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* Replace USES=libtool:oldver with USES=libtool or USES=libtool:keepla inTijl Coosemans2014-12-081-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | the 32 ports that still use it. Bump PORTREVISION on their dependent ports except the ones that depend on these: audio/libogg audio/libvorbis devel/pcre ftp/curl graphics/jpeg graphics/libart_lgpl graphics/tiff textproc/expat2 textproc/libxslt In these cases the same trick as in the recent gettext update is used. The ports install a symlink with the old library version. When enough of their dependent ports have had regular updates the remaining ones can get a PORTREVISION bump and the links can be removed. Also remove the devel/pcre dependency from USE_GNOME=glib20. It causes over 2200 packages to depend on devel/pcre while less than 200 actually link with it. The glib20 package still depends on devel/pcre so this should not make a difference for ports with USE_GNOME=glib20. Also, libdata/pkgconfig/glib-2.0.pc lists pcre as a private library so USE_GNOME=glib20 should not propagate it. PR: 195724 Exp-run by: antoine Approved by: portmgr (antoine) Notes: svn path=/head/; revision=374303
* Update "BSD" license in science categoryMark Felder2014-12-074-4/+4
| | | | Notes: svn path=/head/; revision=374211
* Canonicalize a few licensesAntoine Brodin2014-12-071-1/+1
| | | | Notes: svn path=/head/; revision=374163
* - Update to 1.1.1Sunpoet Po-Chuan Hsieh2014-12-052-20/+15
| | | | | | | | | | | | - Strip shared library Changes: https://github.com/Unidata/netcdf4-python/blob/master/Changelog PR: ports/195356 Submitted by: sunpoet (myself) Approved by: Muhammad Moinur Rahman <5u623l20@gmail.com> (maintainer) Notes: svn path=/head/; revision=374066
* Reset maintainership:Baptiste Daroussin2014-12-023-3/+3
| | | | | | | | | | - Lots of maintainers timeout - unresponsive for almost a year PR: 195059 Notes: svn path=/head/; revision=373790
* Split devel/gettext in devel/gettext-runtime and devel/gettext-tools. TheTijl Coosemans2014-11-292-48/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | first contains runtime libraries such as libintl and the latter contains developer tools such as msgfmt. Ports that use gettext will usually need a LIB_DEPENDS on gettext-runtime and a BUILD_DEPENDS on gettext-tools. USES=gettext-runtime can be used to set a LIB/BUILD/RUN_DEPENDS on devel/gettext-runtime and USES=gettext-tools can be used to set a BUILD/RUN_DEPENDS on devel/gettext-tools. USES=gettext is now the same as "USES=gettext-runtime gettext-tools" meaning a LIB_DEPENDS on devel/gettext-runtime and a BUILD_DEPENDS on devel/gettext-tools. Update gettext to 0.19.3. Remove :oldver from converters/libiconv and devel/gettext-runtime. Leave symlinks with the old library versions to avoid the need to bump PORTREVISION on a large number of dependent ports. When most of the dependent ports have had normal version updates, PORTREVISION can be bumped on the remaining ones (low number) and the links can be removed. Fix some ports that installed files in lib/locale instead of share/locale. PR: 194038 Reviewed by: bapt Exp-run: antoine Approved by: portmgr (antoine) Notes: svn path=/head/; revision=373636
* Deprecated ports broken for more than 6 monthsAntoine Brodin2014-11-271-0/+2
| | | | Notes: svn path=/head/; revision=373522
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-2661-133/+40
