11 that came with 10.6 would remain  
untouched, except for Apple bug-fixes, and future
Xquartz releases would install elsewhere (presumably /opt/X11) to  
avoid clobbering the officially distributed Apple X11.

I think this is a Good Thing, assuming all fink packages work with the  
SL X11.  We should just assume it is there, and not
concern ourselves at all with what gets installed in /opt, or support  
it.  What the end-user does is out of our control, but
in principle there is no reason we would have to worry about this one  
way or the other, as long as we can rely on the
current contents of /etc/X11 being in place.

2. Stable vs. Unstable

I tell people to translate the word unstable as current when  they  
express shyness about using it.  With the SL upgrade, we have, at  
least initially, an inversion, where packages in Unstable may work  
when packages in Stable do not, or are obsolete, etc.

I wonder if it might be worth changing this demarcation to Core and  
Peripheral or some such designation, the main point being to have  
the talents and energy of the core fink team focused on the most  
important packages, and to keep people with limited abilities, like  
me, out.

2.1 Core branch
Put packages including all the core fink packages, gcc44, fftw, tcltk  
and friends, gtk+2, gnome libraries, python, guile, and all the other  
packages that tend to get built primarily as dependencies for other  
packages into this branch.  These are the ones that are by far the  
most critical for end-users, would be of the most use to have  
available as a stable, binary distribution that mainly got updated  
only for bug fixes, and would benefit the most from having the fink  
core maintainers maintaining them.  Then allow the core maintainers  
themselves to decide on whatever policy they think is best for keeping  
the core packages of fink up and running smoothly. Because maintaining  
these packages would be the highest priority, it would be best to  
focus the talents and energy of the best and most capable people on  
these packages to ensure they all work together to form a seamless  
infrastructure.

2.2 Peripheral branch
Put packages that are of use to a subset of end-users (e.g.: my  
crystallography packages come to mind) here.  Mistakes in these  
packages are more easily tolerated, because they do not cripple the  
core infrastructure of fink, and so these can be entrusted to  
peripheral maintainers who possess more limited skills like me.   
Distributing these as binaries is a much less compelling concern.

To decide where a package goes, just ask what would happen if the  
package were to be deleted from fink.  If the answer is that the  
presence isn't critical, then assign it to the Peripheral branch.


3. Let's all take a deep breath

I had the good fortune to have a former Apple VP (who was responsible  
for much of Xcode) as a graduate student in a class last spring.  I  
asked him what it was like, and he described his erstwhile job as  
helping highly creative autistic people to have productive careers.  I  
know it is a bit of a stereotype, but computer people often aren't  
qualified to be Japanese diplomats, and it is also very hard for even  
the most socially adept individuals to infer intent from a pile of  
ascii text characters.  We all need to give each other the benefit of  
the doubt when interpreting each other's words and actions. We all  
want the same thing, after all: a viable, fully-functional and up-to- 
date fink.

Peace and joy,

Bill




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Re: [Fink-devel] scipy-core needs updated in stable

[William G. Scott]

Dear Fink community:

I want to apologize, because I think this is really mostly my fault.

  I made a faulty assumption about ownership of the scipy package  
without looking, and suggested he (Jack) added it to stable because he  
was spending a few hours trying to work out a bug that was preventing  
me from building an NMR package that some of my colleagues here use.   
(scipy-core is a dependency for ccpnmr).

Not being a programmer myself, I've relied heavily on both Jack's  
advice and his packages (especially gcc44), and he has kindly invested  
hours of time in fixing some of the monstrosities that I am  
responsible for.  I would really hate to lose that.

I also get the email digests and tend to miss half of what goes on, so  
again, I apologize, this time for not picking up on this sooner.

Yours sincerely,

Bill Scott




William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott




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Re: [Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit

[William G. Scott]

I also get it on a second machine (installed into /sw instead of / 
sw64).  If I issue the command by hand, it works (or at least there  
is no error reported):

/sw/var/lib/dpkg/info/ccpnmr-py26.postinst: line 15:   474  
Segmentation fault  /sw/bin/python2.6 -O /sw/lib/python2.6/site- 
packages/ccpnmr/ccpnmr2.0/python/ccpnmr/update/UpdateAuto.py
/sw/bin/dpkg: error processing ccpnmr-py26 (--install):
  subprocess post-installation script returned error exit status 139
Errors were encountered while processing:
  ccpnmr-py26
### execution of /sw/bin/dpkg-lockwait failed, exit code 1
Failed: can't install package ccpnmr-py26-2.0.7.1-1
zsh-%
zsh-% sudo  /sw/bin/python2.6 -O /sw/lib/python2.6/site-packages/ 
ccpnmr/ccpnmr2.0/python/ccpnmr/update/UpdateAuto.py
zsh-%
zsh-%

also

BlockFile.so:Mach-O 64-bit bundle x86_64
FitMethod.so:Mach-O 64-bit bundle x86_64
GlHandler.so:Mach-O 64-bit bundle x86_64
MemCache.so: Mach-O 64-bit bundle x86_64
PdfHandler.so:   Mach-O 64-bit bundle x86_64
PsHandler.so:Mach-O 64-bit bundle x86_64
ShapeFile.so:Mach-O 64-bit bundle x86_64
StoreFile.so:Mach-O 64-bit bundle x86_64
StoreHandler.so: Mach-O 64-bit bundle x86_64
TkHandler.so:Mach-O 64-bit bundle x86_64

