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* Update SphinxDanilo G. Baio2020-05-111-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Repocopy textproc/py-sphinx to textproc/py-sphinx18 Update it to 1.8.5 (latest version from 1.8.X). This version supports Python 2 and 3. Add test target. - textproc/py-sphinx: Update to 3.0.2 Python 3 only (3.5+). Add test target. - Mk/Uses/python.mk: Add PY_SPHINX Shared macro to use with flavors and not break ports with USES=python (all versions). Python >=3.5 --> textproc/py-sphinx (v3.0.2) Python < 3.5 --> textproc/py-sphinx18 (v1.8.5) All ports that uses sphinx were changed to use the new variable ${PY_SPHINX} in the dependency line, exceptions: * Ports that fails to build with sphinx 3.0.2 because of code. They are pointing to textproc/py-sphinx18 directly. There aren't many ports. * Ports that doesn't know Python flavors. - Add several patches to fix Sphinx consumers The most common issues are related with pkg-plist, the output files from Sphinx changes between versions, keep this dynamically is the better approach. This will save time in future sphinx updates. PR: 245629 Exp-run by: antoine Notes: svn path=/head/; revision=534966
* biology/hhsuite: fix build on powerpc64 elfv2Piotr Kubaj2020-05-111-1/+4
| | | | | | | | | Use GCC instead of Clang: /usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw' return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); Notes: svn path=/head/; revision=534934
* - Resurrect and unbreak by updating to version 34.0Alexey Dokuchaev2020-05-1012-0/+1774
| | | | | | | | - Stop providing outdated offline PDF documentation, users are advised to use the online files instead Notes: svn path=/head/; revision=534852
* Update devel/gmake to 4.3.Tijl Coosemans2020-05-091-0/+22
| | | | | | | | | | | | | Some changes have been made in this release that break backwards compatibility. Let USES=gmake force users to upgrade to this version so port maintainers don't have to support older versions. PR: 245725 Exp-run by: antoine Approved by: portmgr (antoine) Notes: svn path=/head/; revision=534792
* Update to 7.6.13Mateusz Piotrowski2020-05-092-4/+4
| | | | | | | | Release announcement: https://foldingforum.org/viewtopic.php?f=108&t=34466 Notes: svn path=/head/; revision=534738
* Bump 37 ports depending on math/openblas through USES=blaslapack:openblas ↵Yuri Victorovich2020-05-062-1/+2
| | | | | | | because after the recent math/openblas update the library name changed in openblas Notes: svn path=/head/; revision=534190
* Bump 46 ports depending on math/openblas because the after the recent ↵Yuri Victorovich2020-05-062-1/+2
| | | | | | | math/openblas update the library name changed in openblas. Notes: svn path=/head/; revision=534185
* Preserve Gradle 6.2.2 for biology/gatkTobias Kortkamp2020-05-061-2/+2
| | | | | | | It fails to build with newer Gradle versions again. Notes: svn path=/head/; revision=534171
* Remove expired ports:Rene Ladan2020-05-0535-2475/+0
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months 2020-05-05 textproc/csv2latex: Broken for more than 6 months 2020-05-05 textproc/da-hyphen: Broken for more than 6 months 2020-05-05 textproc/glark: Broken for more than 6 months 2020-05-05 textproc/html2tex: Broken for more than 6 months 2020-05-05 textproc/htmlsection: Broken for more than 6 months 2020-05-05 textproc/kenlm: Broken for more than 6 months 2020-05-05 textproc/libguess: Broken for more than 6 months 2020-05-05 textproc/libxml++26-reference: Broken for more than 6 months 2020-05-05 textproc/no-hunspell: Broken for more than 6 months 2020-05-05 textproc/p5-MARC: Broken for more than 6 months 2020-05-05 textproc/p5-texcount: Broken for more than 6 months 2020-05-05 textproc/pcrs: Broken for more than 6 months 2020-05-05 textproc/pear-Structures_DataGrid_DataSource_RSS: Broken for more than 6 months 2020-05-05 textproc/pear-Structures_DataGrid_DataSource_XML: Broken for more than 6 months 2020-05-05 textproc/permute: Broken for more than 6 months 2020-05-05 textproc/pocketreader: Broken for more than 6 months 2020-05-05 textproc/py-sgrep: Broken for more than 6 months 2020-05-05 textproc/rss2html: Broken for more than 6 months 2020-05-05 textproc/ruby-xmlparser: Broken for more than 6 months 2020-05-05 textproc/sv-hyphen: Broken for more than 6 months 2020-05-05 