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non port: biology/snpeff/Makefile

Number of commits found: 7

Monday, 6 Nov 2023
10:03 Rodrigo Osorio (rodrigo) search for other commits by this committer
*/*: 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
commit hash: 06df180a9e39055026499a326ef67812801a8919 commit hash: 06df180a9e39055026499a326ef67812801a8919 commit hash: 06df180a9e39055026499a326ef67812801a8919 commit hash: 06df180a9e39055026499a326ef67812801a8919 06df180
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
Monday, 19 Dec 2022
18:50 Jason W. Bacon (jwb) search for other commits by this committer
biology/snpeff: Update to 5.1

Unbreak fetch, which depends on an unversioned distfile
Requested version tags upstream and looking at other build options
commit hash: c5835753ea70c074f8796aa1df459838ef61c6f7 commit hash: c5835753ea70c074f8796aa1df459838ef61c6f7 commit hash: c5835753ea70c074f8796aa1df459838ef61c6f7 commit hash: c5835753ea70c074f8796aa1df459838ef61c6f7 c583575
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
Tuesday, 24 May 2022
20:09 Rene Ladan (rene) search for other commits by this committer
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
commit hash: c7d1c247d8ea8f87edd6a5012702a3cd10d99d49 commit hash: c7d1c247d8ea8f87edd6a5012702a3cd10d99d49 commit hash: c7d1c247d8ea8f87edd6a5012702a3cd10d99d49 commit hash: c7d1c247d8ea8f87edd6a5012702a3cd10d99d49 c7d1c24
Monday, 19 Apr 2021
16:41 Jason W. Bacon (jwb) search for other commits by this committer
biology/snpeff: Improvements to Makefile and patches

Reported by:    Omp
commit hash: 3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe commit hash: 3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe commit hash: 3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe commit hash: 3bc87a0f1a1b36d958c9478a0d2feaeebf283dbe 3bc87a0
Sunday, 18 Apr 2021
18:46 Jason W. Bacon (jwb) search for other commits by this committer
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).
commit hash: 5164d38ee538f6791a25b81f28a27126b90444f7 commit hash: 5164d38ee538f6791a25b81f28a27126b90444f7 commit hash: 5164d38ee538f6791a25b81f28a27126b90444f7 commit hash: 5164d38ee538f6791a25b81f28a27126b90444f7 5164d38

Number of commits found: 7