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* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-0/+2
| | | | | | | | | - Bump PORTREVISION for package change Tested by: Christer Edwards <christer.edwards@gmail.com> (maintainer) Notes: svn path=/head/; revision=468304
* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-0/+3
| | | | Notes: svn path=/head/; revision=468303
* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-1/+4
| | | | | | | - Bump PORTREVISION for package change Notes: svn path=/head/; revision=468302
* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-1/+3
| | | | | | | - Bump PORTREVISION for package change Notes: svn path=/head/; revision=468301
* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-1/+3
| | | | | | | - Bump PORTREVISION for package change Notes: svn path=/head/; revision=468300
* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-1/+5
| | | | | | | - Bump PORTREVISION for package change Notes: svn path=/head/; revision=468299
* Fix msgpack dependencySunpoet Po-Chuan Hsieh2018-04-251-0/+4
| | | | Notes: svn path=/head/; revision=468298
* biology/paml: Update to version 4.9hJoseph Mingrone2018-04-253-27/+181
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Port Changes: - Add EXAMPLES option and install most files under EXAMPLESDIR - Add USES=dos2unix to fix DOS line endings Upstream Changes: Version 4.9h, March 2018 (*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for rates for loci. Since 4.9d, the program and the documentation are inconsistent about the two priors, and which value (0 or 1) means which prior. I have now checked the program and the documentation to make sure that they are consistent: prior = 0: gamma-Dirichlet (dos Reis 2014). This is the default. prior = 1: conditional i.i.d. prior (Zhu et al. 2015). I believe these two are similar especially if the number of loci (partitions) is large, but no serious comparisons between the two priors have been published. Thanks to Adnan Moussalli for pointing out the errors. (*) codeml. It was discovered that the mechanistic amino acid substitution model implemented in Yang et al. (1998; see table 3), specified by seqtype = 2 model = 6, has been broken for a long time, since version 3.0 (2000) at least. Version 2.0 (1999) seems to be correct. This means that the model become broken soon since it was published. I have now fixed this. This model of amino acid substitution starts from a Markov chain for codons and then aggregate the states and merge the synonymous codons into one state (the coded amino acid). This is an approximate formulation since the process after state aggregation is not Markovian anymore. I have now added another codon-based amino acid substitution model that treats amino acids as ambiguities codons. The model is specified by seqtype = 2 model = 5. This is an exact formulation. (*) codeml. The number of categories in the BEB calculation under M2 and M8 is unintentionally set to 4 rather than 10. I have changed this back to 10. The details of this calculation are in Yang et al. 2005 MBE. Version 4.9g, December 2017 (*) codeml. A bug caused the BEB calculation under the site model M8 (NSsites = 8) to be incorrect, with the program printing out warming messages like "strange: f[ 5] = -0.0587063 very small." This bug was introduced in version 4.9b and affects versions 4.9b-f. A different bug was introduced in version 4.9f that causes the log likelihood function under the site model M8 (NSsites = 8) to be calculated incorrectly. These are now fixed. Version 4.9f, October 2017 (*) baseml, nonhomogeneous models (nhomo & fix_kappa). Those models allow different branches on the tree to have different Q matrices. Roughly nhomo controls the base frequency parameters while gix_kappa controls kappa or the exchangeability parameters (a b c d e in GTR/REV, for example). I added the option (nhomo = 5, fix_kappa = 2), which lets the user to define branch types, so that branches of the same type have the same