Here's everything python installed, fwiw:


boost1.35.nopython-shlibs
f2py-py26
libxml2-py26
numeric-py26
numpy-py26
pmw-py26
pycairo-py26
pycairo-py26-dev
pygobject2-py26
pygobject2-py26-dev
pygobject2-py26-shlibs
pygtk2-gtk-py26
pygtk2-gtk-py26-dev
pymol-py26
python
python26
python26-shlibs
scientificpython-py26
scipy-core-py26
scipy-py26
system-pkgconfig-xpyb





On Sep 9, 2009, at 6:29 AM, Jack Howarth wrote:

 On Tue, Sep 08, 2009 at 09:36:23PM -0700, William G. Scott wrote:
 This worked ok on my 32-bit install, but ...

 Setting up ccpnmr-py26 (2.0.7.1-1) ...
 cd ../python/memops/c; sh linkSharedObjs
 cd ../python/ccp/c; sh linkSharedObjs
 cd ../python/ccpnmr/c; sh linkSharedObjs
 /sw64/var/lib/dpkg/info/ccpnmr-py26.postinst: line 15: 59735
 Segmentation fault  /sw64/bin/python2.6 -O /sw64/lib/python2.6/
 site-packages/ccpnmr/ccpnmr2.0/python/ccpnmr/update/UpdateAuto.py
 /sw64/bin/dpkg: error processing ccpnmr-py26 (--install):
 subprocess post-installation script returned error exit status 139
 Errors were encountered while processing:
 ccpnmr-py26
 ### execution of /sw64/bin/dpkg-lockwait failed, exit code 1
 Failed: can't install package ccpnmr-py26-2.0.7.1-1

 Bill,
   This looks like the execution of...

 /sw64/bin/python2.6 -O /sw64/lib/python2.6/site-packages/ccpnmr/ 
 ccpnmr2.0/python/ccpnmr/update/UpdateAuto.py

 where the script /sw64/lib/python2.6/site-packages/ccpnmr/ccpnmr2.0/ 
 python/ccpnmr/update/UpdateAuto.py
 should be...

 from ccpnmr.update.UpdateAgent import UpdateAgent,  
 UPDATE_SERVER_LOCATION, UPDATE_DIRECTORY, UPDATE_DATABASE_FILE

 def updateAuto(serverLocation=UPDATE_SERVER_LOCATION,
   serverDirectory=UPDATE_DIRECTORY,
   dataFile=UPDATE_DATABASE_FILE):

  updateAgent = UpdateAgent(serverLocation, serverDirectory,  
 dataFile, isGraphical=False)
  server = updateAgent.server
  if server:
  server.getFileUpdates()
  if not server.fileUpdates:
server.getFileUpdates()
  if server.fileUpdates:
updateAgent.installNewUpdates()

 if __name__ == '__main__':

  updateAuto()

 This looks more like possible breakage of x86_64 python on your  
 machine than
 a problem with ccpnmr-py26 itself. Also, make sure that everything in
 /sw64/lib/python2.6/site-packages/ccpnmr/ccpnmr2.0/python/memops/c
 is built as x86_64 code according to file (although I would think
 that would give an entirely different error).
  Jack


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Re: [Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit

[William G. Scott]

Yes, it works on the i386 fink (which was upgraded from 10.5).

I just recompiled and reinstalled to double-check.


On Sep 9, 2009, at 11:33 AM, Jack Howarth wrote:


 Bill,
   Could you test the ccpnmr-py26 build on one of your
 i386 fink installations? I would assume you would have
 about the same set of python packages installed (just
 to make sure that none of those are the cause).
  Jack


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Re: [Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit

[William G. Scott]

On Sep 9, 2009, at 4:09 PM, Jack Howarth wrote:

 fink --version
 Package manager version: 0.29.99.cvs
 Distribution version: selfupdate-cvs Wed Sep  9 18:42:56 2009, 10.6,  
 x86_64

I think I have the same setup as you.  On this machine, /sw is 64-bit  
and the only fink, and I immediately activated unstable

fink --version
Package manager version: 0.29.99.cvs
Distribution version: selfupdate-cvs Tue Sep  8 17:57:20 2009, 10.6,  
x86_64

The only thing I can think of that might be different is that I did a  
completely fresh install after upgrading to 10.6 in both cases.  Two  
out of two cases, whereas the upgrade from 10.5 pathway has this  
working (32-bit).  That one has Package manager version: 0.29.9

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[Fink-devel] 32-bit SL upgrade vs fresh install

[William G . Scott]

Hi citizens:

On an upgrade 32-bit intel fink from 10.5, I get a problem (compiling  
coot) that I don't encounter on a 32-bit fresh install:

libtool: link: cannot find the library `/usr/X11/lib/libXrender.la'

I suspect this might be carried over from one or more of its 230+  
dependencies, among them pango1-xft2-ft219-shlibs.

