Bio::FeatureIO is an iterator subsystem for genomic sequence features.
Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
format objects, which most people should use.
The Bio::FeatureIO system can be thought of like biological file handles. They
are attached to filehandles with smart formatting rules (eg, GFF format, or BED
format) and can either read or write feature objects (Bio::SeqFeature objects,
or more correctly, Bio::FeatureHolderI implementing objects, of which
Bio::SeqFeature is one such object). If you want to know what to do with a
Bio::SeqFeatureI object, read Bio::SeqFeatureI.
The idea is that you request a stream object for a particular format. All the
stream objects have a notion of an internal file that is read from or written
to. A particular FeatureIO object instance is configured for either input or
output. A specific example of a stream object is the Bio::FeatureIO::gff object.
WWW: http://search.cpan.org/dist/Bio-FeatureIO/
(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
2017-08-23 games/plee-the-bear: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-umicons: Broken for more than 6 months
2017-08-23 lang/bigloo: Broken for more than 6 months
2017-08-23 audio/linux-neroaaccodec: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-dark-glass: Broken for more than 6 months
2017-08-23 misc/fortune-mod-ferengi_rules_of_acquisition: Broken for more than 6 months
2017-08-23 misc/fortune-mod-culmea-culmilor: Broken for more than 6 months
2017-08-23 misc/xyzcmd: Broken for more than 6 months
2017-08-23 russian/fortuneru: Broken for more than 6 months
2017-08-23 security/bdc: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-icosx: Broken for more than 6 months
2017-08-23 devel/insight: Broken for more than 6 months
2017-08-23 devel/gdb66: Broken for more than 6 months
2017-08-23 biology/biojava: Broken for more than 6 months
2017-08-23 games/xroach: Broken for more than 6 months
Update the default Objective-C compiler.
Fix various build failures in GNUstep ports from newer versions of the GNUstep
core libraries and from changes to GNUstep Make.
Update various ports that use GNUstep and bump the portrevision of the ones
that haven't had a new release.
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:
Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
* "Binned bitsets" which act just like chromosome sized bit arrays,
but lazily allocate regions and allow large blocks of all set or
all unset bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve
both query and target intervals and associated annotation
WWW: https://github.com/bxlab/bx-python
PR: 218757
Submitted by: Yuri Victorovich <yuri@rawbw.com>
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
to the command line functionality of the samtools and bcftools packages. The
module supports compression and random access through indexing.
This module provides a low-level wrapper around the htslib C-API as using
cython and a high-level API for convenient access to the data within standard
genomic file formats.
WWW: https://pypi.python.org/pypi/pysam
PR: 218745
Submitted by: Yuri Victorovich <yuri@rawbw.com>
This release introduces some new features and fixes several bugs:
http://savannah.gnu.org/forum/forum.php?forum_id=8751
* update to 2.3 and take maintainership
* update math/py-gsl to 2.2.0 for gsl2 support
* update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support
PR: 218952
Exp-run by: antoine
Reviewed by: mat, rakuco
Approved by: rakuco (mentor)
Differential Revision: https://reviews.freebsd.org/D10522
2017-04-30 devel/py-coil: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/py-cmdln: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/privman: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/c-unit: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/py-px: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/nglogc: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/bncsutil-ghost++: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/liblouisxml: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/nxt-python: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/spdict: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/guiloader-c++: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/streamhtmlparser: Unfetchable for more than six months (google code has gone away)
2017-04-30 devel/winpdb: Unfetchable for more than six months (google code has gone away)
2017-04-30 net/opendpi: Unfetchable for more than six months (google code has gone away)
2017-04-30 net/py-pybeanstalk: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/qwit: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/linux-instantbird: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/jabber-pyicq: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/qwit-devel: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/naim: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-im/pwytter: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/sievelog: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/ldapenter: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/py-danzfs: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/plasma-applet-apcups: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/scanmem: Unfetchable for more than six months (google code has gone away)
2017-04-30 sysutils/pdsh: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/superswitcher: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/plasma-applet-playwolf: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/nagaina: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/vboxgtk: Unfetchable for more than six months (google code has gone away)
2017-04-30 deskutils/libgcal: Unfetchable for more than six months (google code has gone away)
2017-04-30 math/carve: Unfetchable for more than six months (google code has gone away)
2017-04-30 math/foma: Unfetchable for more than six months (google code has gone away)
