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 $300 http://ads.osdn.com/?ad_id=6883alloc_id=15149op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ 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 $300 http://ads.osdn.com/?ad_id=6883alloc_id=15149op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
On Mar 24, 2005, at 10:58 AM, Robert T Wyatt wrote: Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ 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 $300 http://ads.osdn.com/?ad_id=6883alloc_id=15149op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Hi Alexander, I know it's confusing. This machine is 10.2-gcc3.3 (hence the subject line). Naturally, this will change soon, but for now I'm trying to build some unstable stuff in this branch on this machine while I still can (I'm getting a dual 1.8GHz G5 in about two weeks here at work which will use OS10.3.) The eMac at home is the one I've already changed over to 10.3. Thanks much for trying to keep up though! --Robert At 11:04 AM -0500 3/24/05, Alexander K. Hansen wrote: On Mar 24, 2005, at 10:58 AM, Robert T Wyatt wrote: Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ 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 $300 http://ads.osdn.com/?ad_id=6883alloc_id=15149op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
On Mar 24, 2005, at 11:24 AM, Robert T Wyatt wrote: Hi Alexander, I know it's confusing. This machine is 10.2-gcc3.3 (hence the subject line). Naturally, this will change soon, but for now I'm trying to build some unstable stuff in this branch on this machine while I still can (I'm getting a dual 1.8GHz G5 in about two weeks here at work which will use OS10.3.) The eMac at home is the one I've already changed over to 10.3. Thanks much for trying to keep up though! --Robert At 11:04 AM -0500 3/24/05, Alexander K. Hansen wrote: On Mar 24, 2005, at 10:58 AM, Robert T Wyatt wrote: Hmmm, if this doesn't work (and it doesn't): bash-2.05b$ 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 $300 http://ads.osdn.com/?ad_id=6883alloc_id=15149op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
Re: [Fink-devel] Re: dists/10.2-gcc3.3/unstable/main/finkinfo/sci hmmer-2.2g-3.info,1.3,1.4
Yes: bash-2.05b$ 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_ide95alloc_id396op=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=6595alloc_id=14396op=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
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=6595alloc_id=14396op=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
Do y'all know why I am getting this? Thanks, Robert Information about 3326 packages read in 4 seconds. hmmer2.2g-3 Profile HMMs for biological sequence analysis Information about 3326 packages read in 4 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 Wed Mar 23 16:09:20 CST 2005 bash-2.05b$ Daniel Macks wrote: Update of /cvsroot/fink/dists/10.2-gcc3.3/unstable/main/finkinfo/sci In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4315 Modified Files: hmmer-2.2g-3.info Log Message: Cleared BConflicts:fink by fixing Source2 shell metachars Index: hmmer-2.2g-3.info === RCS file: /cvsroot/fink/dists/10.2-gcc3.3/unstable/main/finkinfo/sci/hmmer-2.2g-3.info,v retrieving revision 1.3 retrieving revision 1.4 diff -u -d -r1.3 -r1.4 --- hmmer-2.2g-3.info 20 Jan 2005 20:51:17 - 1.3 +++ hmmer-2.2g-3.info 23 Mar 2005 03:27:13 - 1.4 @@ -3,11 +3,11 @@ Revision: 3 Source: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/%v/hmmer-%v.tar.gz Source-MD5: d7def2007a0aaf2eafb9a96a07986b8c -Source2: http://pfam.wustl.edu/cgi-bin/gethmm?name=7tm_1\type=fs +Source2: http://pfam.wustl.edu/cgi-bin/gethmm?name=7tm_1type=fs Source2Rename: 7tm_1 Source3: http://us.expasy.org/cgi-bin/get-sprot-fasta?P08908 Source3Rename: P08908.fasta -BuildConflicts: fink (= 0.23.5.cvs-20050120.) +BuildDepends: fink (= 0.24) Patch: %f.patch RuntimeVars: HMMERDB: /data/hmmerdb --- 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=6883alloc_id=15149op=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 Wyatt wrote: Do y'all know why I am getting this? Thanks, Robert Did you look at the file to see whether you have the new version? If yes, maybe you need to run fink index. -- 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=6883alloc_id=15149op=click ___ Fink-devel mailing list Fink-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-devel
