| Port details |
- ssaha Very fast matching and alignment of DNA sequences
- 3.1c_6 biology
 =0      3.1c_6Version of this port present on the latest quarterly branch.  BROKEN: No public distfiles
 DEPRECATED: Broken for more than 6 months
 This port expired on: 2018-06-06
 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
- Port Added: 2008-06-21 00:02:14
- Last Update: 2018-06-07 00:34:18
- SVN Revision: 471892
- License: not specified in port
- WWW:
- http://www.sanger.ac.uk/resources/software/ssaha/
- Description:
- 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.
SSAHA: a fast search method for large DNA databases (2001).
Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9.
PMID: 11591649
WWW: http://www.sanger.ac.uk/resources/software/ssaha/
 cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- No installation instructions:
- This port has been deleted.
- PKGNAME: ssaha
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (ssaha_v31c.tar.gz) = 63fa38ccd2725db6ba10881f8cc94d899afd2eba9c2f6436223d9284c5abfced
SIZE (ssaha_v31c.tar.gz) = 251510
No package information for this port in our database- Sometimes this happens. Not all ports have packages.
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake : devel/gmake
- gcc6 : lang/gcc6
- as : devel/binutils
- Runtime dependencies:
-
- gcc6 : lang/gcc6
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- N/A
- USES:
- gmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
3.1c_6
07 Jun 2018 00:34:18
  |
rene |
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  ) |
3.1c_6
05 May 2018 10:49:36
|
antoine |
Deprecate ports broken for more than 6 months |
3.1c_6
10 Mar 2018 17:46:06
|
gerald |
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079). |
3.1c_5
13 Oct 2017 11:14:53
 |
bapt |
Mark as broken ports with no public distfiles |
3.1c_5
24 Sep 2017 18:45:25
|
jbeich |
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 |
3.1c_5
10 Sep 2017 20:55:39
|
gerald |
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 |
3.1c_4
01 Apr 2017 15:23:32
|
gerald |
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 |
3.1c_3
20 Nov 2016 09:38:09
|
gerald |
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. |
3.1c_2
19 May 2016 10:21:25
|
amdmi3 |
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
Approved by: portmgr blanket |
3.1c_2
20 Dec 2014 17:27:09
|
bapt |
Cleanup plist |
3.1c_2
09 Mar 2014 09:39:50
|
rene |
biology/ssaha: undeprecate, this port fetches and builds fine.
Submitted by: Kurt Jaeger via private mail. |
3.1c_2
07 Feb 2014 18:50:30
|
bapt |
Deprecate ports unmaintained for which distillator is not able to find public
distfiles
Reported by: distilator |
3.1c_2
25 Jan 2014 16:48:06
|
miwi |
- 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 |
3.1c_1
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
3.1c_1
01 Oct 2012 14:45:17
|
tabthorpe |
- Reassign to the heap at maintainer's request |
3.1c_1
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
3.1c_1
21 Jun 2008 02:46:21
|
lippe |
- Fix plist files installation.
- Bump PORTREVISION.
Reported by: QA Tindy
Approved by: gabor (mentor, implicit) |
3.1c
21 Jun 2008 00:01:57
|
lippe |
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) |
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