Re: [Fink-devel] [tutors-dev:01049] Package manager: AppBundles feature is buggy
On Tue, Mar 22, 2005 at 05:17:08PM +0900, AIDA Shinra wrote: > I found a the symlink to /sw/Applications/foobar.app is not created if > /Applications/Fink is already exist. I attach a patch. Fixed in CVS HEAD and branch_0_24. drm: if 0.24.2 isn't out yet, want to redo it with this patch? dan -- Daniel Macks [EMAIL PROTECTED] http://www.netspace.org/~dmacks --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] [tutors-dev:01049] Package manager: AppBundles feature is buggy
I found a the symlink to /sw/Applications/foobar.app is not created if /Applications/Fink is already exist. I attach a patch. PkgVersion.pm.diff Description: Binary data
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
This fixed the problem (and updated several core files). Thanks Martin! At 8:24 PM +0100 3/24/05, Martin Costabel wrote: Robert T Wyatt wrote: Mirror-rsync: rsync://msn.wi.us.finkmirrors.net/finkinfo/ Looking at this rsync mirror, it seems to me indeed that it is taking its spring break since a week or so. Try another one, perhaps master.us.finkmirrors.net to be on the safe side. -- Martin --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Robert T Wyatt wrote: Yes: bash-2.05b$ cat /sw/etc/fink.conf [] Mirror-rsync: rsync://msn.wi.us.finkmirrors.net/finkinfo/ Looking at this rsync mirror, it seems to me indeed that it is taking its spring break since a week or so. Try another one, perhaps master.us.finkmirrors.net to be on the safe side. -- Martin --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Yes: bash-2.05b$ cat /sw/etc/fink.conf # Fink configuration, initially created by bootstrap.pl Basepath: /sw RootMethod: sudo Trees: local/main stable/main stable/crypto local/bootstrap unstable/main unstable/crypto Distribution: 10.2-gcc3.3 Mirror-cpan: ftp://ftp.duke.edu/pub/perl/ Mirror-ctan: ftp://ctan.math.utah.edu/tex-archive/ Mirror-debian: ftp.debian.org Mirror-gimp: ftp://ftp.cs.umn.edu/pub/gimp/ Mirror-gnome: ftp://ftp.cse.buffalo.edu/pub/Gnome Mirror-gnu: ftp://ftp.cis.ohio-state.edu/mirror/gnu/ Mirror-kde: ftp://ftp.rutgers.edu/pub/kde Mirror-master: http://distfiles.msn.wi.us.finkmirrors.net/ Mirror-rsync: rsync://msn.wi.us.finkmirrors.net/finkinfo/ Mirror-sourceforge: http://umn.dl.sourceforge.net/sourceforge/ MirrorContinent: nam MirrorCountry: nam-us MirrorOrder: MasterLast ProxyPassiveFTP: false Verbose: 3 SelfUpdateMethod: rsync Mirror-apt: http://us.dl.sourceforge.net/fink/direct_download UseBinaryDist: true MatchPackageRegEx: (.*-ssl.*$) DownloadMethod: axel ConfFileCompatVersion: 1 CCacheDir: /sw/var/ccache FetchAltDir: /Users/rgrtw/src bash-2.05b$ ls /users/rgrtw/src io.c ldp.dsl ldp.dsl-1.12 also: b a s h - 2 . 0 5 b $ p r i n t e n v M A N P A T H = / s w / s h a r e / m a n : / s w / m a n : / u s r / s h a r e / m a n : / u s r / X 1 1 R 6 / m a n : / s w / l i b / p e r l 5 - c o r e / 5 . 6 . 0 / m a n : / s w / l i b / p e r l 5 / 5 . 6 . 0 / m a n : / s w / l i b / p e r l 5 - c o r e / 5 . 8 . 0 / m a n : / s w / l i b / p e r l 5 / 5 . 8 . 0 / m a n T E R M _ P R O G R A M = A p p l e _ T e r m i n a l H O S T = r e g 1 3 4 . r e g . u t e x a s . e d u T E R M = v t 1 0 0 S H E L L = / b i n / t c s h P E R L 5 L I B = / s w / l i b / p e r l 5 : / s w / l i b / p e r l 5 / d a r w i n T E R M _ P R O G R A M _ V E R S I O N = 8 1 Q T D I R = / s w A N T _ H O M E = / s w / l i b / a n t X A P P L R E S D I R = / s w / e t c / a p p - d e f a u l t s / S G M L _ C A T A L O G _ F I L E S = / s w / e t c / s g m l / c a t a l o g G R O U P = s t a f f U S E R = r g r t w C C A C H E _ D I R = / s w / v a r / c c a c h e G D K _ U S E _ X F T = 1 H O S T T Y P E = m a c i n t o s h T E R M C A P = _ _ C F _ U S E R _ T E X T _ E N C O D I N G = 0 x 1 F 6 : 0 : 0 G N O M E _ D I S A B L E _ C R A S H _ D I A L O G = 1 F L T K _ D O C D I R = / s w / s h a r e / d o c / f l t k - x 1 1 - 4 3 / h t m l P A T H = / s w / b i n : / s w / s b i n : / b i n : / s b i n : / u s r / b i n : / u s r / s b i n : / u s r / X 1 1 R 6 / b i n X M L _ C A T A L O G _ F I L E S = / s w / e t c / x m l / c a t a l o g M A G I C = / s w / s h a r e / l e s s p i p e / m a g i c : / p r i v a t e / e t c / m a g i c P W D = / s w / s r c J A V A _ H O M E = / L i b r a r y / J a v a / H o m e L A N G = e n _ U S Q M A K E S P E C = / s w / s h a r e / q t 3 / m k s p e c s / d a r w i n - g + + S H L V L = 2 H O M E = / U s e r s / r g r t w O S T Y P E = d a r w i n V E N D O R = a p p l e L E S S = - - R A W - C O N T R O L - C H A R S M A C H T Y P E = p o w e r p c L O G N A M E = r g r t w C L A S S P A T H = / s w / s h a r e / j a v a / c o m m o n s - c o l l e c t i o n s / c o m m o n s - c o l l e c t i o n s - 3 . 1 . j a r : / s w / s h a r e / j a v a / c o m m o n s - c o l l e c t i o n s / c o m m o n s - c o l l e c t i o n s - t e s t f r a m e w o r k - 3 . 1 . j a r : / s w / s h a r e / j a v a / c o m m o n s - l o g g i n g / c o m m o n s - l o g g i n g - a p i . j a r : / s w / s h a r e / j a v a / c o m m o n s - l o g g i n g / c o m m o n s - l o g g i n g . j a r : / s w / s h a r e / j a v a / d b 4 2 - s s l - j a v a / d b . j a r : / s w / s h a r e / j a v a / j u n i t / j u n i t . j a r : / s w / s h a r e / j a v a / l o g 4 j / l o g 4 j - 1 . 2 . 8 . j a r : . L E S S O P E N = | / s w / b i n / l e s s p i p e . s h % s I N F O P A T H = / s w / s h a r e / i n f o : / s w / i n f o : / u s r / s h a r e / i n f o D I S P L A Y = : 0 . 0 _ = / u s r / b i n / p r i n t e n v O L D P W D = / s w At 11:33 AM -0500 3/24/05, Alexander K. Hansen wrote: On _this_ machine, does the Distribution: line say 10.2-gcc3.3 (similar upgrade issue)? --- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_ide95&alloc_id396&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
On Mar 24, 2005, at 11:24 AM, Robert T Wyatt wrote: Hi Alexander, I know it's confusing. This machine is 10.2-gcc3.3 (hence the subject line). Naturally, this will change soon, but for now I'm trying to build some unstable stuff in this branch on this machine while I still can (I'm getting a dual 1.8GHz G5 in about two weeks here at work which will use OS10.3.) The eMac at home is the one I've already changed over to 10.3. Thanks much for trying to keep up though! --Robert At 11:04 AM -0500 3/24/05, Alexander K. Hansen wrote: On Mar 24, 2005, at 10:58 AM, Robert T Wyatt wrote: Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ fink purge hmmer; fink scanpackages; fink selfupdate; fink index; fink dumpinfo hmmer What am I doing wrong? Would my environment or fink.conf be out of whack? (Everything else seems to build okay.) Perhaps it has not made it to the mirror yet? Thanks, Robert It could well be fink.conf, since you've changed OS versions. Check that the Distribution: line says 10.3. Ah--I'm with you now (clearly actually reading the subject is too much!). On _this_ machine, does the Distribution: line say 10.2-gcc3.3 (similar upgrade issue)? -- Alexander Hansen Fink Documentarian [Day Job] Levitated Dipole Experiment http://www.psfc.mit.edu/LDX --- This SF.net email is sponsored by Microsoft Mobile & Embedded DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more about the latest Windows Embedded(r) & Windows Mobile(tm) platforms, applications & content. Register by 3/29 & save $300 http://ads.osdn.com/?ad_id=6883&alloc_id=15149&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Hi Alexander, I know it's confusing. This machine is 10.2-gcc3.3 (hence the subject line). Naturally, this will change soon, but for now I'm trying to build some unstable stuff in this branch on this machine while I still can (I'm getting a dual 1.8GHz G5 in about two weeks here at work which will use OS10.3.) The eMac at home is the one I've already changed over to 10.3. Thanks much for trying to keep up though! --Robert At 11:04 AM -0500 3/24/05, Alexander K. Hansen wrote: On Mar 24, 2005, at 10:58 AM, Robert T Wyatt wrote: Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ fink purge hmmer; fink scanpackages; fink selfupdate; fink index; fink dumpinfo hmmer What am I doing wrong? Would my environment or fink.conf be out of whack? (Everything else seems to build