10:03 Rodrigo Osorio (rodrigo) 

*/*: Update WWW to use HTTPS for sourceforge.net projects

Homepage link is permanent redirected to its HTTPS counterpart
Issue reported by repology : https://repology.org/repository/freebsd/problems

Approved by:	portmgr (blanket)
PR:		274888

    06df180

19:34 Rene Ladan (rene) 

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>

    3d9a815

18:50 Jason W. Bacon (jwb) 

biology/snpeff: Update to 5.1

Unbreak fetch, which depends on an unversioned distfile
Requested version tags upstream and looking at other build options

    c583575

21:10 Stefan Eßer (se) 

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)

    b7f0544

20:09 Rene Ladan (rene) 

cleanup: remove expired versions of OpenJDK (12 through 16)

Adjust ports depending on expired versions of OpenJDK:
- biology/snpeff: 12+ -> 17+
- devel/RStudio: 12 -> 11
- www/closure-compiler: 13 -> 11+

Allow java/openjdk17 to use java/openjdk17-bootstrap on i386
too, this builds just fine on 13.1-i386

Remove jdk12-doc as it is no longer relevant.

Clean up Java version calculations in bsd.java.mk

Reviewed by: jwb, java (glewis)

Differential Revision: https://reviews.freebsd.org/D35280

    c7d1c24

16:41 Jason W. Bacon (jwb) 

biology/snpeff: Improvements to Makefile and patches

Reported by:    Omp

    3bc87a0

18:46 Jason W. Bacon (jwb) 

biology/snpeff: Genetic variant annotation and effect prediction toolbox

Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).

    5164d38