So I tried to re-build pango1-xft2-ft219, which was carried over from  
10.5 prior to the upgrade.

grep: /usr/lib/libiconv.la: No such file or directory
/sw/bin/sed: can't read /usr/lib/libiconv.la: No such file or directory
libtool: link: `/usr/lib/libiconv.la' is not a valid libtool archive
make[4]: *** [libharfbuzz-1.la] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
### execution of /var/tmp/tmp.2.K8ulmC failed, exit code 2

This sort of recursive foray to the gates of Hell makes me wonder if  
the 10.5 upgrade path is viable.  Even if I manage to figure out which  
packages need to be rebuilt, I worry that there is no mechanism to  
trigger for the general user to do this.

The path of my [32-bit upgrade] is strewn with cow-pats from the  
devil's own satanic herd.

Cheerio.

Bill



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[Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit

[William G. Scott]

This worked ok on my 32-bit install, but ...

Setting up ccpnmr-py26 (2.0.7.1-1) ...
cd ../python/memops/c; sh linkSharedObjs
cd ../python/ccp/c; sh linkSharedObjs
cd ../python/ccpnmr/c; sh linkSharedObjs
/sw64/var/lib/dpkg/info/ccpnmr-py26.postinst: line 15: 59735  
Segmentation fault  /sw64/bin/python2.6 -O /sw64/lib/python2.6/ 
site-packages/ccpnmr/ccpnmr2.0/python/ccpnmr/update/UpdateAuto.py
/sw64/bin/dpkg: error processing ccpnmr-py26 (--install):
  subprocess post-installation script returned error exit status 139
Errors were encountered while processing:
  ccpnmr-py26
### execution of /sw64/bin/dpkg-lockwait failed, exit code 1
Failed: can't install package ccpnmr-py26-2.0.7.1-1

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Re: [Fink-devel] [Fwd: zsh as shell in compilescript on 10.6 breaks 32bit Fink]

[William G. Scott]

On Sep 7, 2009, at 5:23 AM, Martin Costabel wrote:


 Somehow one needs to place that path-prefix back in front of the PATH,
 but since this is distribution and architecture dependent, to do so  
 can
 become quite a mess.

Hi Martin:

I am working on pdb2pqr, an apbs dependency that uses gfortran, gcc,  
and g++

It is currently broken on 23-bit 10.6 but works fine on the other  
platforms.

If the first three lines are

#!/bin/zsh -f
source %p/bin/init.sh
PATH=%p/bin:%p/sbin:${PATH} ; export PATH

this appears to put everything right, at least in my experiment.

Because of zsh's path anti-metastasis feature, I HAD to do this  
explicitly with the path, e.g., this

set +x
print 
print  
~
print 
print source %p/bin/init.sh
source %p/bin/init.sh
print The path after sourcing the %p/bin/init.sh file
print starts with $path[1,6]
print 
PATH=%p/bin:%p/sbin:${PATH} ; export PATH
print now path starts with $path[1,6]
print VERSIONER_PERL_PREFER_32_BIT is $VERSIONER_PERL_PREFER_32_BIT
print 
print  
~
print 
sleep 10
set -x





gives the following output:

~

source /sw/bin/init.sh
The path after sourcing the /sw/bin/init.sh file
starts with /usr/bin /bin /usr/sbin /sbin /usr/local/bin /usr/X11/bin

now path starts with /sw/bin /sw/sbin /usr/bin /bin /usr/sbin /sbin
VERSIONER_PERL_PREFER_32_BIT is yes

~

This, however, wasn't enough to get gfortran to do the right thing


 On a related note: How does one tell gfortran (from Fink's gcc44) to
 build either 32bit or 64bit executables?

so I am left having to do a hackish conditional test
  [[ %m != x86_64 ]] and manually introducing -m32 where  
appropriate.



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Re: [Fink-devel] [Fwd: zsh as shell in compilescript on 10.6 breaks 32bit Fink]

[William G. Scott]

Hi Martin:

Fortunately the fix was much simpler for apbs.

I just started the CompileScript with

#!/bin/bash -efv
source %p/bin/init.sh
PATH=%p/bin:%p/sbin:${PATH} ; export PATH

the last two lines are probably overkill, but to be on the safe side...

Thanks (and sorry!!!).

