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non port: biology/haplohseq/Makefile

Number of commits found: 19

Tuesday, 13 Feb 2024
14:44 Dima Panov (fluffy) search for other commits by this committer
devel/boost: bump consumers after library update
commit hash: db616534ff99d6268997e2f30858891e20641a1e commit hash: db616534ff99d6268997e2f30858891e20641a1e commit hash: db616534ff99d6268997e2f30858891e20641a1e commit hash: db616534ff99d6268997e2f30858891e20641a1e db61653
Wednesday, 27 Sep 2023
14:36 Dima Panov (fluffy) search for other commits by this committer
devel/boost*: bump all consumers after 1.83.0
commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 21d8008
Sunday, 9 Jul 2023
16:37 Jason W. Bacon (jwb) search for other commits by this committer
biology/haplohseq: Fix build on FreeBSD 14

Add -std=c++14 to override clang 16 default

Reported by:    pkg-fallout
commit hash: 3df899be41477eac63133c5a618947719ae04f9e commit hash: 3df899be41477eac63133c5a618947719ae04f9e commit hash: 3df899be41477eac63133c5a618947719ae04f9e commit hash: 3df899be41477eac63133c5a618947719ae04f9e 3df899b
Tuesday, 27 Jun 2023
19:34 Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb 3d9a815
Thursday, 27 Apr 2023
18:25 Dima Panov (fluffy) search for other commits by this committer
*/*: bump all direct Boost cunsumers
commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 3e45e8e
Sunday, 23 Apr 2023
09:09 Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b 8d3e020
Monday, 16 Jan 2023
19:32 Dima Panov (fluffy) search for other commits by this committer
*/*:	bump libboost*.so libraries consumert after Boost upgrade
commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b e1287d0
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
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
Saturday, 23 Jan 2021
19:31 jwb search for other commits by this committer
biology/haplohseq: Fix example scripts for python 3

Also clean up plist
Original commitRevision:562414 
Friday, 15 Jan 2021
00:08 jwb search for other commits by this committer
biology/haplohseq: Restrict to python3

Also remove extraneous @dir from plist

Reported by:    rene
Original commitRevision:561615 
Thursday, 14 Jan 2021
15:51 jwb search for other commits by this committer
biology/haplohseq: Resurrect and fix python2 dependency

Move upstream to Github fork
Original commitRevision:561567 
Sunday, 8 Mar 2020
17:01 antoine search for other commits by this committer
Deprecate some ports using deprecated version of python

With hat:	portmgr
Original commitRevision:528058 
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 
Sunday, 17 Nov 2019
15:00 jwb search for other commits by this committer
biology/haplohseq: Switch to distfile with example data

Add script to run on example input
Minor fix to report inadequate VCF input
Original commitRevision:517828 
Monday, 16 Sep 2019
01:07 jwb search for other commits by this committer
biology/haplohseq: Identify regions of allelic imbalance

Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample.  Input to the software includes a VCF file
of genotypes and estimated phased genotypes.
Original commitRevision:512137 

Number of commits found: 19