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Before, we had: site_perl : lib/perl5/site_perl/5.18 site_perl/perl_arch : lib/perl5/site_perl/5.18/mach perl_man3 : lib/perl5/5.18/man/man3 Now we have: site_perl : lib/perl5/site_perl site_arch : lib/perl5/site_perl/mach/5.18 perl_man3 : lib/perl5/site_perl/man/man3 Modules without any .so will be installed at the same place regardless of the Perl version, minimizing the upgrade when the major Perl version is changed. It uses a version dependent directory for modules with compiled bits. As PERL_ARCH is no longer needed in plists, it has been removed from PLIST_SUB. The USE_PERL5=fixpacklist keyword is removed, the .packlist file is now always removed, as is perllocal.pod. The old site_perl and site_perl/arch directories have been kept in the default Perl @INC for all Perl ports, and will be phased out as these old Perl versions expire. PR: 194969 Differential Revision: https://reviews.freebsd.org/D1019 Exp-run by: antoine Reviewed by: perl@ Approved by: portmgr Notes: svn path=/head/; revision=373448
* - Add LICENSESunpoet Po-Chuan Hsieh2014-11-242-9/+3
| | | | | | | - Cleanup PLIST Notes: svn path=/head/; revision=373315
* Fix build with Perl 5.18+. While there, add a runtime dependency on Perl, aMathieu Arnold2014-11-243-3/+41
| | | | | | | | | few installed scripts need it. Sponsored by: Absolight Notes: svn path=/head/; revision=373223
* - Update to 1.3.6Olivier Duchateau2014-11-153-4/+4
| | | | | | | - Update website in WWW entry (pkg-descr) Notes: svn path=/head/; revision=372591
* science/kst2:Max Brazhnikov2014-11-131-1/+3
| | | | | | | | | | - NetCDF 4 is not supported yet, set INGORE if NETCDF option is requested. PR: 194936 Reported by: nwhitehorn Notes: svn path=/head/; revision=372521
* Cleanup plistAntoine Brodin2014-11-1256-736/+23
| | | | Notes: svn path=/head/; revision=372500
* - Update to 1.81.02Wen Heping2014-11-082-5/+4
| | | | Notes: svn path=/head/; revision=372333
* Remove expired ports:Rene Ladan2014-11-0714-158/+0
| | | | | | | | | | | 2014-11-07 math/elmer-umfpack: Obsoleted by cad/elmerfem 2014-11-07 science/elmer-eio: Obsoleted by cad/elmerfem 2014-11-07 science/elmer-matc: Obsoleted by cad/elmerfem 2014-11-07 science/elmer-meshgen2d: Obsoleted by cad/elmerfem 2014-11-07 science/elmergrid: Obsoleted by cad/elmerfem Notes: svn path=/head/; revision=372273
* science/kst2:Max Brazhnikov2014-11-079-121/+61
| | | | | | | | | - Update to 2.0.8 - Remove now needless patches - Add option for building with Qt 5 Notes: svn path=/head/; revision=372255
* - Update to version 2.38Pawel Pekala2014-11-023-68/+42
| | | | | | | | | | | - Sort option helpers - Clean pkg-plist PR: 194170 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=372080
* - Update to 5.0.2Wen Heping2014-10-303-74/+16
| | | | | | | | PR: 193902 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=371747
* Explicitly link with libblas to avoid errors likeDmitry Sivachenko2014-10-302-6/+10
| | | | | | | | | | | | | import sklearn.decomposition.pca ImportError: /usr/local/lib/libcblas.so.2: Undefined symbol "cgemv_" due to it trying to import pairwise_fast.so PR: 194683 Update to version 0.15.2. Notes: svn path=/head/; revision=371746
* - Convert ports of science/ and security to new USES=pythonMarcus von Appen2014-10-2428-77/+50
| | | | | | | Approved by: portmgr (implicit) Notes: svn path=/head/; revision=371453
* Fix compilation after recent numpy patch.Dmitry Sivachenko2014-10-231-0/+2
| | | | | | | Patch by thierry@FreeBSD.org, pointed out by antoine. Notes: svn path=/head/; revision=371398
* science/gromacs: Fix build on DragonFly (fix from dports)John Marino2014-10-201-0/+11
| | | | Notes: svn path=/head/; revision=371267
* Add USES=alias to several portsJohn Marino2014-10-201-1/+1
| | | | | | | | | | | Alias is a new USES tool that allows DragonFly to masquerade as FreeBSD by setting CFLAGS+= -D__FreeBSD__. For some ports, this fixes the build without the need for additional patches. Approved by: portmgr (bapt, blanket) Notes: svn path=/head/; revision=371252