Bill



On Sep 7, 2009, at 5:23 AM, Martin Costabel wrote:

 Here is the first mail in that thread:

  Original Message 
 Subject: [Fink-devel] zsh as shell in compilescript on 10.6 breaks  
 32bit Fink
 Date: Mon, 31 Aug 2009 09:42:21 +0200
 From: Martin Costabel costa...@wanadoo.fr
 To: Fink fink-devel@lists.sourceforge.net


 After spending time trying to build apbs in SnowLeopard 32-bit Fink, I
 have identified a source of breakage, but I have not yet found a good
 solution:

 CompileScripts that run in zsh, like apbs which has
 #!/bin/zsh -efv
 have a good chance to break on 32-bit Fink on SL. The reason is the
 following:

 SL has /etc/zshenv, which didn't exist before. This script is always
 executed at startup of zsh, and according to man zsh, this behavior
 cannot be overridden. Now /etc/zshenv runs /usr/libexec/path_helper,  
 and
 this places the system path /usr/bin in front of Fink's path.

 In particular, gcc will then be /usr/bin/gcc, and not the carefully
 crafted /sw/var/lib/fink/path-prefix-10.6/gcc, and therefore it will  
 not
 have the -arch i386 flag, and it will build for the x86_64
 architecture, which causes breakage in 32bit Fink.

 Somehow one needs to place that path-prefix back in front of the PATH,
 but since this is distribution and architecture dependent, to do so  
 can
 become quite a mess.

 On a related note: How does one tell gfortran (from Fink's gcc44) to
 build either 32bit or 64bit executables? It does not seem to  
 understand
 the -arch flag. The same question goes for all Fink-built compilers.  
 If
 there is no reasonable answer, then this would be a further argument
 against keeping 32bit Fink on SnowLeopard.

 -- 
 Martin




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Re: [Fink-devel] [Fwd: zsh as shell in compilescript on 10.6 breaks 32bit Fink]

[William G. Scott]

On Sep 7, 2009, at 10:08 AM, Martin Costabel wrote:

 William G. Scott wrote:

 #!/bin/zsh -f
 source %p/bin/init.sh
 PATH=%p/bin:%p/sbin:${PATH} ; export PATH
 this appears to put everything right, at least in my experiment.

 But on 10.6 gcc then would still be /usr/bin/gcc (which produces  
 64bit binaries) and not /usr/bin/gcc -arch i386 as it should. Hard  
 to see how this can work.

Well, with apbs, it just did :)   (I switched it to /bin/bash for good  
measure).

I think switching the second and third lines (setting the $PATH first)  
would probably be better.  I assume source %p/bin/init.sh is doing the  
right thing as it sets VERSIONER_PERL_PREFER_32_BIT to yes.




 Because of zsh's path anti-metastasis feature, I HAD to do this

 Are you saying that with zsh, /sw/bin/init.sh does not place Fink's  
 paths in front of PATH?

If the user has any instance of

  typeset -U path

then only the original entry is preserved, as shown in this example.

I've contrived it by putting /sw/bin and /sw/sbin at the end to begin  
with, and then I just print the first five elements of the path array  
for clarity:

sage-% print $path[1,5]
/usr/local/phenix-1.4-4/build/mac-intel-osx/bin /usr/bin /bin /usr/ 
sbin /sbin

sage-% source /sw/bin/init.sh

sage-% print $path[1,5]
/usr/local/phenix-1.4-4/build/mac-intel-osx/bin /usr/bin /bin /usr/ 
sbin /sbin

Now reset the $PATH and $path:

sage-% PATH=/usr/bin:/bin

sage-% print $path[1,5]
/usr/bin /bin

sage-% source /sw/bin/init.sh

sage-% print $path[1,5]
/sw/bin /sw/sbin /usr/bin /bin /usr/X11R6/bin



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[Fink-devel] rxvt on 64-bit: gets packaged, but it ain't there (fix included)

[William G. Scott]

rxvt compile fails, but package gets installed (consisting of a man  
page):

% dpkg -c /sw/fink/dists/unstable/main/binary-darwin-x86_64/x11/ 
rxvt_2.7.10-3_darwin-x86_64.deb
drwxr-xr-x root/admin0 2009-09-01 22:14 ./
drwxr-xr-x root/admin0 2009-09-01 22:14 ./sw/
drwxr-xr-x root/admin0 2009-09-01 22:14 ./sw/bin/
drwxr-xr-x root/admin0 2009-09-01 22:14 ./sw/share/
drwxr-xr-x root/admin0 2009-09-01 22:14 ./sw/share/man/
drwxr-xr-x root/admin0 2009-09-01 22:14 ./sw/share/man/man1/
-rw-r--r-- root/admin40639 2009-09-01 22:14 ./sw/share/man/man1/ 
rxvt.1



creating librxvt.la
(cd .libs  rm -f librxvt.la  ln -s ../librxvt.la librxvt.la)
/bin/sh ../libtool --mode=link gcc -g -O2  -L/sw/lib rxvt.o  
librxvt.la  -lX11   -o rxvt
gcc -g -O2 rxvt.o -o rxvt  -L/sw/lib ./.libs/librxvt.a -lX11
ld: library not found for -lX11
collect2: ld returned 1 exit status
make[1]: *** [rxvt] Error 1

This is solved with

SetCPPFLAGS: -I/usr/X11/include -I/usr/X11R6/include
SetLDFLAGS:  -L/usr/X11/lib -L/usr/X11R6/lib



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Re: [Fink-devel] [cvs] dists/10.4/unstable/main/finkinfo/sci mosflm.info, 1.23, 1.24

[William G. Scott]

Hi Dave:

It is working fine for me on my ppc.  (Just built it now). Is there a  
64-bit fink option for ppc?  I couldn't find it in the documentation  
for the %m expansion.