okay.) Perhaps it has not made it to the mirror yet? Thanks, Robert It could well be fink.conf, since you've changed OS versions. Check that the Distribution: line says 10.3. -- Alexander Hansen Fink Documentarian [Day Job] Levitated Dipole Experiment http://www.psfc.mit.edu/LDX --- This SF.net email is sponsored by Microsoft Mobile & Embedded DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more about the latest Windows Embedded(r) & Windows Mobile(tm) platforms, applications & content. Register by 3/29 & save $300 http://ads.osdn.com/?ad_id=6883&alloc_id=15149&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
On Mar 24, 2005, at 10:58 AM, Robert T Wyatt wrote: Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ fink purge hmmer; fink scanpackages; fink selfupdate; fink index; fink dumpinfo hmmer What am I doing wrong? Would my environment or fink.conf be out of whack? (Everything else seems to build okay.) Perhaps it has not made it to the mirror yet? Thanks, Robert It could well be fink.conf, since you've changed OS versions. Check that the Distribution: line says 10.3. -- Alexander Hansen Fink Documentarian [Day Job] Levitated Dipole Experiment http://www.psfc.mit.edu/LDX --- This SF.net email is sponsored by Microsoft Mobile & Embedded DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more about the latest Windows Embedded(r) & Windows Mobile(tm) platforms, applications & content. Register by 3/29 & save $300 http://ads.osdn.com/?ad_id=6883&alloc_id=15149&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ fink purge hmmer; fink scanpackages; fink selfupdate; fink index; fink dumpinfo hmmer What am I doing wrong? Would my environment or fink.conf be out of whack? (Everything else seems to build okay.) Perhaps it has not made it to the mirror yet? Thanks, Robert At 4:29 PM +0100 3/24/05, Martin Costabel wrote: On 24 mars 2005, at 15:56, Robert Wyatt wrote: Fink index did not seem to help. I apologize because clearly dumpinfo was too heavy-handed, but I wanted to try to show that I do have the correct file (did I accomplish that?). No. This is the old version: buildconflicts: fink (>= 0.23.5.cvs-20050120.) The new one (as of yesterday) has builddepends: fink (>= 0.24) instead. You need another selfupdate. -- Martin --- This SF.net email is sponsored by Microsoft Mobile & Embedded DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more about the latest Windows Embedded(r) & Windows Mobile(tm) platforms, applications & content. Register by 3/29 & save $300 http://ads.osdn.com/?ad_id=6883&alloc_id=15149&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
On 24 mars 2005, at 15:56, Robert Wyatt wrote: Fink index did not seem to help. I apologize because clearly dumpinfo was too heavy-handed, but I wanted to try to show that I do have the correct file (did I accomplish that?). No. This is the old version: buildconflicts: fink (>= 0.23.5.cvs-20050120.) The new one (as of yesterday) has builddepends: fink (>= 0.24) instead. You need another selfupdate. -- Martin --- This SF.net email is sponsored by Microsoft Mobile & Embedded DevCon 2005 Attend MEDC 2005 May 9-12 in Vegas. Learn more about the latest Windows Embedded(r) & Windows Mobile(tm) platforms, applications & content. Register by 3/29 & save $300 http://ads.osdn.com/?ad_id=6883&alloc_id=15149&op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
[Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Fink index did not seem to help. I apologize because clearly dumpinfo was too heavy-handed, but I wanted to try to show that I do have the correct file (did I accomplish that?). bash-2.05b$ fink index Reading package info... Updating package index... done. bash-2.05b$ date Thu Mar 24 08:50:22 CST 2005 bash-2.05b$ fink -V Package manager version: 0.24.1 Distribution version: 0.6.3.rsync Copyright (c) 2001 Christoph Pfisterer Copyright (c) 2001-2005 The Fink Package Manager Team This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. bash-2.05b$ fink install hmmer Information about 3326 packages read in 2 seconds. The package 'hmmer' will be built and installed. The following package will be installed