* KDE/FreeBSD team presents KDE SC 4.14.2 and KDE Workspace 4.11.13!Max Brazhnikov2014-10-196-51/+14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | USE_KDE4=kdehier component has been deprecated, new components added: baloo - Baloo core libraries baloo-widgets - Baloo widgets library kfilemetadata - KDE library for extracting file metadata New ports: graphics/kqtquickcharts - QtQuick plugin to render interactive charts misc/artikulate - Pronunciation trainer for KDE (not usable currently, links to both GStreamer 1.x and 0.10.x via dependencies) sysutils/baloo[-widgets] - KDE framework for searching and managing user metadata sysutils/kfilemetadata - Library for extracting file metadata l10n ports: - Farsi (Persian) and Indonesian translations has been readded - Vietnamese didn't pass threshold for inclusion into release astro/kstars: - switch dependency from math/eigen2 to math/eigen3 - add PYKDE option for updating supernovae data deskutils/kdepim4: - update dependencies: add libkgapi and baloo, remove now needless clucene, link-grammar, strigi - add patch to fix build with gcc42 - update COMMENT and description for all KDE PIM ports devel/ruby-krossruby: - remove BROKEN, it builds with ruby 2.x now editors/kate: - add patch to disable memory-hungry build of the kate tests [1] graphics/okular: - add dependency on graphics/libkscreen math/cantor: - add optional dependency on lang/luajit for LuaJIT backend - fix gfortran detection [2] misc/kdehier4: - adapt to new pkg world. Now the purpose of kdehier4 only to link some stuff between KDE4_PREFIX and LOCALBASE. science/kalzium: - switch dependency from math/eigen2 to math/eigen3 - add dependence on science/chemical-mime-data x11-themes/kdeartwork4 - switch dependency from math/eigen2 to math/eigen3 among other changes: - drop deprecated USE_KDE4=kdehier - drop @dirrm from plist - clean up pkg-descr - convert to options helpers - other portlint fixes The area51 repository features commits by alonso, rakuco and myself. PR: 187150 [1] Reported by: pe.freethread@live.com Patch by: Tobias Berner <tcberner@gmail.com> PR: 180674 [2] Reported by: torsten.eichstaedt@web.de PR: 194316 Exp-run: antoine Notes: svn path=/head/; revision=371193
* Allow staging as a regular userAntoine Brodin2014-10-191-3/+0
| | | | Notes: svn path=/head/; revision=371189
* - Drop @dirrm* from plistDmitry Marakasov2014-10-181-88/+0
| | | | Notes: svn path=/head/; revision=371127
* - Fix buildWen Heping2014-10-171-4/+3
| | | | Notes: svn path=/head/; revision=371026
* - Update to 0.99.28Stephen Hurd2014-10-144-31/+16
| | | | | | | | | | | ChangeLog summary: Minor bug fixes, use the new g_object format to supress warnings about deprecated calls. PR: 191376 Submitted by: tkato432@yahoo.com (ie: Ports Fury) Notes: svn path=/head/; revision=370829
* - Upgrade to 0.9.5Thierry Thomas2014-10-1212-571/+474
| | | | | | | - Switch to the options framework. Notes: svn path=/head/; revision=370688
* Force freetype's headers detection.Thierry Thomas2014-10-072-149/+4
| | | | | | | Submitted by: maintainer Notes: svn path=/head/; revision=370399
* Mark the old elmer-* ports as deprecated: they are obsoleted byThierry Thomas2014-10-074-1/+13
| | | | | | | | | cad/elmerfem. Reported by: pfg Notes: svn path=/head/; revision=370390
* science/psychopy: switch from py-imaging to py-pillowWilliam Grzybowski2014-10-071-6/+4
| | | | | | | | | | - USES python With hat: python Approved by: portmgr (bdrewery, implicit) Notes: svn path=/head/; revision=370369
* Fix build after r369447Dmitry Sivachenko2014-09-301-0/+2
| | | | | | | Patch by Thierry Thomas <thierry@FreeBSD.org> Notes: svn path=/head/; revision=369576
* - Update net/openmpi from 1.8.2 to 1.8.3Danilo Egea Gondolfo2014-09-287-5/+7
| | | | Notes: svn path=/head/; revision=369434
* science/jstrack: Unbreak; author verified distfile was rerolledJohn Marino2014-09-253-116/+3
| | | | | | | | | | PR: 193425 Submitted by: Muhammad Rahman While here, remove redundant @dirrm from pkg-plist Notes: svn path=/head/; revision=369274
* - Set CPPFLAGS and LIBS in a number of ports so configure can find libintl.hTijl Coosemans2014-09-252-20/+5
