[Fink-users] PHASE phylogenetics package
Has anyone successfully compiled the phylogenetics package PHASE (Ben Hines, Maintainer) recently? I have scanned the fink archives but see nothing apart from minor updates to the .patch and .info files last year. Below is the output (edited) I get when I try to install it. I am on OS X 10.4.6, PPC. It looks to me like the files are not found because they are not being sought in the right directory, but I'm not sure how to correct this. The files it complains are absent are present in the right folder, and can be seen in the unpacking stages (shown below). For example, the first 'absent' file, has a path: /sw/src/fink.build/phase-1.1-1/phase-1.1/include/Models/DnaModel.h Any help would be appreciated. Mike Dyall-Smith ---From the 'fink install phase' command, it downloads OK: The following package will be installed or updated: phase curl -f -L -O http://distfiles.bne.qld.au.finkmirrors.net/phase-1.1.tgz ---Then it unpacks the downloaded package Unpacking fink-buildlock-phase-1.1-1 (from .../fink-buildlock- phase-1.1-1_2006.06.12-21.57.39_darwin-powerpc.deb) ... Setting up fink-buildlock-phase-1.1-1 (2006.06.12-21.57.39) ... gzip -dc /sw/src/phase-1.1.tgz | /sw/bin/tar -xvf - --no-same-owner --no-same-permissions phase-1.1/ phase-1.1/blas/ phase-1.1/blas/Makefile . . . phase-1.1/include/Models/DnaModel.h . phase-1.1/include/Models/MixedPerturbator.h . . . ---Then it patches the makefile OK . phase-1.1/LICENSING phase-1.1/README patch -p1 /sw/fink/dists/unstable/main/finkinfo/sci/phase.patch patching file include/Models/Model.h patching file makefile /var/tmp/tmp.1.y4WwdA + make g++ -funroll-all-loops -O4 -fstrength-reduce -fexpensive- optimizations -I./include -I./include/Models -I./include/Tree -I./ include/Util -I./include/Sequence -o obj/MCMCphase.o -c src/MCMCphase.cc g++ -funroll-all-loops -O4 -fstrength-reduce -fexpensive- optimizations -I./include -I./include/Models -I./include/Tree -I./ include/Util -I./include/Sequence -o obj/Phase.o -c src/Phase.cc g++-3.3 -I/sw/include -c -o src/Models/DnaModel.o src/Models/ DnaModel.cc src/Models/DnaModel.cc:1:29: Models/DnaModel.h: No such file or directory src/Models/DnaModel.cc:7:36: Sequence/SequenceTable.h: No such file or directory src/Models/DnaModel.cc:9:32: Models/Perturbator.h: No such file or directory src/Models/DnaModel.cc:10:31: Util/ModelFactory.h: No such file or directory src/Models/DnaModel.cc:12:37: PatternDesign/Singleton.h: No such file or directory src/Models/DnaModel.cc:13:26: Util/statlib.h: No such file or directory [snip - lots of similar errors] src/Models/DnaModel.cc:599: error: syntax error before `' token src/Models/DnaModel.cc:601: error: syntax error before `' token src/Models/DnaModel.cc:602: error: syntax error before `.' token make: *** [src/Models/DnaModel.o] Error 1 ### execution of /var/tmp/tmp.1.y4WwdA failed, exit code 2 Removing build lock... /sw/bin/dpkg-lockwait -r fink-buildlock-phase-1.1-1 (Reading database ... 19431 files and directories currently installed.) Removing fink-buildlock-phase-1.1-1 ... Failed: phase compiling: phase-1.1-1 failed ___ ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] PHASE phylogenetics package
On 6/12/06, Mike Dyall-Smith [EMAIL PROTECTED] wrote: Has anyone successfully compiled the phylogenetics package PHASE (Ben Hines, Maintainer) recently? I have scanned the fink archives but see nothing apart from minor updates to the .patch and .info files last year. Below is the output (edited) I get when I try to install it. I am on OS X 10.4.6, PPC. It looks to me like the files are not found because they are not being sought in the right directory, but I'm not sure how to correct this. The files it complains are absent are present in the right folder, and can be seen in the unpacking stages (shown below). For example, the first 'absent' file, has a path: /sw/src/fink.build/phase-1.1-1/phase-1.1/include/Models/DnaModel.h Any help would be appreciated. Mike Dyall-Smith ---From the 'fink install phase' command, it downloads OK: The following package will be installed or updated: phase curl -f -L -O