EXPIRATION_DATE at the end of April 2017.
In the past six months, about a third of the ports marked BROKEN because
they were hosted on Google Code have been fixed. The remaining must not
be of use to anyone.
With hat: portmgr
Sponsored by: Absolight
Upstream changelog:
- Added compositional score adjustments (option --comp-based-stats
(0,1)). This is a useful feature for filtering false positive hits and
is enabled by default.
- Removed --single-domain option and replaced by --max-hsps, to set the
maximum number of Hsps per query/subject pair, to be consistent with
BLAST. This option is set to 1 by default as getting more than 1 Hsp
per subject seems to be confusing users.
- Added option --no-self-hits to filter identical self-hits.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D9134
If you want to set WRKSRC, set GH_PROJECT instead.
- The GitHub URLs are case insensitive, but the distribution files you
get out of them are not.
- If the repository was renamed, the old URL will still work, but the
distribution name will be ith the new name.
Sponsored by: Absolight
Many ports passed ZLIB_CFLAGS="-I/usr/include" ZLIB_LIBS="-L/usr/lib -lz"
which is unsafe at least with lang/gcc* that override some system headers
and have newer libgcc_s.so that our old version in base may not be
forward-compatible with.
Upstream changes:
- slightly improved sensitivity
- added option to report unaligned queries: --unal (0=no, 1=yes)
- pairwise, XML and SAM format will report unaligned queries by default
- added option to filter alignments by subject cover (--subject-cover)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9000
Changes in version 4.6.6:
Bug fix for cd-hit-dup in variable length input when write out R1 reads
Changes in version 4.6.5:
Add filter for -aL option so that short sequences will be skipped if not
satisfy representative sequences' -aL requirement. This will make compute
faster in clustering settings where sequences in the same cluster are
required to have similar length using -aL -AL option (e.g. -aL 0.9).
Approved by: AMDmi3 (mentor) swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8186
Upstream changes since version 2.2.4:
- Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1).
- Fix bug in parsing function that made it stop on sequences that consist
of only empty lines.
- New methods in bindings to enumerate the mers of a string.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8204
Bio::Coordinate classes are used for working with various biological coordinate
systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
WWW: http://search.cpan.org/dist/Bio-Coordinate/
- Change MASTER_SITES back to CPAN
- Update LICENSE
- Add LICENSE_FILE
- Use PORTDOCS
- Convert to options target helper
- Use INSTALL_SCRIPT
- Pet portlint: fix diff header of patch file
Changes: http://search.cpan.org/dist/BioPerl-Run/Changes
- Update *_DEPENDS
- Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies
- Use PORTDATA, PORTDOCS and PORTEXAMPLES
Changes: http://search.cpan.org/dist/BioPerl/Changes
Upstream change: fixed an issue that could cause a crash when using view on
incomplete DAA files
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8832