| | | | | | | | | | | | | | | | | | | | | and libintl.so. This fixes a problem where DATADIRNAME gets an incorrect value which causes locale files to be installed in the wrong place. - The only configure checks that still need to be patched are related to intltool so move DATADIRNAME patching from USES=pathfix to USE_GNOME=intlhack. - games/klavaro: remove excessive dependencies - japanese/libskk: add INSTALL_TARGET=install-strip - math/libqalculate: add INSTALL_TARGET=install-strip and remove pthread patching - multimedia/freetuxtv: remove excessive dependencies - science/gramps: fix shared-mime-info use Exp-run by: antoine Approved by: portmgr (antoine) Notes: svn path=/head/; revision=369260
* science/mpqc: Don't override libtool -version-info, bump dependent portsJohn Marino2014-09-254-60/+55
| | | | | | | | | | | | We accept SHLIB version changes when moving to USE=libtool, so stop overriding it with the intent of prevent library version changes, which is considered the better approach over the long term. Two ports are dependent on mpqc, so bump them for the second time today. requested by: tijl@ Notes: svn path=/head/; revision=369254
* science: Fix mpqc, libint and unbreak ghemical, and libghemical atomicallyJohn Marino2014-09-258-92/+80
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | science/ghemical would not link because libghemical.so (from science/ libghemical port) had never been properly linked. Links to all mpqc "SC" libraries were added to LDFLAGS to rectify this. The configure breakage and solution is described below. After the version of lang/gcc was bumped from 4.7 to 4.8, science/libghemical ceased to configure and it was marked broken. After recreating the conftest, it was discovered that two versions incompatible versions of libgcc_s.so were getting pulled in by the realtime linker: the base version and the gcc48 ports version. The base version was getting pulled in by science/libint. To unbreak libghemical, libint is now built with lang/gcc. It was necessary to force libtool to link with LDFLAGS that Mk/bsd.gcc.mk sets so that the runpaths match across libraries used by libghemical. When science/mpqc was staged, it utilized libtool which renumbered all the library versions from 8.0.1 to 7.1.0. This was caused by the age component being greater than 0. By patching configure.in with a new version, we can generate major SHLIB of 8 again. While here, fix the bin/sc-config tool to remove a bad include cflag. With this fixes, science/ghemical builds successfully. Bump all 4 of these ports, remove any BROKEN designation and remove redundant @dirrm in pkg-plist Notes: svn path=/head/; revision=369236
* - Drop @dirrm* from plistDmitry Marakasov2014-09-241-67/+0
| | | | Notes: svn path=/head/; revision=369142
* Remove expired portsRene Ladan2014-09-2014-292/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Keep some which are optional dependencies of non-expired ports 2014-09-18 sysutils/moreutils-parallel: Use moreutils-parallel in sysutils/moreutils instead 2014-09-20 science/ruby-netcdf: Depends on deprecated math/ruby-narray 2014-09-20 x11-toolkits/ruby-fox16: RubyForge shutdown May 15 2014 2014-09-20 math/ruby-gnuplot: Depends on deprecated math/ruby-narray 2014-09-20 science/ruby-gphys: Depends on deprecated math/ruby-narray 2014-09-20 math/ruby-fftw3: Depends on deprecated math/ruby-narray 2014-09-20 science/ruby-dcl: Depends on deprecated math/ruby-narray 2014-09-20 math/ruby-numru_misc: Depends on deprecated math/ruby-narray 2014-09-20 math/ruby-narray: RubyForge shutdown May 15 2014 2014-09-20 textproc/ruby-liquid: RubyForge shutdown May 15 2014 2014-09-20 comms/callsign: RubyForge shutdown May 15 2014 2014-09-20 misc/ruby-vpim: RubyForge shutdown May 15 2014 2014-09-20 net/ruby-ldap: RubyForge shutdown May 15 2014 2014-09-20 devel/rubygem-echoe: Depends on deprecated rubyforge 2014-09-20 www/ruby-borges: RubyForge shutdown May 15 2014 2014-09-20 www/ruby-fcgiwrap: RubyForge shutdown May 15 2014 2014-09-20 www/rubygem-scrubyt: RubyForge shutdown May 15 2014 