Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine
Also:
- update license since upstream changed to GPLv3
- only build/package for amd64, since it is untested on other architectures
and currently does not build on i386
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.23
- The base compilers meet all of Diamond's requirements, so remove
compiler:c++11-lang from USES definition.
- Upstream release notes:
https://github.com/bbuchfink/diamond/releases/tag/v0.8.38
Approved by: swills (mentor, implicit)
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
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
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
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
Correct LICENSE and set LICENSE_FILE
Upstream changelog:
- support for gzip compressed files containing multiple gzip streams
- support for the BLAST pairwise format (option -f 0)
- slightly improved sensitivity
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8652
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.
WWW: http://ab.inf.uni-tuebingen.de/software/diamond/
PR: 208998
Submitted by: jrm@ftfl.ca