Current possible values are 'powerpc' for ppc machines and either  
'i386' or 'x86_64' for x86 machines. The choice 'x86_64' is only  
available if the machine is capable of running 64-bit libraries and  
executables.

  (If so, I will fix the conditional test, or gladly incorporate  
something less hackish.)

Bill


On Sep 6, 2009, at 8:21 PM, David R. Morrison wrote:

 Bill,

 Isn't that going to break on powerpc?

  -- Dave


 On Sep 6, 2009, at 11:09 PM, William Scott wrote:

 Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
 In directory fdv4jf1.ch3.sourceforge.com:/tmp/cvs-serv9438

 Modified Files:
  mosflm.info
 Log Message:
 fix to force 32-bit compilation on 10.6 when appropriate

 Index: mosflm.info
 ===
 RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ 
 mosflm.info,v
 retrieving revision 1.23
 retrieving revision 1.24
 diff -u -d -r1.23 -r1.24
 --- mosflm.info  7 Sep 2009 02:22:22 -   1.23
 +++ mosflm.info  7 Sep 2009 03:09:19 -   1.24
 @@ -12,6 +12,10 @@
 CompileScript: 
 #!/bin/zsh -efv
 source %p/bin/init.sh
 +if [[ %m != x86_64 ]]; then
 +perl -pi -e 's|gfortran|gfortran -m32|g' fink_gfortran.zsh
 +perl -pi -e 's|gcc |gcc -m32 |g' fink_gfortran.zsh
 +fi
 source fink_gfortran.zsh
 make
 cd bin


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[Fink-devel] gcc44 in stable needs

[William G. Scott]

Hi folks:

I started a clean stable 64-bit for 10.6 for purposes of testing  
migration of some of my packages to stable.

Although gcc44 is in stable, its dependency libmpfr1  is not, so gcc44  
won't build in stable.

HTH,

Bill







William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/



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[Fink-devel] stable wish list: fftw, swig, pygtk2-gtk-py2 and its dep.

[William G. Scott]

I'm trying to migrate coot to stable, but several dependencies are in  
unstable, so if there is any change of migrating these, I can verify  
they work:

These include current  or recent versions (see below) of:

fftw,
swig,
pygtk2-gtk-py26

and

atk1
freetype219
glib2 (dev)
gtk+2
libffi
libglade2
libmpfr1  (needed for gcc44)
libpng3
pango1-xft2-ft219
pycairo-py (26)
pygobject2-py (26)
pygtk2-gtk-py (26)
scipy-core-py (26)


Most are dependencies for pygtk2-gtk-py:

atk1-shlibs (= 1.26.0-1) for package pygtk2-gtk-py26-2.15.2-1
glib2-dev (= 2.20.0-1) for package atk1-1.26.0-2
freetype219-shlibs (= 2.3.8-2) for package pygtk2-gtk-py26-2.15.2-1
gtk+2-shlibs (= 2.16.0-1) for package pygtk2-gtk-py26-2.15.2-1
pango1-xft2-ft219 (= 1.24.0-1) for package gtk+2-2.16.6-1
libpng3 (= 1:1.2.35-2) for package gtk+2-2.16.6-1
libglade2-shlibs (= 2.6.4-1) for package pygtk2-gtk-py26-2.15.2-1
scipy-core-py26 for package pygtk2-gtk-py26-2.15.2-1
pycairo-py26 (= 1.8.4-1) for package pygtk2-gtk-py26-2.15.2-1
pygobject2-py26 (= 2.18.0-1) for package pygtk2-gtk-py26-2.15.2-1
  

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Re: [Fink-devel] SL X11.app regressions relative to X11.app

[William G. Scott]

Having opened this can of worms (sorry), may I add two humble  
suggestions:

1. Roll-your-own X11, I agree, would best be avoided. Instead, let's  
take advantage of the stability of X11 in 10.6.

My understanding from Jeremy, once he got done working me over, was  
that the idea is to have a comparatively immutable system X11 that  
resides in /usr/X11 and won't get clobbered, and then unofficial  
updates can go elsewhere, presumably /opt.  The SL-supplied X11.app  
seems perfectly adequate, so why not take advantage of the stability  
and insist all fink packages simply stick to /usr/X11 (which is  
presumably the path of least action (in the classical limit)).

Many of us updated X11.app on 10.5 because the original one supplied  
with 10.5.0 was a mess.  Now it is cleaned up, as far as I can tell.