http://distfiles.bne.qld.au.finkmirrors.net/phase-1.1.tgz ---Then it unpacks the downloaded package Unpacking fink-buildlock-phase-1.1-1 (from .../fink-buildlock- phase-1.1-1_2006.06.12-21.57.39_darwin-powerpc.deb) ... Setting up fink-buildlock-phase-1.1-1 (2006.06.12-21.57.39) ... gzip -dc /sw/src/phase-1.1.tgz | /sw/bin/tar -xvf - --no-same-owner --no-same-permissions phase-1.1/ phase-1.1/blas/ phase-1.1/blas/Makefile . . . phase-1.1/include/Models/DnaModel.h . phase-1.1/include/Models/MixedPerturbator.h . . . ---Then it patches the makefile OK . phase-1.1/LICENSING phase-1.1/README patch -p1 /sw/fink/dists/unstable/main/finkinfo/sci/phase.patch patching file include/Models/Model.h patching file makefile /var/tmp/tmp.1.y4WwdA + make g++ -funroll-all-loops -O4 -fstrength-reduce -fexpensive- optimizations -I./include -I./include/Models -I./include/Tree -I./ include/Util -I./include/Sequence -o obj/MCMCphase.o -c src/MCMCphase.cc g++ -funroll-all-loops -O4 -fstrength-reduce -fexpensive- optimizations -I./include -I./include/Models -I./include/Tree -I./ include/Util -I./include/Sequence -o obj/Phase.o -c src/Phase.cc g++-3.3 -I/sw/include -c -o src/Models/DnaModel.o src/Models/ DnaModel.cc src/Models/DnaModel.cc:1:29: Models/DnaModel.h: No such file or directory src/Models/DnaModel.cc:7:36: Sequence/SequenceTable.h: No such file or directory src/Models/DnaModel.cc:9:32: Models/Perturbator.h: No such file or directory src/Models/DnaModel.cc:10:31: Util/ModelFactory.h: No such file or directory src/Models/DnaModel.cc:12:37: PatternDesign/Singleton.h: No such file or directory src/Models/DnaModel.cc:13:26: Util/statlib.h: No such file or directory [snip - lots of similar errors] src/Models/DnaModel.cc:599: error: syntax error before `' token src/Models/DnaModel.cc:601: error: syntax error before `' token src/Models/DnaModel.cc:602: error: syntax error before `.' token make: *** [src/Models/DnaModel.o] Error 1 ### execution of /var/tmp/tmp.1.y4WwdA failed, exit code 2 Removing build lock... /sw/bin/dpkg-lockwait -r fink-buildlock-phase-1.1-1 (Reading database ... 19431 files and directories currently installed.) Removing fink-buildlock-phase-1.1-1 ... Failed: phase compiling: phase-1.1-1 failed ___ Try looking in the build directory for DnaModel.h to see if it is in fact present but in some other location. -- Alexander K. Hansen Fink Documenter (still) ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] kde removal
Is there a simple one line command (or thereabouts) to remove all of kde? ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] kde removal
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 William Scott wrote: Is there a simple one line command (or thereabouts) to remove all of kde? fink info kdelibs3 (or any kde package) says: To remove all of the official KDE packages, you can remove the KDE libraries and anything that depends on them by running, in a terminal: sudo apt-get remove kdelibs3-universal-shlibs - -- Benjamin Reed a.k.a. Ranger Rick http://ranger.befunk.com/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEjYNqUu+jZtP2Zf4RAtYJAJ0XFLHhxtoQo0lfLskS5/B2nAwZAQCffu6U a2oIB+Z0cqn1NDpnHjvzmmc= =5Xid -END PGP SIGNATURE- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] kde removal
Thanks. I found fink remove -r packagename, and a little persistance, finally did the trick. (I decided I didn't want to update KDE in the transitional tree since I am hoping to be rid of it soon.) Thanks. Bill On Mon, 12 Jun 2006, Benjamin Reed wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 William Scott wrote: Is there a simple one line command (or thereabouts) to remove all of kde? fink info kdelibs3 (or any kde package) says: To remove all of the official KDE packages, you can remove the KDE libraries and anything that depends on them by running, in a terminal: sudo apt-get remove kdelibs3-universal-shlibs - -- Benjamin Reed a.k.a. Ranger Rick http://ranger.befunk.com/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFEjYNqUu+jZtP2Zf4RAtYJAJ0XFLHhxtoQo0lfLskS5/B2nAwZAQCffu6U a2oIB+Z0cqn1NDpnHjvzmmc= =5Xid -END PGP SIGNATURE- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
