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The cause of the slowdown was a change to the ZFS dataset. In conjunction with the database server, very little caching was being done. This combination resulted in increased disk I/O as the system churned through the database. Details in the blog post which outlines the various things which changed. Many graphs.

Port details
dotter Viewer for multiple sequence alignments
20021204 biology Deleted on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 20021204Version of this port present on the latest quarterly branch.
Broken BROKEN: checksum mismatch
Deprecated DEPRECATED: Broken for more than 6 month
Expired This port expired on: 2013-12-18
Ignore IGNORE: is marked as broken: checksum mismatch
Maintainer: fbsd-ports@opsec.eu search for ports maintained by this maintainer
Port Added: 2006-03-15 10:36:50
Last Update: 2013-11-10 11:01:03
SVN Revision: 333374
License: not specified in port
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • dotter>0:biology/dotter
No installation instructions: this port has been deleted.
The package name of this deleted port was: dotter
PKGNAME: dotter
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: i386
distinfo:
There is no distinfo for this port.

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Runtime dependencies:
  1. fedora-release : emulators/linux_base-f10
There are no ports dependent upon this port

Configuration Options
Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/dotter-20021204/
  2. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  3. ftp://ftp.cn.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  4. ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  5. ftp://ftp.ru.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  6. ftp://ftp.se.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  7. ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  8. ftp://ftp.uk.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  9. http://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  10. http://sonnhammer.sbc.su.se/download/software/dotter/
Port Moves
  • port moved to biology/seqtools on 2013-11-10
    REASON: Replaced with biology/seqtools

Number of commits found: 19

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Nov 2013 11:01:03
Original commit files touched by this commit  20021204
Revision:333374
wg search for other commits by this committer
biology/seqtools: Tools for visualising sequence alignments

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>
07 Nov 2013 13:18:51
Original commit files touched by this commit  20021204
Revision:333091
bsam search for other commits by this committer
. give maintainership to the submitter;
. add one month to DEPRACATION_DATE;

while here: strip the indefinite article from COMMENT.

PR:		ports/183742
Submitted by:	Kurt Jaeger <fbsd-ports@opsec.eu> (assigned maintainer)
18 Oct 2013 07:19:26
Original commit files touched by this commit  20021204
Revision:330726
bapt search for other commits by this committer
Deprecated some ports broken for more than 6 month
20 Sep 2013 15:55:44
Original commit files touched by this commit  20021204
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
25 Mar 2013 01:41:32
Original commit files touched by this commit  20021204
Revision:315188
miwi search for other commits by this committer
- Mark broken checksum mismatch

Reported by:	pointyhat
http://pointyhat.freebsd.org/errorlogs/i386-errorlogs/a.8.20130324140101.pointyhat/dotter-20021204.log
01 Oct 2012 14:45:17
Original commit files touched by this commit  20021204
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
22 Apr 2011 18:59:11
Original commit files touched by this commit  20021204

glarkin search for other commits by this committer
- Updated WWW: to a working link
- Copied unbranded distfile (dotter.LIN) to LOCAL/glarkin for mirroring to
  MASTER_SITE_LOCAL and prevention of fetch checksum error. [1]

Reported by:    pointyhat (via miwi)
19 Mar 2011 12:38:54
Original commit files touched by this commit  20021204

miwi search for other commits by this committer
- Get Rid MD5 support
28 Apr 2010 22:37:11
Original commit files touched by this commit  20021204

glarkin search for other commits by this committer
- Removed BROKEN because file fetches and checksums correctly
- Added another MASTER_SITES for redundancy

PR:             ports/144733
Submitted by:   Fernan Aguero <fernan.aguero@gmail.com> (maintainer)
19 Nov 2009 12:43:06
Original commit files touched by this commit  20021204

miwi search for other commits by this committer
- broken checksum mismatch
16 Sep 2009 15:57:19
Original commit files touched by this commit  20021204

garga search for other commits by this committer
UNBREAK: Probably was a temporary failure, checksums are ok now.

Feature safe:   yes
22 Aug 2009 08:45:12
Original commit files touched by this commit  20021204

miwi search for other commits by this committer
- BROKEN checksum mismatch
17 Aug 2009 15:38:37
Original commit files touched by this commit  20021204

miwi search for other commits by this committer
- Fix fetch

PR:             137840
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
27 Jan 2008 11:26:35
Original commit files touched by this commit  20021204

erwin search for other commits by this committer
Umark BROKEN, stale distfile removed from ftp-master.
25 Jan 2008 20:05:06
Original commit files touched by this commit  20021204

erwin search for other commits by this committer
Mark BROKEN: does not fetch
09 Aug 2007 01:00:45
Original commit files touched by this commit  20021204

kris search for other commits by this committer
Replace IGNORE with ONLY_FOR_ARCHS for this binary port.

Submitted by:   maintainer
03 Aug 2006 20:28:00
Original commit files touched by this commit  20021204

erwin search for other commits by this committer
Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master.
03 Aug 2006 19:06:04
Original commit files touched by this commit  20021204

erwin search for other commits by this committer
Mark BROKEN: checksum mismatch
15 Mar 2006 10:35:24
Original commit files touched by this commit  20021204

garga search for other commits by this committer
Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.

PR:             ports/93055
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

Number of commits found: 19

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