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2012-09-14Import PLINK 1.07 as biology/plinkasau6-0/+134
From Jason Bacon via pkgsrc-wip. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
2012-09-14Updated audio/py-audiotools to 2.18jakllsch1-1/+2
2012-09-14py-audiotools (sometimes) needs py-urwid at runtimejakllsch1-1/+4
pkgrev++
2012-09-14Add p5-biblatex-biberis1-1/+2
2012-09-14Revert previous patch, keeping PKGREVISION.taca1-2/+1
I completely forget where take this patch.
2012-09-14Note update of devel/ruby-gettext package to 2.3.1.taca1-1/+2
2012-09-14Update ruby-gettext to 2.3.1.taca3-19/+18
## 2.3.1: 2012-09-13 It's a Bug and package fix release. Then, it's also encoding support release, only if you use Ruby 1.9. ### Improvements * [xgettext] Added backword compatibility method (GetText::RGetText.run). [Suggested by Fotos Georgiadis] * [xgettext] Removed deprecated parse argument support. * [erb parer] Assumed the encoding in the magic comment of the input file as the encoding of it. * [ruby parser] Assumed the encoding in the magic comment of the input file as the encoding of it. * [xgettext] Added the "--output-encoding" option to set encoding of output pot file. * [xgettext] Used UTF-8 as the default encoding of output pot file. * [xgettext] Supported multiple encoding sources. ### Changes * [MoFile] Returned nil instead of "" as msgstr when its msgid isn't translated (when this msgstr is ""). * [PoParser] Converted msgstr from "" to nil when parsing. ### Fixes * Added missing .yardopts file. [Reported by Takahiro Kambe] * [news] Fixed Eddie Lau name instead of github name. * [msginit] Added the "Plural-Forms:" entry to the header even if a pot file doesn't have it. * [msgmerge] Fixed the bug the new line between a header and contents doesn't exist. * [msginit] Fixed the bug that msgstr with msgid_plural aren't generated in output po file. * [xgettext] Supported class based xgettext parser add API. [GitHub #10] [Suggested by Michael Grosser] * [erb parer] Fixed erb parser bug with unicode msgid in Ruby 1.9 ERB templates. [Github #9] [Patch by Fotos Georgiadis] * Added missing documents for GetText::Tools::XGetText. ### Thanks * Takahiro Kambe * Michael Grosser * Fotos Georgiadis
2012-09-14Note update of lang/ruby18-base package to 1.8.7.370nb1.taca1-1/+2
2012-09-14Add a patch to fix bignum problem on OS X 10.8, clang.taca3-2/+40
Bump PKGREVISION.
2012-09-14Note update of PHP language packages:taca1-1/+3
lang/php53 5.3.17 lang/php54 5.4.7
2012-09-14Update PHP53_VERSION and PHP54_VERSION.taca1-3/+3
2012-09-14Reset PKGREVISION.taca1-2/+1
2012-09-14Update php54 to 5.4.7 (PHP 5.4.7).taca2-6/+6
13 Sep 2012, PHP 5.4.7 - Core: . Fixed bug (segfault while build with zts and GOTO vm-kind). (Laruence) . Fixed bug #62955 (Only one directive is loaded from "Per Directory Values" Windows registry). (Felipe) . Fixed bug #62844 (parse_url() does not recognize //). (Andrew Faulds). . Fixed bug #62829 (stdint.h included on platform where HAVE_STDINT_H is not set). (Felipe) . Fixed bug #62763 (register_shutdown_function and extending class). (Laruence) . Fixed bug #62725 (Calling exit() in a shutdown function does not return the exit value). (Laruence) . Fixed bug #62744 (dangling pointers made by zend_disable_class). (Laruence) . Fixed bug #62716 (munmap() is called with the incorrect length). (slangley@google.com) . Fixed bug #62358 (Segfault when using traits a lot). (Laruence) . Fixed bug #62328 (implementing __toString and a cast to string fails) (Laruence) . Fixed bug #51363 (Fatal error raised by var_export() not caught by error handler). (Lonny Kapelushnik) . Fixed bug #40459 (Stat and Dir stream wrapper methods do not call constructor). (Stas) - CURL: . Fixed bug #62912 (CURLINFO_PRIMARY_* AND CURLINFO_LOCAL_* not exposed). (Pierrick) . Fixed bug #62839 (curl_copy_handle segfault with CURLOPT_FILE). (Pierrick) - DateTime: . Fixed bug #62852 (Unserialize invalid DateTime causes crash). (reeze.xia@gmail.com) - Intl: . Fixed Spoofchecker not being registered on ICU 49.1. (Gustavo) . Fix bug #62933 (ext/intl compilation error on icu 3.4.1). (Gustavo) . Fix bug #62915 (defective cloning in several intl classes). (Gustavo) - Installation: . Fixed bug #62460 (php binaries installed as binary.dSYM). (Reeze Xia) - PCRE: . Fixed bug #55856 (preg_replace should fail on trailing garbage). (reg dot php at alf dot nu) - PDO: . Fixed bug #62685 (Wrong return datatype in PDO::inTransaction()). (Laruence) - Reflection: . Fixed bug #62892 (ReflectionClass::getTraitAliases crashes on importing trait methods as private). (Felipe) . Fixed bug #62715 (ReflectionParameter::isDefaultValueAvailable() wrong result). (Laruence) - Session: . Fixed bug (segfault due to retval is not initialized). (Laruence) . Fixed bug (segfault due to PS(mod_user_implemented) not be reseted when close handler call exit). (Laruence) - SPL: . Fixed bug #62904 (Crash when cloning an object which inherits SplFixedArray) (Laruence) . Implemented FR #62840 (Add sort flag to ArrayObject::ksort). (Laruence) - Standard: . Fixed bug #62836 (Seg fault or broken object references on unserialize()). (Laruence) - FPM: . Merged PR 121 by minitux to add support for slow request counting on PHP FPM status page. (Lars)
2012-09-14Update php53 to 5.3.17 (PHP 5.3.17).taca2-9/+6
13 Sep 2012, PHP 5.3.17 - Core: . Fixed bug (segfault while build with zts and GOTO vm-kind). (Laruence) . Fixed bug #62955 (Only one directive is loaded from "Per Directory Values" Windows registry). (aserbulov at parallels dot com) . Fixed bug #62763 (register_shutdown_function and extending class). (Laruence) . Fixed bug #62744 (dangling pointers made by zend_disable_class). (Laruence) . Fixed bug #62716 (munmap() is called with the incorrect length). (slangley@google.com) . Fixed bug ##62460 (php binaries installed as binary.dSYM). (Reeze Xia) - CURL: . Fixed bug #62839 (curl_copy_handle segfault with CURLOPT_FILE). (Pierrick) - DateTime: . Fixed bug #62852 (Unserialize invalid DateTime causes crash). (reeze.xia@gmail.com) - Intl: . Fix null pointer dereferences in some classes of ext/intl. (Gustavo) - MySQLnd: . Fixed bug #62885 (mysqli_poll - Segmentation fault). (Laruence) - PDO: . Fixed bug #62685 (Wrong return datatype in PDO::inTransaction()). (Laruence) - Session: . Fixed bug (segfault due to retval is not initialized). (Laruence) - SPL: . Fixed bug #62904 (Crash when cloning an object which inherits SplFixedArray) (Laruence) - Enchant: . Fixed bug #62838 (enchant_dict_quick_check() destroys zval, but fails to initialize it). (Tony, Mateusz Goik). 16 Aug 2012, PHP 5.3.16 - Core: . Fixed bug #60194 (--with-zend-multibyte and --enable-debug reports LEAK with run-test.php). (Laruence) - CURL: . Fixed bug #62499 (curl_setopt($ch, CURLOPT_COOKIEFILE, "") returns false). (r.hampartsumyan@gmail.com, Laruence) - DateTime: . Fixed Bug #62500 (Segfault in DateInterval class when extended). (Laruence) - Reflection: . Fixed bug #62715 (ReflectionParameter::isDefaultValueAvailable() wrong result). (Laruence) - SPL: . Fixed bug #62616 (ArrayIterator::count() from IteratorIterator instance gives Segmentation fault). (Laruence, Gustavo)
2012-09-14Note update of F-PROT Antivirus to 6.2.2:taca1-1/+4
security/f-prot-antivirus6-fs-bin security/f-prot-antivirus6-ms-bin security/f-prot-antivirus6-ws-bin
2012-09-14Update F-PROT Antivirus to 6.2.2.taca4-14/+14
Quote from release announce: The only changes in this version are licensing information updates in the documentation.
2012-09-14+ffmpeg010drochner1-1/+2
2012-09-14prepare a pkg for ffmpeg-0.10.4drochner11-0/+551
The idea is to iron out build problems and replace the old ffmpeg pkg after the freeze.
2012-09-14Updated graphics/enblend-enfuse to 4.0nb6obache1-1/+2
2012-09-14After update of recent boost, -lboost_system is required.obache1-2/+5
PR 46873 by Tero Kivinen. Bump PKGREVISION.
2012-09-14Better point to the index page rather than wiki.asau1-2/+2
From Snader_LB via IRC.