textproc/tclExpat: Broken for more than 6 months 2020-05-05 textproc/tex2im: Broken for more than 6 months 2020-05-05 textproc/topic: Broken for more than 6 months 2020-05-05 textproc/uz-hunspell: Broken for more than 6 months 2020-05-05 textproc/xmlprpr: Broken for more than 6 months 2020-05-05 www/ach: Broken for more than 6 months 2020-05-05 www/apache-forrest: Broken for more than 6 months 2020-05-05 www/apercu: Broken for more than 6 months 2020-05-05 www/cblog: Broken for more than 6 months 2020-05-05 www/drood: Broken for more than 6 months 2020-05-05 www/drraw: Broken for more than 6 months 2020-05-05 www/flood: Broken for more than 6 months 2020-05-05 www/grafana2: Broken for more than 6 months 2020-05-05 www/imgsizer: Broken for more than 6 months 2020-05-05 www/jdresolve: Broken for more than 6 months 2020-05-05 www/linkcheck: Broken for more than 6 months 2020-05-05 www/madsonic-standalone: Broken for more than 6 months 2020-05-05 www/mod_auth_external2: Broken for more than 6 months 2020-05-05 www/mod_chroot: Broken for more than 6 months 2020-05-05 www/mod_cvs2: Broken for more than 6 months 2020-05-05 www/mod_domaintree: Broken for more than 6 months 2020-05-05 www/mod_encoding: Broken for more than 6 months 2020-05-05 www/mod_flickr: Broken for more than 6 months 2020-05-05 www/mod_gzip2: Broken for more than 6 months 2020-05-05 www/mod_layout22: Broken for more than 6 months 2020-05-05 www/mod_proctitle: Broken for more than 6 months 2020-05-05 www/mod_tsa: Broken for more than 6 months 2020-05-05 www/mod_vhs: Broken for more than 6 months 2020-05-05 www/p5-AnyEvent-Mojo: Broken for more than 6 months 2020-05-05 www/p5-Apache-Gallery: Broken for more than 6 months 2020-05-05 www/p5-WWW-Google-Video: Broken for more than 6 months 2020-05-05 www/p5-WWW-Shorten-KUSO: Broken for more than 6 months 2020-05-05 www/p5-WWW-Shorten-isgd: Broken for more than 6 months 2020-05-05 www/photo_gallery: Broken for more than 6 months 2020-05-05 www/pwebstats: Broken for more than 6 months 2020-05-05 www/py-django-profiles: Broken for more than 6 months 2020-05-05 www/red5: Broken for more than 6 months 2020-05-05 www/redmine-sidebar_hide: Broken for more than 6 months 2020-05-05 www/rssowl: Broken for more than 6 months 2020-05-05 www/skytemplate: Broken for more than 6 months 2020-05-05 www/surfraw: Broken for more than 6 months 2020-05-05 www/sws: Broken for more than 6 months 2020-05-05 www/tickr: Broken for more than 6 months 2020-05-05 www/tinytinyhttpd: Broken for more than 6 months 2020-05-05 www/udmsearch: Broken for more than 6 months 2020-05-05 www/vee: Broken for more than 6 months 2020-05-05 www/webreport: Broken for more than 6 months 2020-05-05 www/webstats: Broken for more than 6 months 2020-05-05 www/www6to4: Broken for more than 6 months 2020-05-05 x11/deskpaint: Broken for more than 6 months 2020-05-05 x11/dmenu2: Broken for more than 6 months 2020-05-05 x11/gcb: Broken for more than 6 months 2020-05-05 x11/gpctool: Broken for more than 6 months 2020-05-05 x11/ipager: Broken for more than 6 months 2020-05-05 x11/keylaunch: Broken for more than 6 months 2020-05-05 x11/props: 64-bit unsupported 2020-05-05 x11/roxbg: Broken for more than 6 months 2020-05-05 x11/sisctrl: Broken for more than 6 months 2020-05-05 x11/wdm: Broken for more than 6 months 2020-05-05 x11/xaniroc: Broken for more than 6 months 2020-05-05 x11/xmove: Broken for more than 6 months 2020-05-05 x11/xnodecor: Broken for more than 6 months 2020-05-05 x11/xvattr: Broken for more than 6 months 2020-05-05 x11-clocks/tktz: Broken for more than 6 months 2020-05-05 x11-clocks/xtimer: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-dropline-neu: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-dropline-nou: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-gion: Broken for more than 6 months 2020-05-05 x11-themes/gnome-icons-jini: Broken for more than 6 months 2020-05-05 x11-themes/gtk-aurora-engine: Broken for more than 6 months 2020-05-05 x11-themes/gtk-blueprint-engine: Broken for more than 6 months 2020-05-05 x11-themes/gtk-murrina-fancy-clearlooks: Broken for more than 6 months 2020-05-05 x11-themes/gtk-murrina-lightblue: Broken for more than 6 months 2020-05-05 x11-themes/gtk-murrine-themes: Broken for more than 6 months 2020-05-05 x11-themes/murrine-configurator: Broken for more than 6 months 