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non port: biology/canu/Makefile

Number of commits found: 32

Thursday, 20 Jul 2023
17:42 Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/canu: Fix build with llvm16

- Pet portclippy

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
commit hash: d92c0802eadd8d10118f3237e96de9580a6770bb commit hash: d92c0802eadd8d10118f3237e96de9580a6770bb commit hash: d92c0802eadd8d10118f3237e96de9580a6770bb commit hash: d92c0802eadd8d10118f3237e96de9580a6770bb d92c080
11:20 Jason W. Bacon (jwb) search for other commits by this committer
biology/canu: Fix build under clang 16

Also add cpu_any.c to theoretically support any 64-bit CPU
Drop unused simde patches

Reported by:    pkg-fallout
commit hash: 290833541264e265124451053d402f61e2313504 commit hash: 290833541264e265124451053d402f61e2313504 commit hash: 290833541264e265124451053d402f61e2313504 commit hash: 290833541264e265124451053d402f61e2313504 2908335
Tuesday, 4 Apr 2023
18:10 Muhammad Moinur Rahman (bofh) search for other commits by this committer
*/*: Refactor java/openjdk7 removal

- java/openjdk7* has been removed from the tree since 2022-09-03 however
  the relevant codebases in bsd.java.mk has not been removed and the
  consumers has also not been updated to use the next jdk version. This
  commit updates all relevant consumers to use JAVA_VERSION=8 instead of
  JAVA_VERSION=1.7
- Since the introduction of jdk version 18 it looks like similar with
  jdk version 8(java version string 1.8). This is prone to error as it
  looks similar and is only seperated by a '.'. Remove using
  JAVA_VERSION with dotted fomat of java version string and update all
  consumers to utilize version 8 instead of 1.8.

Approved by:	portmgr (blanket)
commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3 commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3 commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3 commit hash: 4cda17ab14588e6e4fdac7f697e246554ce82af3 4cda17a
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Friday, 12 Aug 2022
14:46 Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed 4cf39de
Sunday, 22 May 2022
20:17 Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd b082b3d
Monday, 20 Dec 2021
12:59 Antoine Brodin (antoine) search for other commits by this committer
biology/canu: fix CATEGORIES
commit hash: b2dab386316742576c3fc3fd7a3ed0284c919683 commit hash: b2dab386316742576c3fc3fd7a3ed0284c919683 commit hash: b2dab386316742576c3fc3fd7a3ed0284c919683 commit hash: b2dab386316742576c3fc3fd7a3ed0284c919683 b2dab38
Sunday, 19 Dec 2021
21:06 Jason W. Bacon (jwb) search for other commits by this committer
biology/canu: Update to 2.2

FreeBSD port: Add support for aarch64 and powerpc64 using simde
Not yet supported upstream

Several upstream bug fixes and minor enhancements since 2.1

Changes: https://github.com/marbl/canu/tags
commit hash: b9105b7ef1e91bce177273f3031a98781ca6faf7 commit hash: b9105b7ef1e91bce177273f3031a98781ca6faf7 commit hash: b9105b7ef1e91bce177273f3031a98781ca6faf7 commit hash: b9105b7ef1e91bce177273f3031a98781ca6faf7 b9105b7
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Monday, 11 Jan 2021
16:51 jwb search for other commits by this committer
biology/canu: Drop dependency on gcc

Replace compiler:openmp with compiler:c++11-lang and localbase

PR:             port/247753, ports/252379
Original commitRevision:561227 
Monday, 14 Sep 2020
22:27 jwb search for other commits by this committer
biology/canu: Upgrade to 2.1

Numerous functional improvements for ease of use and output quality
A few bug fixes

Reported by:    portscout
Original commitRevision:548685 
Sunday, 17 May 2020
02:25 linimon search for other commits by this committer
Mark as BROKEN on powerpc64:

  utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error:
'get_deleter' declared as a 'virtual' field

This may have something to do with compiler:openmp in USES.  However,
it has broken for more than 6 months at this point.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:535507 
Friday, 20 Mar 2020
18:14 jwb search for other commits by this committer
biology/canu: Upgrade to 2.0

Several routine enhancements and bug fixes

Reported by:    portscout
Original commitRevision:528792 
Wednesday, 11 Dec 2019
17:53 jbeich search for other commits by this committer
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
Original commitRevision:519824 
Friday, 8 Nov 2019
14:03 jwb search for other commits by this committer
biology/canu: Upgrade to 1.9

Numerous bug fixes and enhancements

Reported by:    portscout
Original commitRevision:517066 
Monday, 19 Aug 2019
15:35 jbeich search for other commits by this committer
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
Original commitRevision:509290 
Friday, 26 Jul 2019
20:46 gerald search for other commits by this committer
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
Original commitRevision:507372 
Thursday, 18 Apr 2019
12:15 jwb search for other commits by this committer
biology/canu: Fix build on powerpc64 and aarch64

Should also work on powerpc and arm*, but unable to test

PR:             237105
Reported by:    pkubaj
Original commitRevision:499251 
Friday, 12 Apr 2019
06:36 jbeich search for other commits by this committer
devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303
Original commitRevision:498698 
Wednesday, 12 Dec 2018
01:35 gerald search for other commits by this committer
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
Original commitRevision:487272 
00:15 jbeich search for other commits by this committer
devel/boost-*: update to 1.69.0

Changes:	http://www.boost.org/users/history/version_1_69_0.html
PR:		232525
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D17645
Original commitRevision:487266 
Sunday, 4 Nov 2018
14:29 jwb search for other commits by this committer
biology/canu: Upgrade to 1.8, add experimental SLURM integration

Solves build issue with gcc8.

PR:             232930
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
Original commitRevision:484077 
Thursday, 9 Aug 2018
06:58 jbeich search for other commits by this committer
devel/boost-*: update to 1.68.0

- Switch to C++14 for libboost_system to support C++14 consumers

Changes:	http://www.boost.org/users/history/version_1_68_0.html
PR:		229569
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D16165
Original commitRevision:476723 
Sunday, 29 Jul 2018
22:18 gerald search for other commits by this committer
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
Original commitRevision:475857 
Thursday, 21 Jun 2018
23:52 linimon search for other commits by this committer
Mark as broken on aarch64, and, where appropriate, armvX.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:473009 
Thursday, 26 Apr 2018
04:16 jwb search for other commits by this committer
biology/canu: Upgrade to 1.7 release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15201
Original commitRevision:468321 
Wednesday, 18 Apr 2018
13:57 jbeich search for other commits by this committer
devel/boost-*: update to 1.67.0

Changes:	http://www.boost.org/users/history/version_1_67_0.html
PR:		227427
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D15030
Original commitRevision:467711 
Saturday, 10 Mar 2018
17:46 gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
Original commitRevision:464084 
Thursday, 18 Jan 2018
04:11 jbeich search for other commits by this committer
devel/boost-*: update to 1.66.0

Changes:	http://www.boost.org/users/history/version_1_66_0.html
PR:		223922
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D13279
Original commitRevision:459315 
Friday, 22 Dec 2017
14:14 jwb search for other commits by this committer
biology/canu: Replace += with = for depends

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D13574
Original commitRevision:456982 
01:30 jwb search for other commits by this committer
[new port] biology/canu: Single molecule sequence assembler

Approved by: jrm (mentor) or wen (mentor)
Differential Revision:  https://reviews.freebsd.org/D13574
Original commitRevision:456950 

Number of commits found: 32