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Port details
ssaha Very fast matching and alignment of DNA sequences
3.1c_6 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 3.1cVersion of this port present on the latest quarterly branch.
Broken BROKEN: No public distfiles
Deprecated DEPRECATED: Broken for more than 6 months
Expired This port expired on: 2018-06-06
Ignore IGNORE: is marked as broken: No public distfiles
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
search for ports maintained by this maintainer
Port Added: 2008-06-21 00:02:14
Last Update: 2018-06-07 01:34:18
SVN Revision: 471892
License: not specified in port
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (8 items)
  1. bin/ssaha
  2. share/ssaha/testSSAHA.csh
  3. share/ssaha/test.fasta
  4. share/ssaha/test_extract.fasta
  5. share/ssaha/test_filter.fail
  6. share/ssaha/test_filter.fastq
  7. share/ssaha/test_protein.fasta
  8. share/ssaha/README
Collapse this list.
Dependency lines:
  • ssaha>0:biology/ssaha
No installation instructions: this port has been deleted.
The package name of this deleted port was:
PKGNAME: ssaha
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. gcc6 : lang/gcc6
  3. as : devel/binutils
Runtime dependencies:
  1. gcc6 : lang/gcc6
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha/
Port Moves
  • port deleted on 2018-06-07
    REASON: Has expired: Broken for more than 6 months

Number of commits found: 18

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Jun 2018 00:34:18
Original commit files touched by this commit  3.1c_6
Revision:471892
rene search for other commits by this committer
Remove expired ports:
2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring
comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
05 May 2018 10:49:36
Original commit files touched by this commit  3.1c_6
Revision:469100
antoine search for other commits by this committer
Deprecate ports broken for more than 6 months
10 Mar 2018 17:46:06
Original commit files touched by this commit  3.1c_6
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
13 Oct 2017 11:14:53
Original commit files touched by this commit  3.1c_5
Revision:451982  Sanity Test Failure
bapt search for other commits by this committer
Mark as broken ports with no public distfiles
24 Sep 2017 18:45:25
Original commit files touched by this commit  3.1c_5
Revision:450500
jbeich search for other commits by this committer
biology/ssaha: unbreak with gcc7

In file included from Binary/..//Global/SSAHAMain.cpp:51:0:
Binary/..//Global/SSAHAMain.cpp: In function 'void
processQuery(QueryParameterStruct&)':
Binary/..//Global/SSAHAMain.cpp:968:23: error: ISO C++ forbids comparison
between pointer and integer [-fpermissive]
     assert( pAligner!=false);
                       ^

PR:		222542
10 Sep 2017 20:55:39
Original commit files touched by this commit  3.1c_5
Revision:449591
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
01 Apr 2017 15:23:32
Original commit files touched by this commit  3.1c_4
Revision:437439
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
20 Nov 2016 09:38:09
Original commit files touched by this commit  3.1c_3
Revision:426566
gerald search for other commits by this committer
Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
19 May 2016 10:21:25
Original commit files touched by this commit  3.1c_2
Revision:415498
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
20 Dec 2014 17:27:09
Original commit files touched by this commit  3.1c_2
Revision:375014
bapt search for other commits by this committer
Cleanup plist
09 Mar 2014 09:39:50
Original commit files touched by this commit  3.1c_2
Revision:347560
rene search for other commits by this committer
biology/ssaha: undeprecate, this port fetches and builds fine.

Submitted by:	Kurt Jaeger via private mail.
07 Feb 2014 18:50:30
Original commit files touched by this commit  3.1c_2
Revision:343287
bapt search for other commits by this committer
Deprecate ports unmaintained for which distillator is not able to find public
distfiles

Reported by:	distilator
25 Jan 2014 16:48:06
Original commit files touched by this commit  3.1c_2
Revision:341053
miwi search for other commits by this committer
- Fix build on -current
- Update MASTER_SITES and WWW: line
- Support CXX/CXXFLAGS properly
- Support PLIST_FILES
- Stage support

PR:		184852
Submitted by:	Ports Fury
20 Sep 2013 15:55:44
Original commit files touched by this commit  3.1c_1
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)
01 Oct 2012 14:45:17
Original commit files touched by this commit  3.1c_1
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
19 Mar 2011 12:38:54
Original commit files touched by this commit  3.1c_1

miwi search for other commits by this committer
- Get Rid MD5 support
21 Jun 2008 02:46:21
Original commit files touched by this commit  3.1c_1

lippe search for other commits by this committer
- Fix plist files installation.
- Bump PORTREVISION.

Reported by:    QA Tindy
Approved by:    gabor (mentor, implicit)
21 Jun 2008 00:01:57
Original commit files touched by this commit  3.1c

lippe search for other commits by this committer
SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.

WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/

PR:             ports/124525
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:    gabor (mentor, implicit)

Number of commits found: 18

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