2. The 10.6 64-bit tree of fink is in a situation where things in  
unstable work but in stable don't (older versions, no gfortran  
4.4, etc). Maybe this is a good chance to move everything en masse  
that works into stable.


 Message: 1
 Date: Sat, 29 Aug 2009 02:07:19 -0400
 From: Jack Howarth
 Subject: Re: [Fink-devel] SL X11.app regressions relative to X11.app
   2.4.0
 To: fink-devel@lists.sourceforge.net
 Message-ID: 20090829060719.ga19...@bromo.med.uc.edu
 Content-Type: text/plain; charset=us-ascii

   My own instinct is that (considering the lack of
 manpower in fink these days) rolling our own X11 is
 only asking for trouble. Also do we know for certain
 that there won't be beta releases of a Xquartz
 release for Snow Leopard much sooner than that? I would
 think our resources would be better utilized by focusing
 on the x86_64 transition.
Jack

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Re: [Fink-devel] SL X11.app regressions relative to X11.app

[William G. Scott]

On Aug 30, 2009, at 8:58 PM, David R. Morrison wrote:


 On Aug 31, 2009, at 11:48 AM, William G. Scott wrote:


 2. The 10.6 64-bit tree of fink is in a situation where things in
 unstable work but in stable don't (older versions, no gfortran
 4.4, etc). Maybe this is a good chance to move everything en masse
 that works into stable.


 Bill,

 Yes, in a rush to get the stable tree into usable shape in a very  
 short period of time, I didn't check to see which unstable packages  
 were ready.  I'm asking people to hold off moving things to stable  
 for another day or two while I finish my pruning job, but after that  
 I imagine that quite a few things can be moved (with adequate  
 testing on so on, please!).

  -- Dave


Dear Dave:

Sorry, didn't mean to alarm anyone.  I am just feeling guilty for  
having not invested any time in the stable tree (and am in no danger  
of messing with it any time soon).

You can pretty much assume anything in stable with my name on it  
__isn't__ good for 10.6, fwiw.


Bill



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Re: [Fink-devel] SL X11.app regressions relative to X11.app 2.4.0

[William G. Scott]

 This isn't any different than the usual issues we've had on 10.5, when
 you get down to it.  System updates cause regressions with respect the
 libraries in Xquartz, and Xcode updates regress the headers and  
 libtool
 archives (not to mention just clobbering them outright).

One HUGE important difference is before, one could always simply  
reinstall the Xquartz latest version, but in this case, the installer  
prevents you from doing so (it has to be 10.5) and no 10.6-compatible  
update is planned prior to December.

As a maintainer, it looks as if the only thing I can do is to throw  
everything into the fire and recompile fink from scratch, to find out  
if they still compile.


 The position has always been:  users are free to use the unofficial
 Xquartz update, but they need to reinstall it after updating anything,
 as is explicitly mentioned on its download page.

That's the rub.  You _can't_ reinstall, (and there is no prior warning  
of this).

 What would solve this problem, in my opinion, would be

 1)  More virtual packages, corresponding to libraries from X11
 2)  Getting automatic shlibs resolution working.


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[Fink-devel] SL X11.app regressions relative to X11.app 2.4.0

[William G. Scott]

Hi folks:

After upgrading, I discovered that the SL (10.6) distributed X11.app  
clobbers the X11.app v. 2.4.0 I had installed, and (unlike with 10.5.X  
point updates), there are no plans to release an X11.app update before  
ca. December. So this means users who linked to recently released  
X11.app libraries will likely experience problems.

Is this something we should address?

The libraries in question appear to include the following:

Regressions from X11.app 2.4.0 to SL X11.app

/usr/X11/lib/libOSMesa.4.dylib not present in SL X11
/usr/X11/lib/libxcb-xlib.0.dylib not present in SL X11
/usr/X11/lib/libxcb-keysyms.1.dylib not present in SL X11

/usr/X11/lib/libfontconfig.1.dylib  (compatibility version 5.0.0 vs   
6.0.0 in X11 2.4.0)
/usr/X11/lib/libpng.3.dylib (compatibility version 39.0.0 vs 41.0.0 in  
X11 2.4.0)
/usr/X11/lib/libpng12.0.dylib (compatibility version 36.0.0, vs 38.0.0  
in X11 2.4.0)
/usr/X11/lib/libxcb-randr.0.dylib  (compatibility version 1.0.0 vs  
2.0.0 in X11 2.4.0)


Of these, I've only run into problems with /usr/X11/lib/libfontconfig. 
1.dylib so far (and lazily swiped the later version from another  
computer to resolve the problem).

The X11.app upgrade pathway appears to be a source of user frustration.

Would fink be better served to have its own X11 installation, as we  
did back with 10.4 and earlier?