2020-05-05 x11-themes/nimbus: Broken for more than 6 months 2020-05-05 x11-themes/openbox-themes: Broken for more than 6 months 2020-05-05 x11-themes/rezlooks: Broken for more than 6 months 2020-05-05 x11-themes/ubuntulooks: Broken for more than 6 months 2020-05-05 x11-toolkits/slingshot: 64-bit unsupported 2020-05-05 x11-toolkits/xview-clients: 64-bit unsupported 2020-05-05 x11-wm/fluxconf: Broken for more than 6 months 2020-05-05 x11-wm/ion: Broken for more than 6 months 2020-05-05 x11-wm/matwm2: Broken for more than 6 months 2020-05-05 x11-wm/nickleby: Broken for more than 6 months 2020-05-05 x11-wm/olvwm: 64-bit unsupported 2020-05-05 x11-wm/ratmenu: Broken for more than 6 months Notes: svn path=/head/; revision=534093
* biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparserRene Ladan2020-05-051-3/+1
| | | | Notes: svn path=/head/; revision=534089
* biology/plink: Whole genome association analysis toolsetJason W. Bacon2020-05-046-0/+94
| | | | | | | | | | | Reversed removal, commit r471892 2018/06/07 Upgraded to 1.90 beta 6.17 PR: ports/243733 Submitted by: mzaki@e-mail.ne.jp Notes: svn path=/head/; revision=533993
* - update libgd to 2.3.0Dirk Meyer2020-05-042-1/+2
| | | | | | | | | - new option RAQM - resurrect deprecated gdlib-config - bump dependend ports Notes: svn path=/head/; revision=533989
* biology/hyphy: Update to version 2.5.12Joseph Mingrone2020-05-033-5/+5
| | | | | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.11 https://github.com/veg/hyphy/releases/tag/2.5.12 Notes: svn path=/head/; revision=533731
* biology/iqtree: Update to version 2.0.4Joseph Mingrone2020-05-022-5/+7
| | | | Notes: svn path=/head/; revision=533706
* biology/hyphy: Update to version 2.5.10Joseph Mingrone2020-04-252-4/+4
| | | | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.9 https://github.com/veg/hyphy/releases/tag/2.5.10 Notes: svn path=/head/; revision=532908
* biology/diamond: Update to version 0.9.32Joseph Mingrone2020-04-242-5/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32 Notes: svn path=/head/; revision=532906
* - Swap back from net/openmpi3 to net/openmpiDanilo Egea Gondolfo2020-04-211-3/+3
| | | | Notes: svn path=/head/; revision=532429
* - Swap back from net/openmpi3 to net/openmpiDanilo Egea Gondolfo2020-04-211-3/+3
| | | | Notes: svn path=/head/; revision=532428
* Update to 7.6.9Mateusz Piotrowski2020-04-192-4/+4
| | | | | | | | Release announcement: https://foldingforum.org/viewtopic.php?f=24&t=34466 Notes: svn path=/head/; revision=532099
* - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)Danilo Egea Gondolfo2020-04-191-3/+2
| | | | | | | | | - Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is deprecated and will be removed) - Fix science/gromacs plist when MPI option is enabled - Bump PORTREVISION for all the consumers of net/openmpi Notes: svn path=/head/; revision=532095
* Update to 7.6.8Mateusz Piotrowski2020-04-182-6/+5
| | | | Notes: svn path=/head/; revision=532028
* - Move OpenMPI support to net/openmpi3. OpenMPI 1 and 2 were deprecated.Danilo Egea Gondolfo2020-04-151-2/+3
| | | | | | | Approved by: maintainer (e-mail) Notes: svn path=/head/; revision=531784
* biology/gcta: Genome-wide Complex Trait AnalysisJason W. Bacon2020-04-159-0/+218
| | | | | | | | | | | GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. Notes: svn path=/head/; revision=531770
* Correct typo in pkg-message.Michael Gmelin2020-04-141-2/+2
| | | | | | | | | | Accidentally documented fahclient_donor as fahclient_user, which has a different meaning. PR: 245506 Notes: svn path=/head/; revision=531706
* Improve startup script, join "Team FreeBSD" by defaultMichael Gmelin2020-04-143-11/+85
| | | | | | | | PR: 245506 Approved by: 0mp (maintainer) Notes: svn path=/head/; revision=531701
* biology/py-macs2: Upgrade to 2.2.7.1Jason W. Bacon2020-04-143-5/+29
| | | | | | | | | Bug fix release Reported by: portscout Notes: svn path=/head/; revision=531674
* - Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.Danilo Egea Gondolfo2020-04-121-4/+4
| | | | Notes: svn path=/head/; revision=531485
* biology/fastp: Upgrade to 0.20.1Jason W. Bacon2020-04-093-8/+15
| | | | | | | | | Fix the plotly.js CDN issue Reported by: portscout Notes: svn path=/head/; revision=531215
* biology/star: Upgrade to 2.7.3aJason W. Bacon2020-04-092-4/+4
