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* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withtijl2016-09-061-3/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mk/Uses/linux.mk. - Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with USES+=linux:\1 in all ports. - Replace USE_LINUX_APPS with USE_LINUX in all ports. - Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some ports. - When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY are defined. - Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases that it is still necessary ports can run ${BRANDELF} from post-patch. - Remove AUTOMATIC_PLIST handling. Only one port used it. - Fix Linux MASTER_SITES. - Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with default versions framework. - bsd.port.mk: - Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX. - Put USE_LINUX_PREFIX handling after USES processing. - Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can give these variables a different default value. - When a package needs to run Linux ldconfig check before installation if Linux support is enabled. - emulators/linux_base-*: - Use USES=linux and remove duplication. - Remove files/lp. FreeBSD or CUPS lp(1) should work. - Remove files/yp.conf. No longer seems to be used. - Remove pkg-deinstall and move pkg-install into pkg-plist. - Update pkg-descr and pkg-message. - Fix handling of ldconfig cache in pkg-plist. - devel/fb-adb: Use a Linux shell to run a Linux script but patch the script to use FreeBSD mkdir so mkdir -p $path creates $path and not /compat/linux/$path. PR: 211645 Exp-run by: antoine Approved by: portmgr (antoine)
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.mat2016-04-011-2/+2
| | | | | With hat: portmgr Sponsored by: Absolight
* biology/consed: undeprecate, it presumably builds fine but it is restricted.rene2015-12-261-5/+1
| | | | Add a note to ports/LEGAL
* Deprecate ports broken for more than 6 monthsantoine2015-10-261-0/+2
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* ${ENV} does not exist, it is called ${SETENV}.mat2015-04-131-1/+1
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* Mark as broken unfetchable portsbapt2015-04-061-0/+2
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* update ports:pi2014-08-248-1126/+133
| | | | | | | | | | | | biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer)
* Convert a bunch of EXTRACT_SUFX=... into USES=tar:...adamw2014-07-301-2/+1
| | | | Approved by: portmgr (not really, but touches unstaged ports)
* Remove indefinite articles and trailing periods from COMMENT, plusolgeni2014-06-091-1/+1
| | | | | | | minor COMMENT typos and surrounding whitespace fixes. Categories A-C. CR: D196 Approved by: portmgr (bapt)
* Replace maintainer's email address with one that seems to workantoine2014-05-111-1/+1
| | | | With hat: portmgr
* Remove trailing whitespaces from category biologyehaupt2014-02-211-1/+1
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* According to the Porter's Handbook (5.12.2.3.) default options must be added toehaupt2014-02-101-0/+2
| | | | | | | | | | | OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt)
* Convert biology to MDOCS and MEXAMPLESadamw2014-01-031-5/+8
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* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵bapt2013-09-201-5/+2
| | | | biology)
* - convert to the new perl5 frameworkaz2013-09-071-1/+1
| | | | Approved by: portmgr (bapt@, blanket)
* - Get Rid MD5 supportmiwi2011-03-191-1/+0
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* Welcome to the new linux ports infrastructure which allows usingbsam2009-03-201-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | both current (fc4) and future linux (f8) distributions at one ports tree. The patch contains full changes to ports/Mk files and all ports involved. But only infrastructure is changed. The resulting packages are the same as before. Hence no need to bump PORTREVISIONs. The idea was taken from bsd.gnome.mk and others. More than 130 ports are switched to follow a new linux infrastructure introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new bsd.linux-apps.mk. Thanks for all who was involved and helped me with this work. And help from Alexander Leidinger was incredible. Other changes are coming. Stay tuned! PR: ports/132510 Submitted by: bsam (me) Exp-run by: portmgr (pav)
* Teach the building cluster that these ports are not to be buildedwin2008-05-261-0/+3
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* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-248-0/+1173
assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
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