or updated: hmmer The following package will be removed: fink Do you want to continue? [Y/n] n Failed: Package requirements not satisfied bash-2.05b$ fink dumpinfo hmmer Information about 3326 packages read in 2 seconds. infofile: /sw/fink/dists/unstable/main/finkinfo/sci/hmmer-2.2g-3.info package: hmmer version: 2.2g revision: 3 family: hmmer status: latest allversions: 2.2g-3 description: Profile HMMs for biological sequence analysis type: [undefined] license: GPL maintainer: Richard Graul <[EMAIL PROTECTED]> buildconflicts: fink (>= 0.23.5.cvs-20050120.) essential: [undefined] builddependsonly: [undefined] source: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.2g/hmmer-2.2g.tar.gz source-md5: d7def2007a0aaf2eafb9a96a07986b8c nosourcedirectory: [undefined] source2: http://pfam.wustl.edu/cgi-bin/gethmm?name=7tm_1\&type=fs source2rename: 7tm_1 source2-md5: 2267b9803e79806141fd17116e4cb560 source3: http://us.expasy.org/cgi-bin/get-sprot-fasta?P08908 source3rename: P08908.fasta source3-md5: 30eac186ce169f3156bf64bae97a286c updateconfigguess: [undefined] updatelibtool: [undefined] updatepomakefile: [undefined] patch: hmmer-2.2g-3.patch env: ANT_HOME=/sw/lib/ant CCACHE_DIR=/sw/var/ccache CLASSPATH=/sw/share/java/commons-collections/commons-collections-3.1.jar:/sw/share/java/commons-collections/commons-collections-testframework-3.1.jar:/sw/share/java/commons-logging/commons-logging-api.jar:/sw/share/java/commons-logging/commons-logging.jar:/sw/share/java/db42-ssl-java/db.jar:/sw/share/java/junit/junit.jar:/sw/share/java/log4j/log4j-1.2.8.jar:. CPPFLAGS=-I/sw/include FLTK_DOCDIR=/sw/share/doc/fltk-x11-43/html GDK_USE_XFT=1 GNOME_DISABLE_CRASH_DIALOG=1 HOME=/Users/rgrtw INFOPATH=/sw/share/info:/sw/info:/usr/share/info LDFLAGS=-L/sw/lib LD_PREBIND=1 LD_PREBIND_ALLOW_OVERLAP=1 LD_SEG_ADDR_TABLE=/sw/var/lib/fink/prebound/seg_addr_table LESS=--RAW-CONTROL-CHARS LESSOPEN=| /sw/bin/lesspipe.sh %s MACOSX_DEPLOYMENT_TARGET=10.1 MAGIC=/sw/share/lesspipe/magic:/private/etc/magic MANPATH=/sw/share/man:/sw/man:/usr/share/man:/usr/X11R6/man:/sw/lib/perl5-core/5.6.0/man:/sw/lib/perl5/5.6.0/man:/sw/lib/perl5-core/5.8.0/man:/sw/lib/perl5/5.8.0/man PATH=/sw/bin:/sw/sbin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/X11R6/bin PERL5LIB=/sw/lib/perl5:/sw/lib/perl5/darwin PWD=/sw/src QMAKESPEC=/sw/share/qt3/mkspecs/darwin-g++ QTDIR=/sw SGML_CATALOG_FILES=/sw/etc/sgml/catalog SHLVL=2 XAPPLRESDIR=/sw/etc/app-defaults/ XML_CATALOG_FILES=/sw/etc/xml/catalog configureparams: --prefix=/sw --bindir=/sw/src/root-hmmer-2.2g-3/sw/bin --mandir=/sw/src/root-hmmer-2.2g-3/sw/share/man compilescript: ./configure --prefix=/sw --bindir=/sw/src/root-hmmer-2.2g-3/sw/bin --mandir=/sw/src/root-hmmer-2.2g-3/sw/share/man make make check chmod a+r documentation/man/* chmod a+r squid/Man/* noperltests: [undefined] updatepod: [undefined] installscript: install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/bin install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/share/man/man1 mv INSTALL INSTALL.sav make install prefix=/sw/src/root-hmmer-2.2g-3/sw mv INSTALL.sav INSTALL install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/include/hmmer-2.2g install -c -p -m 644 version.h src/*.h /sw/src/root-hmmer-2.2g-3/sw/include/hmmer-2.2g ln -s hmmer-2.2g /sw/src/root-hmmer-2.2g-3/sw/include/hmmer install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/lib install -c -p -m 644 src/libhmmer.a /sw/src/root-hmmer-2.2g-3/sw/lib/libhmmer-2.2g.a ln -s libhmmer-2.2g.a /sw/src/root-hmmer-2.2g-3/sw/lib/libhmmer.a install -d -m 755 /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo install -c -p -m 644 ../7tm_1 /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo install -c -p -m 644 ../P08908.fasta /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo echo "#!/bin/sh" > /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh echo "hmmsearch /sw/share/hmmer/demo/7tm_1 /sw/share/hmmer/demo/P08908.fasta" >> /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh chmod 755 /sw/src/root-hmmer-2.2g-3/sw/share/hmmer/demo/hmmsearch.sh docfiles: 00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf ru