exchangeability parameters (a b c d e for GTR) and base composition parameters, while branches of different types have different parameters. Branch types are labeled (using # and $), 0, 1, 2, .... The labels should be consecutive positive integers. The old options nhomo = 3 or 4 work for some models like GTR, but not some other models which also have base composition parameters. In this update, I think those options should work with all those models. I have also edited the documentation (look for option variable nhomo for baseml). (*) baseml & codeml. i added an option fix_blength = 3 (proportional), which means that branch lengths will be proporational to those given in the tree file, and the proportionality factor is estimated by ML. (*) codeml. The program does not count the parameters correctly for model M0 when fix_kappa = 1. The bug was introduced in version 4.9c and affects versions 4.9c-e. This is now fixed. (*) codeml (seqtype = 2 model = 2). If you are analyzing multiple protein data sets (ndata > 1) under the empirical models such as wag, jtt, dayhoff. The results for the first data set are correct, but all later data sets are analyzed incorrectly under the corresponding +F models, that is, wag+F, jtt+F, dayhoff+F, etc. A bug in the program means that for the second and later data sets, the equilibrium amino acid frequencies are taken from the real data and not correctly set to those specified by the empirical models. I note that this bug was recorded in the update Version 3.14b, April 2005, but it was somehow not fixed, even in that version. This is now fixed. Thanks to Nick Goldman for reporting this again. (*) evolver (options 5, 6, 7 for simulating nucleotide, codon and amino acid alignments). If you choose the option of printing out the site pattern counts instead of the sequences (specified at the beginning of the control file such as MCbase.dat), and if you are simulating two or more alignments, the program crashes after finishing the first alignment. This is now fixed. (*) mcmctree. The program crashes if you have a mixture of morphological loci and molecular loci, if not all the morphological loci are before the molecular loci. I have now fixed this. I think this was never described anyway. Version 4.9e, March 2017 (*) Edited the readme files to change the license to GPL. (*) mcmctree. A bug was introduced in version 4.9b which causes the program to read the fossil calibration information in the tree file incorrectly, if joint (minimum and maximum) bounds are specified using the symbol '<' and '>'. If you use the notation "B()", "L()", and 'U()', the information is read correctly. This bug was introduced in version 4.9b and exists in 4.9c and 4.9d. Versions 4.9a and earlier were correct. Version 4.9d, February 2017 (*) mcmctree. Changed the default prior for rates for loci to gamma-Dirichlet (dos Reis 2014), and updated the documentation as well. It was set to the conditional i.i.d. prior (Zhu et al. 2015). (*) mcmctree. Added Bayes factor calculation. A program called BFdriver is included in the release, as well as a pdf document in the folder examples/DatingSoftBound/BFdriverDOC.pdf. We suggest that you use the exact likelihood calculation when you use this option, since the normal approximation is unreliable when the power posterior is close to the prior (when beta is small). Notes: svn path=/head/; revision=468297
* The newer meson requires 3.5 (setup.py)Bryan Drewery2018-04-251-1/+1
| | | | Notes: svn path=/head/; revision=468295
* devel/py-async_timeout: update to 2.0.1William Grzybowski2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468294
* Update to 0.4.9.Jung-uk Kim2018-04-253-17/+7
| | | | | | | https://sourceforge.net/p/libwps/code/ci/0.4.9/tree/CHANGES Notes: svn path=/head/; revision=468293
* Remove expired ports:Rene Ladan2018-04-2527-585/+3
| | | | | | | | | 2018-04-24 net/google-daemon: Please use sysutils/py-google-compute-engine instead 2018-04-24 net/google-startup-scripts: Please use sysutils/py-google-compute-engine instead 2018-04-24 math/octave-forge-odepkg Notes: svn path=/head/; revision=468292
