ABySS is a de novo, parallel, paired-end sequence assembler that is designed for
short reads. The single-processor version is useful for assembling genomes up to
100 Mbases in size. The parallel version is implemented using MPI and is capable
of assembling larger genomes.
===> The following configuration options are available for abyss-2.3.10_1:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
Mk/bsd.commands.mk: Use absolute path to define GMAKE
Same as BSDMAKE variable. It is needed by some ports.
Some ports needed fixes:
- devel/rcs57: Regenerate configure with newer autoconf so it can deal
with MAKE set to an absolute path. While here fix issues with
(un)escaping double quotes. The warnings about this were in
WRKSRC/src/conf.err.
- lang/gnu-cobol: Patch configure.ac so the MAKE environment variable
can contain an absolute path, and define MAKE before it is used in
AM_INIT_AUTOMAKE. Remove post-patch patching of configure. It appears
to have been fixed upstream.
- math/unuran: Remove post-patch, fixed upstream.
- net-mgmt/kismet: Fix post-patch.
PR: 283534
Exp-run by: antoine
all: drop support for expired FreeBSD 14.0
Simplify expressions for FreeBSD 13.X
Reviewed by: many
Differential Revision: https://reviews.freebsd.org/D46601
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner)
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
Chanse update of devel/libffi
Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.
PR: 247028 (for tracking)
Drop dependency on devel/openmp
- Drop if devel/llvm* was used as a substitute
Approved by: yuri, rene (earlier version)
Differential Revision: https://reviews.freebsd.org/D23020
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
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, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
biology/abyss: fix build on big-endian architectures
Use new GCC from ports on GCC architectures.
Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC
architectures.
Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at
https://github.com/bcgsc/abyss/pull/287 ).
PR: 238737
Approved by: yuri (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D20717
devel/openmp: phase out
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)
PR: 236907
Approved by: bapt (maintainer)
Differential Revision: https://reviews.freebsd.org/D19767
