Re: [Fink-devel] A few 10.11 glitches and possible workarounds
> On Oct 1, 2015, at 8:01 AM, Alexander Hansen > wrote: > > >> On Oct 1, 2015, at 07:59, Hanspeter Niederstrasser >> wrote: >> >> On Thu, October 1, 2015 9:17 am, William G. Scott wrote: >>> >>>> 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 didnât 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? -- ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] A few 10.11 glitches and possible workarounds
> 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. ] -- ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] A few 10.11 glitches and possible workarounds
In the course of building some of my packages, a few dependencies failed to compile, requiring minor tweaks: gtk+2 — I had to change to UseMaxBuildJobs: false libvpx14 — I had to change to UseMaxBuildJobs: false fftw — I had to change it to build with gcc5 Also, $X11_BASE_DIR doesn’t seem to get set. Bill Scott -- ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] command-line tools for 10.10-beta ?
> On Oct 5, 2014, at 5:58 PM, Alexander Hansen
> wrote:
>
> On 10/5/14, 4:05 PM, William G. Scott wrote:
>>
>>
>>> On Oct 5, 2014, at 3:14 PM, Alexander Hansen
>>> 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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Re: [Fink-devel] command-line tools for 10.10-beta ?
> On Oct 5, 2014, at 3:14 PM, Alexander Hansen
> wrote:
>
> Are you using our Yosemite developer branch ('HalfDome')?
Yes. (Sorry, I should have specified this.)
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[Fink-devel] command-line tools for 10.10-beta ?
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 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Fink's blt-2.4z-161 fails - missing dependency?
On Aug 29, 2014, at 8:50 AM, William G. Scott wrote: > > On Aug 29, 2014, at 4:11 AM, Kevin Horton 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 > > I copied tcltk-10.9.info and tcltk-10.9.patch to tcltk-10.10.info and tcltk-10.10.patch (respectively), and changed the Distribution field to 10.10, compiled that, and blt now builds as it should. (maintainer bcc-ed) -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Fink's blt-2.4z-161 fails - missing dependency?
On Aug 29, 2014, at 4:11 AM, Kevin Horton 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] OS X version comparisons (was Re: zsh-templates with OS X 10.10)
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 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" >> 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 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 >> > >> > >> > -- >> > Slashdot TV. Video for Nerds. Stuff that matters. >> > http://tv.slashdot.org/ >> > ___ >> > Fink-devel mailing list >> > Fink-devel@lists.sourceforge.net >> > List archive: >> > http://news.gmane.org/gmane.os.apple.fink.dev l >> > Subscription management: >> > https://lists.sourceforge.net/lists/listinfo/fink-devel >> > >> > >> >> -- >> Daniel Macks >> dma...@netspace.org >> >> >> >> -- >> Slashdot TV. >> Video for Nerds. Stuff that matters. >> http://tv.slashdot.org/ >> ___ >> Fink-devel mailing list >> Fink-devel@lists.sourceforge.net >> List archive: >> http://news.gmane.org/gmane.os.apple.fink.devel >> Subscription management: >> https://lists.sourceforge.net/lists/listinfo/fink-devel -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] zsh-templates with OS X 10.10
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 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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Help with 10.9 g++ errors
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_test' static_assert((is_same::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_check)> \ ^ CXXTorusElement.cpp:259:3: note: in instantiation of template class 'std::__1::list >' requested here list >::iterator matchingTriangle; ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/__config:407:24: note: template is declared here template struct __static_assert_test; ^ CXXTorusElement.cpp:259:53: error: use of class template iterator requires template arguments list >::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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Cannot install fink on a 10.9
On Oct 23, 2013, at 1:27 PM, Alexander Hansen 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. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Cannot install fink on a 10.9
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-% -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] ccp4 package
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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Fink's a2ps-4.14-2 fails deb validation
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 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/ 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 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] boost
On Feb 9, 2013, at 9:16 AM, Martin Costabel 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. -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] boost
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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] ccp4 on 10.6/i386
On Feb 9, 2013, at 4:17 AM, Hanspeter Niederstrasser 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 > 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] xmakemol for 10.8
Does anyone mind if I put xmakemol (no maintainer) into fink's 10.8 branch (sci)? It works, and I had someone email asking me (presumably since i am a chemist) if I could make it available. It seems to work (I am unfamiliar with the program) to his satisfaction. Thanks. 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 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Is it permissible to use hfsCompression in a post-install script?
On Sep 13, 2012, at 2:36 PM, Hanspeter Niederstrasser wrote: > On 9/13/2012 5:31 PM, William G. Scott wrote: >> >> >> >> On Sep 13, 2012, at 2:00 PM, Alexander Hansen >> 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. > > -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Is it permissible to use hfsCompression in a post-install script?
On Sep 13, 2012, at 2:00 PM, Alexander Hansen 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Is it permissible to use hfsCompression in a post-install script?
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] avoiding linking system's python
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] zsh update?
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Fwd: problem with sudo apt-get dist-upgrade
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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] [Fink-announce] fink-0.32.4.1 released
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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] does fink-0.32.4.1 require Xcode? (was fink-0.32.4.1)
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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] numpy in 10.6/5/4 stable needs a nose-py27
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? -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
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 >> >> > -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol in 10.7
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 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] These packages work in 10.7, and I really need them ...
