aboutsummaryrefslogtreecommitdiff
path: root/biology/snpeff
Commit message (Collapse)AuthorAgeFilesLines
* */*: Update WWW to use HTTPS for sourceforge.net projectsRodrigo Osorio2023-11-061-1/+1
| | | | | | | | 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
* all: remove explicit versions in USES=python for "3.x+"Rene Ladan2023-06-271-1/+1
| | | | | | | | | | | | | | | | | | | 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>
* biology/snpeff: Update to 5.1Jason W. Bacon2022-12-192-4/+4
| | | | | Unbreak fetch, which depends on an unversioned distfile Requested version tags upstream and looking at other build options
* Remove WWW entries moved into port MakefilesStefan Eßer2022-09-071-2/+0
| | | | | | | | | | Commit b7f05445c00f has added WWW entries to port Makefiles based on WWW: lines in pkg-descr files. This commit removes the WWW: lines of moved-over URLs from these pkg-descr files. Approved by: portmgr (tcberner)
* Add WWW entries to port MakefilesStefan Eßer2022-09-071-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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)
* cleanup: remove expired versions of OpenJDK (12 through 16)Rene Ladan2022-05-241-1/+1
| | | | | | | | | | | | | | | | | | 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
* biology/snpeff: Improvements to Makefile and patchesJason W. Bacon2021-04-194-12/+13
| | | | Reported by: Omp
* biology/snpeff: Genetic variant annotation and effect prediction toolboxJason W. Bacon2021-04-186-0/+179
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).