| | | | | | | Several compatibility and feature enhancements Notes: svn path=/head/; revision=531206
* Deprecate ports broken for more than 6 monthsAntoine Brodin2020-04-045-0/+10
| | | | Notes: svn path=/head/; revision=530719
* biology/ngs-sdk: Update 2.10.4 -> 2.10.5Yuri Victorovich2020-04-044-12/+12
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=530713
* Cosmetic changeSunpoet Po-Chuan Hsieh2020-04-021-2/+3
| | | | Notes: svn path=/head/; revision=530291
* Cosmetic changeSunpoet Po-Chuan Hsieh2020-04-021-2/+3
| | | | Notes: svn path=/head/; revision=530290
* kallisto: Patch for build with GCCJason W. Bacon2020-04-012-0/+11
| | | | | | | | PR: ports/245240 Submitted by: pkubaj Notes: svn path=/head/; revision=530250
* Update devel/tbb to 2020.2 and bump dependent port's revisionsGanael LAPLANCHE2020-04-011-0/+1
| | | | | | | Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES Notes: svn path=/head/; revision=530219
* Update WWWSunpoet Po-Chuan Hsieh2020-03-311-1/+1
| | | | Notes: svn path=/head/; revision=530167
* biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89Yuri Victorovich2020-03-313-17/+10
| | | | | | | Add the pull request that fixes the boost::thread build failures. Notes: svn path=/head/; revision=529953
* Update WWWMateusz Piotrowski2020-03-302-2/+2
| | | | Notes: svn path=/head/; revision=529890
* biology/hyphy: Update to version 2.5.8Joseph Mingrone2020-03-283-5/+7
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8 Notes: svn path=/head/; revision=529331
* Load appropriate Linuxulator bits automatically when starting serviceMateusz Piotrowski2020-03-232-1/+2
| | | | Notes: svn path=/head/; revision=528977
* Improve pkg-messageMateusz Piotrowski2020-03-221-6/+9
| | | | | | | | | | | - Fix some whitespace issues - Suggest the user to configure their user name and team ID. [1] - Link to a website where statistics are updated more often. Suggested by: netchild [1] Notes: svn path=/head/; revision=528927
* biology/seaview: Update version 5.0=>5.0.2Muhammad Moinur Rahman2020-03-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview Notes: svn path=/head/; revision=528926
* Resurrect biology/linux-foldingathomeMateusz Piotrowski2020-03-217-0/+214
| | | | | | | | | | | Special thanks to netchild for inspiring bringing back this piece software to ports! Reviewed by: netchild, pi, salvadore Differential Revision: https://reviews.freebsd.org/D24127 Notes: svn path=/head/; revision=528886
* biology/diamond: Update to version 0.9.31.2Joseph Mingrone2020-03-212-4/+5
| | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.31 Also include two additional commits that fix a build error. Notes: svn path=/head/; revision=528881
* biology/canu: Upgrade to 2.0Jason W. Bacon2020-03-203-9/+4
| | | | | | | | | Several routine enhancements and bug fixes Reported by: portscout Notes: svn path=/head/; revision=528792
* biology/hyphy: Update to version 2.5.7Joseph Mingrone2020-03-202-4/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.7 Notes: svn path=/head/; revision=528753
* Deprecate java/openjfx8-devel consumersTobias Kortkamp2020-03-191-0/+3
| | | | | | | | | | | Chase r527795 and put a deprecation notice on all openjfx8-devel dependent ports too. Also deprecate devel/gradle4 which is only needed to build igv and openjfx8-devel. Notes: svn path=/head/; revision=528706
* biology/hyphy: Update to version 2.5.6Joseph Mingrone2020-03-173-5/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.6 Notes: svn path=/head/; revision=528590
* Mark BROKEN: fails to buildAntoine Brodin2020-03-101-0/+2
| | | | | | | | | | | ../include/pbcopper/json/internal/json.hpp:1229:9: error: static_assert failed due to requirement 'sizeof(nlohmann::basic_json<std::map, std::vector, std::__1::basic_string<char>, bool, long, unsigned long, double, std::allocator, adl_serializer>) == 0' "could not find from_json() method in T's namespace" static_assert(sizeof(BasicJsonType) == 0, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ Reported by: pkg-fallout Notes: svn path=/head/; revision=528170
* Drop dependency on devel/openmpJan Beich2020-03-083-7/+5
| | | | | | | | | | - Drop if devel/llvm* was used as a substitute Approved by: yuri, rene (earlier version) Differential Revision: https://reviews.freebsd.org/D23020 Notes: svn path=/head/; revision=528082
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