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Port details
hs-bio Bioinformatics library
0.5.3_4 science 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 View this port on Repology. pkg-fallout 0.5.3_4Version of this port present on the latest quarterly branch.
Maintainer: haskell@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2010-01-03 05:02:40
Last Update: 2018-05-25 21:44:13
SVN Revision: 470870
Also Listed In: haskell
License: LGPL21
WWW:
http://biohaskell.org/Libraries/Bio
Description:
This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities. Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also Blast output parsing. Partly implemented single linkage clustering, and multiple alignment. Reading Gene Ontology (GO) annotations (GOA) and definitions hierarchy. WWW: http://biohaskell.org/Libraries/Bio
Homepage    cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (3 items)
Collapse this list.
  1. /usr/local/share/licenses/hs-bio-0.5.3_4/catalog.mk
  2. /usr/local/share/licenses/hs-bio-0.5.3_4/LICENSE
  3. /usr/local/share/licenses/hs-bio-0.5.3_4/LGPL21
Collapse this list.
Dependency lines:
  • hs-bio>0:science/hs-bio
No installation instructions:
This port has been deleted.
PKGNAME: hs-bio
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (cabal/bio-0.5.3.tar.gz) = 42c8f9b83fea6bf51356afe1251910ba4421e0af0bb4f26431eaf385971d7eed SIZE (cabal/bio-0.5.3.tar.gz) = 103707

No package information for this port in our database
Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link: pkg-fallout
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. ghc : lang/ghc
  2. ghc>=8.0.2 : lang/ghc
  3. hs-mtl>=0 : devel/hs-mtl
  4. hs-old-time>=0 : devel/hs-old-time
  5. hs-parallel>=0 : devel/hs-parallel
  6. hs-parsec>=0 : textproc/hs-parsec
  7. hs-QuickCheck>=2 : devel/hs-QuickCheck
  8. hs-random>=0 : devel/hs-random
  9. hs-tagsoup>=0.8 : textproc/hs-tagsoup
Runtime dependencies:
  1. ghc : lang/ghc
  2. ghc>=8.0.2 : lang/ghc
  3. hs-mtl>=0 : devel/hs-mtl
  4. hs-old-time>=0 : devel/hs-old-time
  5. hs-parallel>=0 : devel/hs-parallel
  6. hs-parsec>=0 : textproc/hs-parsec
  7. hs-QuickCheck>=2 : devel/hs-QuickCheck
  8. hs-random>=0 : devel/hs-random
  9. hs-tagsoup>=0.8 : textproc/hs-tagsoup
Library dependencies:
  1. libgmp.so : math/gmp
  2. libiconv.so : converters/libiconv
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for hs-bio-0.5.3_4: DOCS=on: Build and/or install documentation DYNAMIC=on: Add support for dynamic linking HSCOLOUR=off: Colorize generated documentation by HsColour PROFILE=off: Add support for profiling ===> Use 'make config' to modify these settings
Options name:
N/A
USES:
iconv:translit
FreshPorts was unable to extract/find any pkg message
Master Sites:
  1. There is no master site for this port.

Number of commits found: 28

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.5.3_4
25 May 2018 21:44:13
Revision:470870Original commit files touched by this commit
tcberner search for other commits by this committer
Update lang/ghc 8.4.2 and the hs-* ports the newer versions

* Update lang/ghc to 8.4.2
* Update the boostrap compiler to 8.4.1
* Update the many hs-* ports
* Bump the rest

Thanks a lot to arrowd for doing all the heavy lifting :)

PR:		227968
Exp-run by:	antoine
Submitted by:	arrowd
Differential Revision:	https://reviews.freebsd.org/D15005
0.5.3_4
10 Feb 2018 08:03:22
Revision:461362Original commit files touched by this commit
tcberner search for other commits by this committer
Switch C compiler used to compile GHC to base Clang.

This removes build dependency on gcc and runtime dependency on gcc's runtime
libraries.

Big thanks to Gleb for working on this.

PR:		225185
Submitted by:	Gleb Popov <6yearold@gmail.com>
Exp-run by:	antoine
Reviewed by:	pgj
Differential Revision:	https://reviews.freebsd.org/D12043
0.5.3_3
08 Aug 2017 17:21:46
Revision:447548Original commit files touched by this commit
tcberner search for other commits by this committer
- Update The Glorious Glasgow Haskell Compiler to version 8.0.2
- Simplified port by only suporting GCC, and creating a build.mk file
- Update Pandoc to 1.19.2.1
- Update git-annex to 6.20170520
- Update Darcs to 2.12.5
- Update Gtk2Hs to 0.13.2.2
- Update Agda to 2.5.2

Please note that port revisions for all the Haskell ports without version
changes are bumped.

See the UPDATING file for instructions.