* Remove math/octave-forge-ocs, it depends on expired math/octave-forge-odepkgRene Ladan2018-04-255-45/+1
| | | | Notes: svn path=/head/; revision=468291
* mail/up-imapproxy: Take maintainershipBernard Spil2018-04-251-1/+1
| | | | Notes: svn path=/head/; revision=468290
* Clixon is a CLI/network interfaced configuration database toolRenato Botelho2018-04-257-0/+110
| | | | | | | | | | | | | | | Using Clixon you can create CLI, RESTCONF, and NETCONF interfaces to manage a configuration database. It also provides the mechanism to validate and configure system components. WWW: http://www.clicon.org/ PR: 227681 Submitted by: dcornejo@netgate.com Sponsored by: Rubicon Communications, LLC (Netgate) Notes: svn path=/head/; revision=468289
* - Bump PORTREVISION. databases/firebird25-* ports were updatedJose Alonso Cardenas Marquez2018-04-2516-4/+18
| | | | Notes: svn path=/head/; revision=468288
* - Update to 2.5.8Jose Alonso Cardenas Marquez2018-04-253-11/+7
| | | | | | | | | - Take maintainership Release notes: https://www.firebirdsql.org/file/documentation/release_notes/html/en/2_5/rlsnotes25.html Notes: svn path=/head/; revision=468287
* Update the KERB_GSSAPI patch from debian.Bryan Drewery2018-04-252-4/+6
| | | | | | | | | | | | | https://sources.debian.org/data/main/o/openssh/1:7.7p1-2/debian/patches/gssapi.patch is mirrored due to not being filename-unique and not gzipped. PR: 226789 Submitted by: Rick Miller <vmiller@verisign.com> (based on) Tested by: Rick Miller <vmiller@verisign.com> Reported by: david@dcrosstech.com Notes: svn path=/head/; revision=468286
* Set MAINTAINER to dteske@FreeBSD.orgSteven Kreuzer2018-04-251-1/+1
| | | | Notes: svn path=/head/; revision=468285
* x11-toolkits/qwt6 -- flavorize, with qt4 and qt5 variantsTobias C. Berner2018-04-2514-184/+182
| | | | | | | | | Submitted by: lbartoletti@tuxfamily.org (maintainer) Approved by: portmgr (mat) Differential Revision: https://reviews.freebsd.org/D14462 Notes: svn path=/head/; revision=468283
* Switch all pypi.python.org WWWs to a new PyPi home pypi.org whereDmitry Marakasov2018-04-25817-817/+817
| | | | | | | | | | they now redirect to anyway. All new urls checked to return 200, I've fixed a couple of them in the process. Approved by: portmgr blanket, mat Notes: svn path=/head/; revision=468282
* Enable experimental features.Michael Reifenberger2018-04-253-15/+21
| | | | | | | | Make portlint happy. Mark Broken for FreeBSD 10 due to compile/link error. Notes: svn path=/head/; revision=468281
* net/ipxe: Build undionly and EFI imagesTobias Kortkamp2018-04-252-6/+26
| | | | | | | | Submitted by: fabian.freyer@physik.tu-berlin.de Differential Revision: https://reviews.freebsd.org/D15194 Notes: svn path=/head/; revision=468280
* databases/pecl-redis: Update to 4.0.2Jochen Neumeister2018-04-252-4/+4
| | | | | | | | | | Changelog: https://pecl.php.net/package-changelog.php?package=redis&release=4.0.2 PR: 227766 Submitted by: maintainer Notes: svn path=/head/; revision=468279
* www/caddy: update to 0.10.14Jochen Neumeister2018-04-252-4/+4
| | | | | | | | PR: 227764 Submitted by: maintainer Notes: svn path=/head/; revision=468278
* Catch up with changed binutils prefix some moreAlexander Kabaev2018-04-251-2/+1
| | | | | | | | | | | The amd64-gcc needs same treatment as amd64-binutils, we need to override BUTARGET in order to account for amd64 vs x86-64 mismatch. Submitted by: lwhsu Notes: svn path=/head/; revision=468277
* Update Mojolicious to 7.76Adam Weinberger2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468276
* sysutils/runit-faster: Update scripts to 0.1.23Tobias Kortkamp2018-04-253-4/+5
| | | | | | | | | | | | | | - Fix netdata service to not effectively forkbomb the system when it's enabled. - Fix musicpd service - Try and load ukbd(4) before spawning an emergency shell when using a modular kernel in case it's not loaded yet and leaving you stranded with no way out. Notes: svn path=/head/; revision=468275