2017-04-30 math/libjbigi: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/gcap: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/freetuxtv: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/bangarang: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/opencinematools: Unfetchable for more than six months (google code has gone away)
2017-04-30 multimedia/vstream-client: Unfetchable for more than six months (google code has gone away)
2017-04-30 biology/treeviewx: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/pylot: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/xpi-pencil: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_myvhost: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/feedonfeeds: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_jail: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/jspacker: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/cocoon: Overly complex port with no maintainer since 2008, requires openjdk 1.6
2017-04-30 www/mod_authz_unixgroup24: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/trac-down: Upstream is gone
www/tengine
2017-04-30 www/arora: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/py-postmarkup: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/py-dotcloud.cli: deprecated in upstream
2017-04-30 www/closure-linter: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/httpsqs: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/sventon: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_authnz_external22: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_authn_otp: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/php-plurk-api: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/py-django-app-plugins: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_authz_unixgroup22: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/squidstats: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/mod_log_firstbyte: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/gaeo: Unfetchable for more than six months (google code has gone away)
2017-04-30 www/xpi-pentadactyl: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-mgmt/py-flowtools: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/ydict: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/py-cconv: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/fqterm: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/libgooglepinyin: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/p5-cconv: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/fcitx-googlepinyin: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/php-cconv: Unfetchable for more than six months (google code has gone away)
2017-04-30 chinese/ibus-table-chinese: Unfetchable for more than six months (google code has gone away)
2017-04-30 databases/jdbm2: Unfetchable for more than six months (google code has gone away)
2017-04-30 databases/akonadi-googledata: Unfetchable for more than six months (google code has gone away)
2017-04-30 lang/ofc: Unfetchable for more than six months (google code has gone away)
2017-04-30 comms/esmska: Unfetchable for more than six months (google code has gone away)
2017-04-30 x11/keynav: Unfetchable for more than six months (google code has gone away)
2017-04-30 x11/hotwire-shell: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/fuzzdb: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/truecrack: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/skipfish: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/py-yara-editor: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/nmapsi4: Unfetchable for more than six months (google code has gone away)
2017-04-30 security/cmd5checkpw: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-p2p/unworkable: Unfetchable for more than six months (google code has gone away)
2017-04-30 net-p2p/rtgui: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/xpi-musicpm: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/pidgin-musictracker: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/logitechmediaserver-superdatetime: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/last-cmus: Unfetchable for more than six months (google code has gone away)
2017-04-30 audio/mehdiaplayer: Unfetchable for more than six months (google code has gone away)
2017-04-30 japanese/nhocr: Unfetchable for more than six months (google code has gone away)
2017-04-30 misc/xsw: Unfetchable for more than six months (google code has gone away)
2017-04-30 dns/py-adns: Unfetchable for more than six months (google code has gone away)
2017-04-30 dns/py-bonjour: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/robocalypto: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/libfov: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/dcross: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/lostfeathers: Unfetchable for more than six months (google code has gone away)
2017-04-30 games/hexglass: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/ibus-table: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/chm2pdf: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/dtdinst: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/py-xmltv: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/ibus-m17n: Unfetchable for more than six months (google code has gone away)
2017-04-30 textproc/libroxml: Unfetchable for more than six months (google code has gone away)
2017-04-30 mail/gnome-gmail-notifier: Unfetchable for more than six months (google code has gone away)
2017-04-30 irc/py-gozerbot: Unfetchable for more than six months (google code has gone away)
2017-04-30 irc/tircd: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/qiviewer: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/py-gchartwrapper: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/svgfig: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/iulib: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/seam-carving-gui: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/py-pyggel: Unfetchable for more than six months (google code has gone away)
2017-04-30 graphics/rubygem-gemojione2: Use graphics/rubygem-gemojione instead