2012-09-14Updated net/p5-NetAddr-IP to 4.062sno1-1/+2
2012-09-14Updating package for CPAN module NetAddr::IP in net/p5-NetAddr-IP fromsno2-7/+7
4.058 to 4.062. pkgsrc changes: - currect license conditions upstream changes: 4.062 Wed Jun 6 12:34:48 PDT 2012 documentation updates courtesy of Ben Bullock <benkasminbullock@gmail.com> Thank you Ben. 4.061 Tue May 8 16:24:03 PDT 2012 fixed bug in Lite v1.44 that returned $ip->num() = 2^128 for 0.0.0.0/0 Thanks to Sebastian <debug@test1.org> for spotting it. 4.060 Fri Apr 6 16:00:02 PDT 2012 In Lite.pm v1.43, fix bug #75976, change in behavior introduced in v4.050 where an empty string supplied to "new" previously returned 'undef' and now returns 'default' for ipV4 or ipV6 4.059 Wed Mar 7 12:50:04 PST 2012 add is_rfc1918 to Lite.pm v1.42 documentation updates
2012-09-14raros.hpp defines _UNIX on ~everything except Windows, so removewiz2-13/+3
a chunk that shouldn't be necessary.
2012-09-14Add comments to patches.wiz3-5/+9
2012-09-14Resign maintainership -- I haven't been maintaining this really for quitewiz1-2/+2
some time.
2012-09-14Stop maintaining it, dead upstream.wiz1-2/+2
2012-09-14Add comments to patches.wiz5-9/+17
2012-09-14BibLaTeX-Biber package (0.9.9, the last one working with biblatex 1.7).is4-0/+112
This is in modular form, with the necessary dependencies noted.
2012-09-14Remove emacs from dependencies because it may be usedcheusov1-4/+2
by other programs. One example is ssmtp. ++pkgrevision
2012-09-14Add comments to patches.wiz4-7/+14
2012-09-14Add comment to patch.wiz2-3/+5
2012-09-14Updated archivers/unrar to 4.2.4wiz1-1/+2
2012-09-14Update to 4.2.4, changes undocumented.wiz2-6/+6
2012-09-14revbump for poppler updatedrochner3-6/+6
2012-09-14revbump for poppler updatedrochner1-3/+3
also switch to lcms2 - it is pulled in by poppler and picked up by the build anyway
2012-09-14revbump for poppler updatedrochner10-19/+20
2012-09-14bump dependencies for shlib major changedrochner3-6/+6
2012-09-14update to 0.20.4drochner4-11/+11
changes: -Improvements regarding embedded file handling -bugfixes -cleanup pkgsrc note: shlib major changes, revbumps needed. also switch to lcms2 for the "cms" option
2012-09-14Broken upstream and not actively maintainedsno1-1/+3
2012-09-14Added devel/delta version 2006.08.03morr1-1/+2
2012-09-14Add devel/deltamorr1-1/+2
2012-09-14Delta assists you in minimizing "interesting" files subject to a test ofmorr4-0/+38
their interestingness. A common such situation is when attempting to isolate a small failure-inducing substring of a large input that causes your program to exhibit a bug.
2012-09-14Add '-q' to the grep command in GENERATE_PLIST.sbd1-2/+2
2012-09-14Remove this as the last remaining corresponding version of Asteriskjnemeth6-1480/+0
has been removed. This is included in all existing packages and is expected to be included in any new packages.
2012-09-14Removed comms/asterisk-sounds-extrajnemeth1-1/+2
2012-09-14Remove Asterisk 1.6. This version series went end-of-line on Apriljnemeth35-4292/+0
21st, 2012. It most likely has multiple security issues. By this point, all users of this package should have migrated to comms/asterisk18 or comms/asterisk10 as this version has been marked as being deprecated for some time now. Note that this directory is likely to re-appear in late 2017 when Asterisk 16 comes out, assuming the current schedule is followed. However that will be a vastly different version as Asterisk 11 is only in the RC stage now (i.e. it will be five major versions after the one that is expected to be released later this year).
2012-09-14Removed comms/asterisk16jnemeth1-1/+2
2012-09-14Updated comms/asterisk18 to 1.8.16.0jnemeth1-1/+2
2012-09-14Update to Asterisk 1.8.16.0. This release is to fix AST-2012-012 andjnemeth2-9/+9
AST-2012-013, and some general bugs. The Asterisk Development Team has announced the release of Asterisk 1.8.16.0. The release of Asterisk 1.8.16.0 resolves several issues reported by the community and would have not been possible without your participation. Thank you! The following is a sample of the issues resolved in this release: * --- AST-2012-012: Resolve AMI User Unauthorized Shell Access through ExternalIVR * --- AST-2012-013: Resolve ACL rules being ignored during calls by some IAX2 peers * --- Handle extremely out of order RFC 2833 DTMF * --- Resolve severe memory leak in CEL logging modules. * --- Only re-create an SRTP session when needed; respond with correct crypto policy For a full list of changes in this release, please see the ChangeLog: http://downloads.asterisk.org/pub/telephony/asterisk/ChangeLog-1.8.16.0 Thank you for your continued support of Asterisk!
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