2014-09-20 devel/ruby-multi: RubyForge shutdown May 15 2014 2014-09-20 databases/ruby-dbd_sqlite3: RubyForge shutdown May 15 2014 2014-09-20 math/ruby-gsl: RubyForge shutdown May 15 2014 2014-09-20 security/ruby-gpgme: RubyForge shutdown May 15 2014 2014-09-20 multimedia/vodcatcher: RubyForge shutdown May 15 2014 2014-09-20 japanese/ruby-ming: RubyForge shutdown May 15 2014 2014-09-20 devel/ruby-statgrab: RubyForge shutdown May 15 2014 2014-09-20 security/ruby-crypt: RubyForge shutdown May 15 2014 2014-09-20 sysutils/philesight: Depends on deprecated devel/ruby-locale2 2014-09-20 multimedia/podcatcher: RubyForge shutdown May 15 2014 2014-09-20 audio/ruby-mp3info: RubyForge shutdown May 15 2014 2014-09-20 multimedia/ruby-flvtool2: RubyForge shutdown May 15 2014 2014-09-20 audio/ruby-freedb: RubyForge shutdown May 15 2014 2014-09-20 graphics/ruby-ming: RubyForge shutdown May 15 2014 2014-09-20 devel/ruby-locale2: RubyForge shutdown May 15 2014 2014-09-20 devel/rubygem-rubyforge: RubyForge shutdown May 15 2014 2014-09-20 databases/ruby-dbd_odbc: RubyForge shutdown May 15 2014 2014-09-20 devel/ruby-fastri: RubyForge shutdown May 15 2014 2014-09-20 devel/ri-emacs: RubyForge shutdown May 15 2014 2014-09-20 security/p5-openxpki-client-html-mason: security/p5-openxpki-0.15+ abandoned Mason UI technology in favor of FastCGI Notes: svn path=/head/; revision=368630
* - Update to 1.3.5Olivier Duchateau2014-09-182-3/+4
| | | | | | | - Add LICENSE_FILE Notes: svn path=/head/; revision=368420
* Upgrade to version 2.0.7.Thierry Thomas2014-09-145-27/+26
| | | | | | | | | Note: this is not the latest. Now there is no separate release for ncs and the sources are distributed as code_saturne-x.y.z. Next upgrades in preparation! Notes: svn path=/head/; revision=368186
* Upgrade to version 2.0.3.Thierry Thomas2014-09-142-24/+11
| | | | | | | | PR: ports/193296 Submitted by: pfg Notes: svn path=/head/; revision=368185
* Upgrade to version 0.15.4.Thierry Thomas2014-09-142-7/+5
| | | | | | | | PR: ports/193298 Submitted by: pfg Notes: svn path=/head/; revision=368184
* Mark BROKEN: Fails to configureAntoine Brodin2014-09-131-0/+2
| | | | | | | | | | | | | | | checking for main in -llapack... yes checking for sc-config... /usr/local/bin/sc-config checking SC - version... no *** Could not run SC test program, checking why... *** The test program compiled, but did not run. This usually means *** that the run-time linker is not finding SC or finding the wrong *** version of SC. Reported by: pkg-fallout Notes: svn path=/head/; revision=368144
* Use default LIBTOOLIZE_ARGSTijl Coosemans2014-09-131-1/+0
| | | | Notes: svn path=/head/; revision=368126
* - Update to 4.4.1Sunpoet Po-Chuan Hsieh2014-09-132-5/+4
| | | | | | | Changes: https://github.com/Unidata/netcdf-fortran/blob/master/RELEASE_NOTES.md Notes: svn path=/head/; revision=368118
* - Add rubygem-cdo 1.2.3Sunpoet Po-Chuan Hsieh2014-09-134-0/+29
| | | | | | | | | | | | Ruby binding to CDO (Climate Data Operators) GitHub repository at https://github.com/Try2Code/cdo-bindings WWW: https://code.zmaw.de/projects/cdo/wiki/Cdo%7Brbpy%7D RG: https://rubygems.org/gems/cdo Notes: svn path=/head/; revision=368114
* - Add py-cdo 1.2.3Sunpoet Po-Chuan Hsieh2014-09-134-0/+29
| | | | | | | | | | | Python binding to CDO (Climate Data Operators) GitHub repository at https://github.com/Try2Code/cdo-bindings WWW: https://code.zmaw.de/projects/cdo/wiki/Cdo%7Brbpy%7D Notes: svn path=/head/; revision=368113
* - Update to 4.10Jason E. Hale2014-09-124-25/+20
| | | | | | | | | | | | | | | | | | - Update WWW While here: - Update LICENSE - Convert non-functional (since February) USE_FORTRAN to USES=fortran - Convert USE_PYTHON to USES=python:2 (3.x doesn't seem to work) - Further convert to options helpers - FORTRAN and QT4 options seem to build fine together, so make them non-exclusive regular options PR: 193590 Submitted by: pfg Notes: svn path=/head/; revision=368072