Bill



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[Fink-devel] gcc43 vs. gcc44

[William G. Scott]

Hi Citizens:

A number of packages, including fftw, depend on gcc43 instead of  
gcc44, which leads to the rather time-consuming and blood-pressure- 
elevating phenomenon of having not one but two interminable builds for  
packages that depend on fftw and gcc44.  Any chance this can be  
remedied?

Here's a full list (yes two at least are mine):

% grep gcc43-shlibs */*.info | cut -d : -f 1
sci/atlas.info
sci/avl.info
sci/fftw.info
sci/fftw3-x86_64.info
sci/fftw3.info
sci/freefem++.info
sci/geant4.8.info
sci/geant4.9.info
sci/hdf5-1.6.5.info
sci/hdf5-1.6.5.info
sci/modulef.info
sci/molden.info
sci/mopac7.info
sci/octave-forge-image.info
sci/patchy4.info
sci/pgplot.info
sci/plplot.info
sci/qprop.info
sci/r-base.info
sci/refmac.info
sci/root-pythia.info
sci/root5-devel.info
sci/scilab.info
sci/scipy-py.info
sci/tinker.info
sci/xfoil.info
sound/ocp.info
utils/clamav-0.93.3.info
utils/clamav-0.94.2.info

Bill




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[Fink-devel] Is patch behavior on x86_64 different?

[William G. Scott]

I just started playing with x86_64 to see what I need to fix for my  
packages.  One of these (at least) has a portion of the patch file  
that simply corresponds to deletion.  This works fine in the 32- 
branch, but for x86_64, the patch fails.  Chopping this bit out of the  
patch file cures the problem (along with a manual delete of the file),  
but I can't figure out what is different.  Is it fink itself? Oddly,  
it only showed up when I called the prefix directory /sw64.  When I  
changed it to hard-coded /sw, then it (apparently) works.

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[Fink-devel] pygtk2-gtk-py26?

[William G. Scott]

Dear Daniel et al:

Would it be possible to have a version of pygtk2 for python2.6?  I  
made the substitution in the Type field and it appears to be ok.

Thanks.

Bill Scott




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Re: [Fink-devel] libxml (fixed)

[William G. Scott]

OK I have done that.

The real source of the problem was that this came first in $PATH,  
which I hadn't noticed because I change it (back) when I configure my  
shell.

I've now also fixed that (an easy fix, but only if you see that it is  
broke).

Sorry for this.

Bill


On Sep 18, 2008, at 7:48 AM, Alexander Hansen wrote:

 I did, though.  In consultation with Dan Macks we found the following:

 $ type -a xml2-config
 xml2-config is /sw/share/xtal/ccp4-6.0.99e/bin/xml2-config
 xml2-config is /sw/bin/xml2-config
 xml2-config is /usr/bin/xml2-config

 That shadows the normal xml2-config.  A quick hack would  be to  
 rename or remove ccp4's xml2-config.

 In addition to libxml2, ccp4 appears to install its own versions of  
 libraries for fftw, gc, and ssm.

 On Sep 18, 2008, at 10:11 AM, William G. Scott wrote:

 Even better, I can't reproduce the error.




 Alexander K. Hansen
 akh AT finkproject DOT org
 Fink User Liaison and Documenter





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[Fink-devel] MakeListCache:4: no such file or directory: /sw/bin/fink

[William G. Scott]

I just bootstrap-installed fink in a non-/sw  directory (and moved /sw  
out of the way for safety)

MakeListCache called by fink index does this:

% fink index
Scanning package description files..
MakeListCache:4: no such file or directory: /sw/bin/fink
MakeListCache:6: no such file or directory: /sw/bin/fink
MakeListCache:8: no such file or directory: /sw/bin/fink

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Re: [Fink-devel] MakeListCache:4: no such file or directory: /sw/bin/fink

[William G. Scott]

I discovered that soon after I sent it.

I also put a check for $7.5K in the mail without a stamp or address on  
the envelope.

I should have stayed in bed pondering early-onset Altzheimers.

Sorry.

Bill


On Sep 12, 2008, at 4:36 PM, Martin Costabel wrote:

 William G. Scott wrote:
 I just bootstrap-installed fink in a non-/sw  directory (and moved / 
 sw  out of the way for safety)
 MakeListCache called by fink index does this:
 % fink index
 Scanning package description files..
 MakeListCache:4: no such file or directory: /sw/bin/fink
 MakeListCache:6: no such file or directory: /sw/bin/fink
 MakeListCache:8: no such file or directory: /sw/bin/fink

 Funny, the only MakeListCache google knows about is in
 http://www.chemistry.ucsc.edu/~wgscott/mystuff/zsh/zsh-templates-0.5.2/Library/init/zsh/local-functions/fink
  
 

 mystuff, hmm...

 -- 
 Martin




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[Fink-devel] Failed to start message bus: Memory allocation failure in message bus

[William G. Scott]

I just got asked the following by a good friend and colleague and have  
no idea what the answer is.

Can someone help please?