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 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Pymol
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 -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] fftw (ver 2) in 10.7 please?
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. -- Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] [Fink-users] mmdb can't find c++ on 10.4
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 -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] pmw-py.info
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 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 phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax:+1-831-4593139 (fax) -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines
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... -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines
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. -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines
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 $(( $(sysctl -n hw.ncpu) - 1 )) else make fi -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] gcc45 build fails on two 10.6 64-bit machines
Ok, if this build fails, I will give that a try... On Jun 2, 2010, at 4:55 PM, Jack Howarth wrote: > One possible workaround might be to change gcc45.info > to reduce the number of parallel builds so that the > load sensitivity is reduced. So instead of using... > > num_cpu=$(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 -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] gcc45 build fails on two 10.6 64-bit machines
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 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. -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] info and patch files encapsulated in deb archive
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 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] [Fink-users] Please remove screen from fink
On Jan 14, 2010, at 11:08 PM, Michal Suchanek wrote: > 2010/1/15 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... > > 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 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] [Fink-users] Please remove screen from fink
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... -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pymol-py abps_tools.py fix
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 wrote:
>
>> 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. Scot
Re: [Fink-devel] pymol-py abps_tools.py fix
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 -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] pmw-py, blt, and 64-bit fink
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] pmw-py, blt, and 64-bit fink
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] libgegl0.0.0-shlibs-0.0.22-1 fail: 10.6.1 64-bit
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. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] libgegl0.0.0-shlibs-0.0.22-1 fail: 10.6.1 64-bit
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.) -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] libgegl0.0.0-shlibs-0.0.22-1 fail: 10.6.1 64-bit
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 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] x86_64 build of ffmpeg failing (still)
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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Re: [Fink-devel] Problem compiling a2ps
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. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Problem compiling a2ps
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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[Fink-devel] pymol-py26 in stable requires pmw-py26 which is in unstable only
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 -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] coot and gtkglext1
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. -- Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] May I commit this fix for blt-x86_64.info ?
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
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
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] If everyone would just shut up and listen to me ...
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 -- Let Crystal R
Re: [Fink-devel] scipy-core needs updated in stable
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit
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" -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] ccpnmr-py26 post-install script seg-faults on 64-bit
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] 32-bit SL upgrade vs fresh install
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] [Fwd: zsh as shell in compilescript on 10.6 breaks 32bit Fink]
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 $path[1,5]
/sw/bin /sw/sbin /usr/bin /bin /usr/X11R6/bin
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Re: [Fink-devel] [Fwd: zsh as shell in compilescript on 10.6 breaks 32bit Fink]
Hi Martin:
Fortunately the fix was much simpler for apbs.
I just started the CompileScript with
#!/bin/bash -efv
source %p/bin/init.sh
PATH=%p/bin:%p/sbin:${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
> To: Fink
>
>
> 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]
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] [cvs] dists/10.4/unstable/main/finkinfo/sci mosflm.info, 1.23, 1.24
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 >> >> >> -- >> Let Crystal Reports handle the reporting - Free Crystal Reports >> 2008 30-Day >> trial. Simplify your report design, integration and deployment - >> and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> ___ >> Fink-commits mailing list >> fink-comm...@lists.sourceforge.net >> http://news.gmane.org/gmane.os.apple.fink.cvs > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] rxvt on 64-bit: gets packaged, but it ain't there (fix included)
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] stable wish list: fftw, swig, pygtk2-gtk-py2 and its dep.
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" -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] gcc44 in stable needs
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/ -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] SL X11.app regressions relative to X11.app
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] SL X11.app regressions relative to X11.app
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] SL X11.app regressions relative to X11.app 2.4.0
>> > 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. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] SL X11.app regressions relative to X11.app 2.4.0
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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] gcc43 vs. gcc44
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 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Is patch behavior on x86_64 different?
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. -- Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://www.creativitycat.com ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
[Fink-devel] pygtk2-gtk-py26?
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 -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] libxml (fixed)
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 > > > - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] MakeListCache:4: no such file or directory: /sw/bin/fink
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 > > - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
[Fink-devel] MakeListCache:4: no such file or directory: /sw/bin/fink
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 - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] Failed to start message bus: Memory allocation failure in message bus
>>> > 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? - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
[Fink-devel] Failed to start message bus: Memory allocation failure in message bus
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 > > - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
Re: [Fink-devel] guile-18 question
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
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?
Bill
>
>
>
>
>
>
-
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Re: [Fink-devel] guile-18 question
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/ >>>> >>>> >>>> >>>> - >>>> This SF.Net email is sponsored by the Moblin Your Move >>>> Developer's challenge >>>> Build the coolest Linux based applications with Moblin SDK & win >>>> great prizes >>>> Grand prize is a trip for two to an Open Source event anywhere in >>>> the world >>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>> ___ >>>> Fink-devel mailing list >>>> Fink-devel@lists.sourceforge.net >>>> http://news.gmane.org/gmane.os.apple.fink.devel >>> >>> Alexander K. Hansen >>> akh AT finkproject DOT org >>> Fink User Liaison and Documenter >>> >>> >>> >> > > Alexander K. Hansen > akh AT finkproject DOT org > Fink User Liaison and Documenter > > > - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
[Fink-devel] a problem when linking fftw dynamic libraries
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 William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.devel