* editors/kakoune: Fix tmux-repl.kakTobias Kortkamp2018-04-252-3/+24
| | | | | | | | It fails on FreeBSD and claims that tmux' version is too old even though tmux >= 2 is installed. Notes: svn path=/head/; revision=468274
* devel/awscli: Update 1.15.7 -> 1.15.8Bradley T. Hughes2018-04-252-5/+5
| | | | Notes: svn path=/head/; revision=468273
* databases/pecl-redis: Update and split into new portJochen Neumeister2018-04-257-4/+48
| | | | | | | | | | | | | This update consists of two parts which updates current port and creates a new port with the old version as there are breaking changes in the new version. PR: 227396 Submitted by: Daniel Ylitalo <daniel@blodan.se> (maintainer) Differential Revision: https://reviews.freebsd.org/D15146 Notes: svn path=/head/; revision=468272
* devel/py-botocore: Update 1.10.7 -> 1.10.8Bradley T. Hughes2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468271
* - Update to 3.6.6TAKATSU Tomonari2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468270
* www/mod_auth_gssapi: Update to 1.6.1Jochen Neumeister2018-04-252-4/+4
| | | | | | | | PR: 227736 Submitted by: maintainer Notes: svn path=/head/; revision=468269
* lang/php72: Add missing lmdb support for php72-dbaTorsten Zuehlsdorff2018-04-251-1/+7
| | | | | | | | | | PHP 7.2 adds lmdb support to its dba module. Add support via OPTION. PR: 227732 Submitted by: Waitman Gobble <uzimac@da3m0n8t3r.com> Notes: svn path=/head/; revision=468268
* www/matomo: Fix wrong entries in pkg-plistTorsten Zuehlsdorff2018-04-252-112/+112
| | | | | | | | | | | | Some "www" strings where replaced with %%%WWWDIR%%% causing build failures, if %%%WWWDIR%%% is something other than "www". PR: 226668 Submitted by: freebsd-bugs@cklie.de MFH: 2018Q2 Notes: svn path=/head/; revision=468267
* - Update WWWDmitry Marakasov2018-04-251-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=468266
* www/ufdbguard: update to 1.33.5Jochen Neumeister2018-04-252-4/+4
| | | | | | | | | | | Changelog: https://www.urlfilterdb.com/products/releases.html PR: 227661 Reported by: ncrogers@gmail.com Approved by: maintainer Notes: svn path=/head/; revision=468265
* - Add LICENSEDmitry Marakasov2018-04-252-0/+5
| | | | | | | | | - Add WWW Approved by: portmgr blanket Notes: svn path=/head/; revision=468264
* - Switch to new test frameworkDmitry Marakasov2018-04-251-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=468263
* Update devel/erlang-recon to version 2.3.5.Jimmy Olgeni2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468262
* Update devel/etcd32 to version 3.2.19.Jimmy Olgeni2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468261
* Fix plist after r468231.Raphael Kubo da Costa2018-04-252-0/+2
| | | | Notes: svn path=/head/; revision=468260
* - Update to 0.93-0TAKATSU Tomonari2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468259
* - Update to 1.2TAKATSU Tomonari2018-04-252-4/+4
| | | | Notes: svn path=/head/; revision=468258
* devel/gsoap: Update version 2.8.59=>2.8.66Muhammad Moinur Rahman2018-04-259-53/+53
| | | | | | | Relnotes: https://www.genivia.com/changelog.html#latest Notes: svn path=/head/; revision=468257
* devel/icmake: Update version 9.02.04=>9.02.07Muhammad Moinur Rahman2018-04-252-6/+12
| | | | | | | | | | | - Fix build on MIPS64 [1] PR: 227667 [1] Submitted by: loader [1] Relnotes: https://github.com/fbb-git/icmake/releases/tag/9.02.07 Notes: svn path=/head/; revision=468256
* math/libRmath: Update to version 3.5.0Joseph Mingrone2018-04-252-8/+8
| | | | Notes: svn path=/head/; revision=468255
* databases/geoserver-mysql-plugin: Update version 2.12.1=>2.13.0Muhammad Moinur Rahman2018-04-252-5/+5
| | | | Notes: svn path=/head/; revision=468254
* graphics/geoserver: Update version 2.12.1=>2.13.0Muhammad Moinur Rahman2018-04-253-105/+113
| | | | | | | Relnotes: http://blog.geoserver.org/2018/03/20/geoserver-2-13-0-released/ Notes: svn path=/head/; revision=468253
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