New ports (63):
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.3_2
20 Aug 2015 23:02:17
Revision:394918Original commit files touched by this commit
pgj search for other commits by this committer
- Update The Glorious Glasgow Haskell Compiler to version 7.10.2
- Include a patch for addressing timer issues [1]
- Add support for building both GHC and Haskell ports with Clang, either from
  ports or the base system
- Discontinue supporting Haskell Platform, use Stackage instead as a
  reference
- Drop support for FreeBSD 8.x, optimize bootstrap compiler tarballs
- Update Gtk2Hs to version 0.13 [2]
- Update Pandoc to version 1.15.0.6
- Update git-annex to version 5.20150727
- Update Darcs to 2.10 [3]
- Unbreak wxHaskell ports

Please note that port revisions for all the Haskell ports without version
changes are bumped.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.3_1
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
0.5.3
10 Aug 2014 22:34:52
Revision:364579Original commit files touched by this commit
pgj search for other commits by this committer
- Update The Glorious Glasgow Haskell Compiler to version 7.8.3
- Update Haskell Platform to version 2014.2.0.0
- Update Yesod Platform to version 1.2.13
- Update Gtk2Hs to version 0.12.5
- Update Pandoc to version 1.12.4.2
- Update git-annex to version 5.20140717
- Unbreak wxHaskell ports

Please note that port revisions for all the Haskell ports without version
changes are bumped.

New ports (69):

databases/hs-esqueleto: Type-safe EDSL for SQL queries on persistent backends
devel/hs-Glob: Globbing library
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_8
29 Mar 2014 00:52:55
Revision:349475Original commit files touched by this commit
pgj search for other commits by this committer
- Reroll and update bootstrap Haskell compilers to GHC 7.6.3 on 8.x and
  9.x in order to prevent run-time breakage after the recent changes in
  libiconv
- Bump port revision for lang/ghc and all dependents, as a consequence

Obtained from:	FreeBSD Haskell
0.5.2_7
10 Mar 2014 20:55:22
Revision:347809Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
0.5.2_6
09 Jan 2014 21:32:14
Revision:339286Original commit files touched by this commit
pgj search for other commits by this committer
- Stagify lang/ghc and all the Haskell Cabal ports
- Update HACKAGE_SITE to follow changes in upstream
- MAKE_ENV now sets LC_ALL and DESTDIR for Haskell Cabal ports
- Further minor cosmetical changes: replace USE_GMAKE with USES, get rid of
  ${DO_NADA}, some refactoring

Obtained from:	FreeBSD Haskell
0.5.2_6
09 Jan 2014 21:29:40
Revision:339285Original commit files touched by this commit
pgj search for other commits by this committer
- Fix a run-time problem with lang/ghc on FreeBSD 10.0 and later, caused by
  the iconv changes (basically GHCi was rendered unusable)
- Fix build for x11-toolkits/hs-wxc, while here
- Bump port revision for all Haskell Cabal ports as they have to be rebuilt

PR:		ports/184806
Reported by:	many
Obtained from:	FreeBSD Haskell
MFH:		2014Q1
0.5.2_5
26 Oct 2013 00:52:36
Revision:331644Original commit files touched by this commit
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_4
20 Sep 2013 22:48:31
Revision:327767Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
science)
0.5.2_4
04 Jun 2013 18:53:41
Revision:319894Original commit files touched by this commit
pgj search for other commits by this committer
- Update The Glorious Glasgow Haskell Compiler to version 7.6.3
- Update Haskell Platform to version 2013.2.0.0

Please note that port revisions for all the Haskell ports without version
changes are bumped.

Some highlights of the update:

- Fix PDF generation for pandoc [1]
- From now on, PREFIX/{lib,share,share/doc}/cabal/ghc-GHC_VERSION are used for
  hs- ports (Cabal packages) as prefixes to avoid problems when upgrading with
  portmaster(8) [2]
- Experimental support for LLVM-based code generation (disabled by default)
- Many simplifications, refactoring in bsd.cabal.mk
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_3
05 Feb 2013 22:26:32
Revision:311736Original commit files touched by this commit
pgj search for other commits by this committer
- Fix breakage in the DYNAMIC-enabled ports triggered by the recent
  devel/libffi update
- Enable multithreaded build for lang/ghc (i.e. mark MAKE_JOBS_SAFE)

Please note that port revision for all the Haskell ports without version
changes are bumped.

New ports (20):

devel/hs-MonadRandom                     0.1.8
devel/hs-base64-conduit                  0.5.1
devel/hs-bifunctors                      3.2
devel/hs-either                          3.1
devel/hs-errors                          1.3.1
devel/hs-generic-deriving                1.4.0
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_2
20 Dec 2012 02:23:06
Revision:309275Original commit files touched by this commit
pgj search for other commits by this committer
- Update The Glorious Glasgow Haskell Compiler to version 7.4.2
- Update Haskell Platform to version 2012.4.0.0
- Update Gtk2Hs to 0.12.4
- Transfer maintainership of math/hs-math-functions to haskell@ [1]

Please note that port revisions for all the Haskell ports without version
changes are bumped.