Begin forwarded message:


In the last week or two I've started seeing an error message  
 following
 any re-boot on any of three Macs that I use (all running 10.4.11,  
 one is an
 Intel iMac, one a G5 iMac, the third is a G5 PowerMac).  It shows up  
 only in
 the first terminal or X11 window that gets opened after reboot, and  
 it says:

 Failed to start message bus: Memory allocation failure in message bus
 EOF in dbus-launch reading address from bus daemon

I also noticed that dbus had been updated in fink at around the  
 time
 this symptom appeared (present version 1.2.3-4 under unstable),  
 and all
 three machines got the update.  I never selected dbus for  
 installation, so
 presumably it must be there because it is a dependency of some other
 program(s).  I suspect there might be a permissions problem, as I also
 started seeing an error on my automatic backup program, which told  
 me it
 could not read the file dbus-daemon-launch-helper.  The directory  
 entry for
 this file looks like this:

 mac6010-3:/sw/sbin dn$ ls -al dbus-*
 -rwsr-x---   1 root  messageb  830632 Sep  4 14:38 dbus-daemon- 
 launch-helper



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Re: [Fink-devel] Failed to start message bus: Memory allocation failure in message bus

[William G. Scott]

 This has been reported on -users, too:

 http://article.gmane.org/gmane.os.macosx.fink.user/27068

 although that poster claims that the issue doesn't occur under
 Terminal.app  It doesn't seem to occur on 10.5 as best as I can tell.


Thanks.  Sorry I missed that.

Both are in Cambridge.  Coincidence or conspiracy?



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Re: [Fink-devel] guile-18 question

[William G. Scott]

On Sep 3, 2008, at 9:24 AM, Charles Lepple wrote:

 On Wed, Sep 3, 2008 at 10:22 AM, William G. Scott
 [EMAIL PROTECTED] wrote:


 On Sep 3, 2008, at 4:54 AM, Martin Costabel wrote:

 William G. Scott wrote:

 Apparently gmp compiled on my G5 ppc is not compatible with a  
 G4

 Yes, this is an old problem. Often it gives bus errors or illegal
 instruction errors. The G5 build apparently uses ppc machine
 instructions that don't exist on G4.

 In principle, gmp has some code to ask for a less optimized build  
 (-
 force_cpusubtype_ALL compiler flag), but this doesn't work as
 intended, probably because the flag is not used when the dylibs are
 linked.

 --
 Martin


 Is there a way to deal with this gracefully in a binary debian
 redistribution?

 I think that's what the -64bit variant is supposed to handle. (There's
 a virtual package called 64bit-cpu.)

 It's possible that the packages which depend on gmp may need their
 dependencies adjusted, though.

 -- 
 - Charles Lepple


In my case, it was gmp/gmp-shlibs itself that needed to be recompiled  
from what I had built (and serve) from my G5 ppc.  The dependency  
(guile18) did not.  Since G4s are becoming rare (all but one of mine  
died recently), it probably isn't worth going to extremes for this.


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Re: [Fink-devel] guile-18 question

[William G. Scott]

recompiling gmp on the G4 was the key to getting it to work.

Apparently gmp compiled on my G5 ppc is not compatible with a G4


On Sep 2, 2008, at 4:08 PM, Alexander Hansen wrote:

 My guile18 was built locally on my G4, so it seems like there may be  
 even more to it.

 On Sep 2, 2008, at 6:56 PM, William Scott wrote:

 Yes, 10.5.4, most current everything.

 I've used debian archives compiled on my G5 ppc on my G4 laptop,  
 which may be relevant.


 On Sep 2, 2008, at 3:29 PM, Alexander Hansen wrote:

 Which OS version?  10.5?

 On Sep 2, 2008, at 5:41 PM, William Scott wrote:

 Hi folks:

 I am trying to debug a package I maintain. It runs some scheme
 scripting files using guile-1.8 (of which I know nothing).

 On my G4 laptop, the line

 (set! *random-state* (seed-random-state (current-time)))

 causes guile-1.8 to report (cryptically) a hardware  
 incompatibility.

 On all my other computers, it runs without complaint.

 Am I missing a dependency, or is something more fundamental amiss?

 Thanks.

 Bill


 William G. Scott

 Contact info:
 http://chemistry.ucsc.edu/~wgscott/



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 Fink User Liaison and Documenter





 Alexander K. Hansen
 akh AT finkproject DOT org
 Fink User Liaison and Documenter





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[Fink-devel] a problem when linking fftw dynamic libraries

[William G. Scott]

Hi folks:

I need some advice.

The program coot, which I maintain, links to fftw, which it uses to  
calculate crystallographic electron density maps.

If I link to fftw's dynamic libraries, I run into a memory problem  
that causes the program to seg fault.  If I link to static fftw  
libraries only, the program works.

I have reported this to the program's author.  I have no ability to  
tell whether this is a problem with coot or with fftw (except I am not  
aware of any other problems with fftw).

Meanwhile, is there a way to force the compiler to link only to the  
fftw static libraries?

Many thanks in advance.

Bill



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