/commits.php is going away

biology/ncbi-blast+: Update to 2.12.0

Changes:        https://www.ncbi.nlm.nih.gov/books/NBK131777/
Reported by:    portscout

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/ncbi-blast+: Drop dependency on gcc

Replace compiler:openmp with compiler:c++14-lang
Clang build also requires localbase:ldflags and a source patch to explicitly
set variables to shared
GCC-based platforms still require -latomic

PR:             port/247753, ports/252379

biology/ncbi-blast+: Upgrade to 2.11.0

A few bug fixes and performance improvements since 2.10.0
Also overcomes GCC 10 build issues

PR:             ports/246700
Reported by:    linimon

Chase security/p11-kit update

After switch to meson libp11-kit.so no longer has symbols
in the LIBP11_KIT_1.0 namespace. As a workaround, bump
PORTREVISION of consumers to get those rebuilt.

See more details in the comments of the linked PR.

PR:		248819
Reported by:	John Hein

Bump PORTREVISION for security/nettle shlib change

biology/ncbi-blast+: Upgrade to 2.10.0

Numerous minor bug fixes, enhancements and dependency upgrades
Minor port clean-up
1 patch from previous version upstreamed

Reported by:    portscout

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

ncbi-blast+: Unbreak build with gcc8 following gcc9 patch

GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none).  All const variables default to shared even with default(none)
present.  8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.

Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.

Reported by:    jrm

ncbi-blast+: Fix build with gcc9

GCC 9 requires OpenMP variables to be explicitly defined as shared or private
where earlier versions fell back on default.  New patch sent upstream.

PR:             238471
Reported by:    gerald

Update security/nettle to 3.5.1

- Bump PORTREVISION of dependent ports for shlib change
- Fix build of devel/pijul [1]

Changes:	https://git.lysator.liu.se/nettle/nettle/blob/master/NEWS
PR:		238991
Exp-run by:	antoine
Thanks to:	tobik [1]

biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl

biology/ncbi-blast+: Upgrade to 2.9.0

Fixes build issue with gcc9

PR:             238471
Reported by:    gerald

Update dns/libidn2 to 2.1.1

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://gitlab.com/libidn/libidn2/blob/master/NEWS

Update dns/libidn2 to 2.1.0

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://gitlab.com/libidn/libidn2/blob/master/NEWS

biology/ncbi-blast+: Upgrade to 2.8.1

Remove hacks that are no longer needed
New patch for endian.h location

Approved by:    jrm (mentor, implicit)

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 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, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542

Mark as broken on powerpc64.  The entire, unhelpful, error message is:

# gmake[2]: Leaving directory
'/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.5.0+-src/c++/ReleaseMT/build'
# gmake[1]: *** [Makefile:24: all] Error 2

Approved by:	portmgr (tier-2 blanket)

biology/ncbi-blast+: Upgrade to 2.7.1

Patch Makefile.in.top to cleanly support DESTDIR

Also resolves 225002, conflict with libproj

PR:             226037
Reported by:    wen
Reviewed by:    mat rene
Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14854

Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).

Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128

Bump PORTREVISION for ports depending on the canonical version of GCC
(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

Bump PORTREVISIONs for ports depending on the canonical version of GCC and
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

biology/ncbi-blast+: Add MAKE_JOBS_UNSAFE

PR:		214997
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8882

- Update to 2.5.0

PR:		214997
Submitted by:	mzaki@e-mail.ne.jp
Approved by:	maintainer(timeout, > 14 days)

Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.

biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)

All support platforms have libbz2.so in base, so this port will never
pull in archivers/bzip2.

Approved by:	just-fix-it

Most commonly used build systems support silent builds, when they
hide actual commands executed and only show short summary line (like
"CC foo.c"). CMake and ninja enable this by default, some autotools
using ports do as well. This is unacceptable because we need complete
build logs at any time, so we now switch to verbose build logs
unconditionally. Note that this change deliberately affects ALL
builds and not only package builds on cluster, because we need to
be sure that user experiencing failure can always provide informative
build log regardless of settings and without rerunning the build.

Change summary:

- Always do verbose builds for cmake, ninja and GNU configure (the
  latter includes check if --disable-silent-rules is actually supported
  by the configure script; there are isolated cases when it's not true)

- Make configure script handle --disable-silent-rules gracefully

PR:		212075
Approved by:	portmgr blanket

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

Add Public Domain support to ports license framework. You can now use

    LICENSE=  PD

Note that although Public Domain is not technically a license, it's
handled in the same way as licenses here, which is a common practice
(Arch, Gentoo, Fedora, Debian, even FOSSology do the same).

Convert all ports which redefine Public Domain LICENSE to LICENSE=PD.

Approved by:	portmgr (bapt)
Differential Revision:	D4149

- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

- Unbreak

PR:		199734
Submitted by:	jwbacon@tds.net(maintainer)

Mark BROKEN: fails to configure

===>  Configuring for ncbi-blast+-2.2.30_2
configure: error: --localstatedir=/var:  unknown option;  use --help to show
usage

Reported by:	pkg-fallout

biology/ncbi-blast+: Add additionl MASTER_SITE to unbreak fetch

The distfile was rerolled but nobody knows why (not a good sign).  The
maintainer has added a new MASTER_SITE with the original distfile in
order to unbreak fetch.

PR:		199474
Submitted by:	maintainer (Jason Bacon)

Mark as broken unfetchable ports

Add a run dependency used by update_blastdb.pl

PR:		198331
Submitted by:	maintainer

Fix PKGNAMEPREFIX of biology/ncbi-blast+, so that the resulting package is
named like the port.

Approved by:	mentors (implicit)

Rename biology/ncbi-blast to biology/ncbi-blast+

Approved by:	mentors (implicit)