Some further highlights of the update:
- Trim Makefile headers
- Enable dynamic libraries and dynamic linking by default
- Enable bootstrapping by versions of GHC and HsColour already installed
- Use GCC and binutils from ports

New ports (32):
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.5.2_1
03 Aug 2012 02:30:11
Original commit files touched by this commit
pgj search for other commits by this committer
- Teach the Haskell Cabal ports to use the new options framework
- Remove some cruft

Obtained from:	FreeBSD Haskell
0.5.2
03 Jun 2012 22:21:27
Original commit files touched by this commit
pgj search for other commits by this committer
- Update to 0.5.2

Obtained from:  FreeBSD Haskell
0.5.1
13 Feb 2012 05:20:41
Original commit files touched by this commit
pgj search for other commits by this committer
- Update to 0.5.1

Obtained from:  FreeBSD Haskell
0.5.0.1
10 Jul 2011 01:03:33
Original commit files touched by this commit
ashish search for other commits by this committer
- Update to 0.5.0.1

Obtained from:  FreeBSD Haskell
0.5_2
03 Jul 2011 22:30:23
Original commit files touched by this commit
ashish search for other commits by this committer
- Update textproc/hs-tagsoup to 0.12.2.
- Bump PORTREVISION of dependent ports on textproc/hs-tagsoup, i.e.
  devel/h-hoogle, science/hs-bio, and textproc/pandoc.

PR:             ports/157826
Submitted by:   Jin-Sih Lin <linpct@gmail.com>
0.5_1
26 May 2011 00:51:15
Original commit files touched by this commit
ashish search for other commits by this committer
Bump PORTREVISION of all ports dependent on lang/ghc as during
upgrade, lang/ghc cabal package cache gets invalidated causing all
dependent ports to be reinstalled.

Obtained from:  FreeBSD Haskell
0.5
09 May 2011 05:28:57
Original commit files touched by this commit
ashish search for other commits by this committer
- Please welcome GHC 7.0.3

GHC in the ports tree has been updated to 7.0.3 and all other Haskell ports
are also updated to their corresponding Haskell Platform versions, or latest
versions.

We would like to acknowledge the support of the FreeBSD Donations Team and
Eotvos Lorand University, Faculty of Informatics who contributed to the server
that we used for testing.

We would also like to thank all the testers who tested FreeBSD Haskell ports
and provided their feedback.

PR:             ports/156642
Approved by:    tabthorpe (mentor)
Obtained from:  FreeBSD Haskell
0.4.6
08 Aug 2010 08:49:38
Original commit files touched by this commit
pgj search for other commits by this committer
- Add DIST_SUBDIR for Haskell Cabal ports (with default of "cabal")

Suggested by:   admi3
0.4.6
30 Jul 2010 09:14:14
Original commit files touched by this commit
pgj search for other commits by this committer
- Update to 0.4.6
0.4_1
26 May 2010 11:18:46
Original commit files touched by this commit
jacula search for other commits by this committer
- Pass maintainership to haskell@FreeBSD.org:

    audio/hs-ALUT, audio/hs-OpenAL, benchmarks/hs-criterion
    converters/hs-json, devel/hs-DeepArrow, devel/hs-FileManip
    devel/hs-MemoTrie, devel/hs-MissingH, devel/hs-MonadCatchIO-mtl
    devel/hs-ObjectName, devel/hs-QuickCheck, devel/hs-StateVar
    devel/hs-Tensor, devel/hs-TypeCompose, devel/hs-arrows
    devel/hs-checkers, devel/hs-convertible, devel/hs-datetime
    devel/hs-deepseq, devel/hs-fgl, devel/hs-ghc-mtl, devel/hs-ghc-paths
    devel/hs-ghc-paths-docs, devel/hs-haskeline
    devel/hs-haskell-src-exts, devel/hs-hint, devel/hs-hoogle
    devel/hs-hslogger, devel/hs-mmap, devel/hs-mueval, devel/hs-reactive
    devel/hs-readline, devel/hs-safe, devel/hs-show, devel/hs-smallcheck
    devel/hs-split, devel/hs-testpack, devel/hs-transformers
    devel/hs-unamb, devel/hs-uniplate, devel/hs-unix-compat
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.4_1
20 May 2010 10:39:45
Original commit files touched by this commit
pgj search for other commits by this committer
- Fix build problem caused by the recent textproc/hs-tagsoup update
- Port PORTREVISION
- Tidy up pkg-descr

Reported by:    LambdaBSD-exp
Approved by:    jacula (maintainer)
0.4
12 May 2010 16:33:59
Original commit files touched by this commit
pgj search for other commits by this committer
Introduce a new (and hopefully better) ports infrastructure for Haskell Cabal
ports which makes possible the direct translation of Cabal package
descriptions to FreeBSD ports.  It promises both easier addition and
maintenance for Cabal-based ports.
0.4
03 Jan 2010 05:02:13
Original commit files touched by this commit
pgj search for other commits by this committer
This is a collection of Haskell data structures and algorithms useful for
building bioinformatics-related tools and utilities.
Current list of features includes: a Sequence data type supporting
protein and nucleotide sequences and conversion between them.

WWW: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/

PR:             ports/142187
Submitted by:   Jacula Modyun <jacula(at)gmail.com>

Number of commits found: 28