<precise description of the problem (multiple lines)> FASTA is reportedly broken, as the old distfiles have been removed from upstream sources. http://pointyhat-west.isc.freebsd.org/errorlogs/amd64-errorlogs/a.7.4-release.20110113192327.pointyhat-west/fasta3-35.4.9.log Upgrade FASTA to latest v.36, and fix the fetch issue Fix: <how to correct or work around the problem, if known (multiple lines)> --0003255763fe784d3e049a98d5d1 Content-Type: text/x-patch; charset=US-ASCII; name="fasta3.diff" Content-Disposition: attachment; filename="fasta3.diff" Content-Transfer-Encoding: base64 X-Attachment-Id: f_gjbi3uoe0 ZGlmZiAtLWV4Y2x1ZGUgQ1ZTIC11IC91c3IvcG9ydHMvYmlvbG9neS9mYXN0YTMvTWFrZWZpbGUg ZmFzdGEzL01ha2VmaWxlCi0tLSAvdXNyL3BvcnRzL2Jpb2xvZ3kvZmFzdGEzL01ha2VmaWxlCTIw MDktMDgtMjMgMTI6NDc6MzcuMDAwMDAwMDAwIC0wMzAwCisrKyBmYXN0YTMvTWFrZWZpbGUJMjAx MS0wMS0yMSAxODoxNTo0NC4wMDAwMDAwMDAgLTAzMDAKQEAgLTcsOSArNyw5IEBACiAjCiAKIFBP UlROQU1FPQlmYXN0YTMKLVBPUlRWRVJTSU9OPQkzNS40LjkKK1BPUlRWRVJTSU9OPQkzNi4zLjIK 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http://faculty.virginia.edu/wrpearson/fasta/fasta3/ +MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/ DISTNAME= fasta-${PORTVERSION} MAINTAINER= fernan@iib.unsam.edu.ar @@ -34,12 +34,12 @@ DATA= data/*.mat EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib -MAN1= fasta35.1 map_db.1 ps_lav.1 pvcomp.1 -MLINKS= fasta35.1 tfasta35.1 fasta35.1 fastx35.1 fasta35.1 tfastx35.1 \ - fasta35.1 fasty35.1 fasta35.1 tfasty35.1 fasta35.1 ssearch35.1 \ - fasta35.1 fastf35.1 fasta35.1 fasts35.1 fasta35.1 tfasts35.1 \ - fasta35.1 fastm35.1 fasta35.1 tfastf35.1 fasta35.1 ggsearch35.1 \ - fasta35.1 lalign35.1 fasta35.1 prss35.1 fasta35.1 prfx35.1 +MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 +MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \ + fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \ + fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \ + fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \ + fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1 PLIST_SUB= VER=${PORTVERSION:R:R} post-patch: diff --exclude CVS -u /usr/ports/biology/fasta3/distinfo fasta3/distinfo --- /usr/ports/biology/fasta3/distinfo 2009-08-23 12:47:37.000000000 -0300 +++ fasta3/distinfo 2011-01-21 18:03:08.000000000 -0300 @@ -1,3 +1,2 @@ -MD5 (fasta-35.4.9.tar.gz) = 6bf19b771f2c64287b7713864b9f0a69 -SHA256 (fasta-35.4.9.tar.gz) = 4beaed42557572a1c8e5480e93641af175fa43c545f75c4bf06db62dced6bd39 -SIZE (fasta-35.4.9.tar.gz) = 630748 +SHA256 (fasta-36.3.2.tar.gz) = 1eddb7dac3a52311d43bac854b2153c13aa23cbb163952c9e385a75aa2b9e446 +SIZE (fasta-36.3.2.tar.gz) = 711876 Common subdirectories: /usr/ports/biology/fasta3/files and fasta3/files diff --exclude CVS -u /usr/ports/biology/fasta3/pkg-plist fasta3/pkg-plist --- /usr/ports/biology/fasta3/pkg-plist 2009-06-09 04:53:37.000000000 -0300 +++ fasta3/pkg-plist 2011-01-21 18:26:39.000000000 -0300 @@ -17,7 +17,6 @@ bin/lalign%%VER%% bin/lav2ps bin/lav2svg -bin/list_db bin/map_db bin/ssearch%%VER%% bin/ssearch%%VER%%_t @@ -39,10 +38,6 @@ %%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc %%PORTDOCS%%%%DOCSDIR%%/fasta20.doc %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc -%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3 -%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2 -%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3 -%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4 %%PORTDOCS%%%%DOCSDIR%%/readme.v30 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7 @@ -52,12 +47,14 @@ %%PORTDOCS%%%%DOCSDIR%%/readme.v33t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v34t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v35 +%%PORTDOCS%%%%DOCSDIR%%/readme.v36 %%PORTDOCS%%%%DOCSDIR%%/readme.w32 %%PORTDOCS%%%%DOCSDIR%%/fasta.defaults %%PORTDOCS%%%%DOCSDIR%%/fasta.options %%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html %%PORTDOCS%%%%DOCSDIR%%/changes_v34.html %%PORTDOCS%%%%DOCSDIR%%/changes_v35.html +%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html %%EXAMPLESDIR%%/egmsmg.aa %%EXAMPLESDIR%%/gstt1_drome.aa %%EXAMPLESDIR%%/gtm1_human.aa @@ -95,6 +92,7 @@ %%EXAMPLESDIR%%/hsgstm1b.seq %%EXAMPLESDIR%%/humgstd.seq %%EXAMPLESDIR%%/mgstm1.seq +%%EXAMPLESDIR%%/mgstm1_genclone.seq %%EXAMPLESDIR%%/mgtt2_x.seq %%EXAMPLESDIR%%/titin_hum.seq %%EXAMPLESDIR%%/mu.lib How-To-Repeat: <code/input/activities to reproduce the problem (multiple lines)>
Class Changed From-To: maintainer-update->change-request Fix category (submitter is not maintainer) (via the GNATS Auto Assign Tool)
Maintainer of biology/fasta3, Please note that PR ports/154267 has just been submitted. If it contains a patch for an upgrade, an enhancement or a bug fix you agree on, reply to this email stating that you approve the patch and a committer will take care of it. The full text of the PR can be found at: http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/154267 -- Edwin Groothuis via the GNATS Auto Assign Tool edwin@FreeBSD.org
State Changed From-To: open->feedback Awaiting maintainers feedback (via the GNATS Auto Assign Tool)
On Mon, Jan 24, 2011 at 12:31 PM, Edwin Groothuis <edwin@freebsd.org> wrote= : > Maintainer of biology/fasta3, > > Please note that PR ports/154267 has just been submitted. > > If it contains a patch for an upgrade, an enhancement or a bug fix > you agree on, reply to this email stating that you approve the patch > and a committer will take care of it. > > The full text of the PR can be found at: > =A0 =A0http://www.freebsd.org/cgi/query-pr.cgi?pr=3Dports/154267 It was me that submitted the patch, from a different email address. Sorry. Approved, thanks! --=20 fernan
State Changed From-To: feedback->open Submitter is maintainer from another address.
Responsible Changed From-To: freebsd-ports-bugs->beat I'll take it.
beat 2011-01-26 20:26:36 UTC FreeBSD ports repository Modified files: biology/fasta3 Makefile distinfo pkg-plist Log: - Update to 36.3.2 to fix distfile fetching on pointyhat PR: ports/154267 Submitted by: Fernan Aguero <fernan AT iib.unsam.edu.ar> (maintainer) Feature safe: yes Revision Changes Path 1.27 +8 -8 ports/biology/fasta3/Makefile 1.22 +2 -3 ports/biology/fasta3/distinfo 1.8 +3 -5 ports/biology/fasta3/pkg-plist _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
State Changed From-To: open->closed Committed. Thanks!