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* */*: Remove redundant '-[0-9]*' from CONFLICTSStefan Eßer2021-10-291-1/+1
| | | | | | | | | | | | | The conflict checks compare the patterns first against the package names without version (as reported by "pkg query "%n"), then - if there was no match - agsinst the full package names including the version (as reported by "pkg query "%n-%v"). Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter for the bash package in any version. But that pattern is functionally identical with just "bash". Approved by: portmgr (blanket)
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/seqan-apps, biology/seqan: Update to 2.4.0Yuri Victorovich2018-03-104-1252/+75
| | | | | | | | | | | | | | | | | | | | | | | Port changes for biology/seqan-apps: * Changed to DISTVERSION * Updated COMMENT * Added USES=compiler:openmp * Removed BROKEN_xx (upstream now claims support for these architectures) * Removed USE_GCC * Added SSE4/AVX2/NATIVE SIMD options Port changes for biology/seqan: * Changed to DISTVERSION * Added NO_ARCH * Added PORTDOCS=* * Updated do-install PR: 225682 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer) Approved by: tcberner (mentor, implicit) Notes: svn path=/head/; revision=464043
* - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]Pawel Pekala2016-09-143-24/+34
| | | | | | | | | | - Fix spelling in pkg-descr PR: 212682 [1] Submitted by: Hannes Hauswedell (maintainer) [1] Notes: svn path=/head/; revision=422156
* - Do install cmake and pkgconfig modulesDmitry Marakasov2016-05-272-3/+8
| | | | | | | | | | - While here, switch to options helpers PR: 209710 Submitted by: h2+fbsdports@fsfe.org (maintainer) Notes: svn path=/head/; revision=415945
* biology/seqan: update 1.3.1 -> 2.1.1Jason Unovitch2016-05-107-1915/+1679
| | | | | | | | | | | biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> Notes: svn path=/head/; revision=414898
* biology/segan: Limit GCC to 4.8 while waiting for updateJohn Marino2015-03-211-1/+1
| | | | | | | | | | | | Due to questionable c++, GCC 4.9 and newer cannot build seqan. An update has been in the works that will enable clang compilers and all versions of GCC to build seqan, but it is not quite ready yet. While waiting for it, limit the version of GCC used to 4.8. PR: 196851 Notes: svn path=/head/; revision=381791
* Cleanup plistBaptiste Daroussin2014-10-201-34/+0
| | | | Notes: svn path=/head/; revision=371237
* - Convert ports from benchmarks/ and biology/ to new USES=pythonMarcus von Appen2014-10-191-2/+1
| | | | | | | Approved by: portmgr (implicit) Notes: svn path=/head/; revision=371171
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-101-1/+1
| | | | | | | | | | | | | to GCC 4.8.3. Part II, Bump PORTREVISIONs. PR: 192025 Tested by: antoine (-exp runs) Approved by: portmgr (implicit) Notes: svn path=/head/; revision=367888
* Use gcc on all platforms.Adam Weinberger2014-07-101-6/+1
| | | | | | | | PR: 191692 Submitted by: maintainer Notes: svn path=/head/; revision=361497
* - add stage supportOlli Hauer2014-06-011-5/+1
| | | | | | | - adjust BSDn license Notes: svn path=/head/; revision=356100
* Update the default version of GCC used in the Ports Collection fromGerald Pfeifer2014-03-101-1/+1
| | | | | | | | | | | | | | GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as well as changing the default in Mk/bsd.default-versions.mk. Part II, Bump PORTREVISIONs. PR: 182136 Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports) Tested by: bdrewery (two -exp runs) Notes: svn path=/head/; revision=347809
* Convert b* to USES=zipBaptiste Daroussin2014-03-071-3/+1
| | | | Notes: svn path=/head/; revision=347402
* Update to libmpc version 1.0.1 which brings the following fixes:Gerald Pfeifer2013-10-261-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Switched to automake 1.11.6, see CVE-2012-3386. - #14669: Fixed extraction of CC from gmp.h. - Fixed case of intermediate zero real or imaginary part in mpc_fma, found by hydra with GMP_CHECK_RANDOMIZE=1346362345. This is on top of the following changes from version 1.0 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no invariant sections) for the documentation. - 100% of all lines are covered by tests - Renamed functions . mpc_mul_2exp to mpc_mul_2ui . mpc_div_2exp to mpc_div_2ui - 0^0, which returned (NaN,NaN) previously, now returns (1,+0). - Removed compatibility with K&R compilers, which was untestable due to lack of such compilers. - New functions . mpc_log10 . mpc_mul_2si, mpc_div_2si - Speed-ups . mpc_fma - Bug fixes . mpc_div and mpc_norm now return a value indicating the effective rounding direction, as the other functions. . mpc_mul, mpc_sqr and mpc_norm now return correct results even if there are over- or underflows during the computation. . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has infinite part and equals output variable is corrected. . mpc_fr_sub: Wrong return value for imaginary part is corrected. Convert to the new LIB_DEPENDS standard and remove hard-coded .so versions from a couple of dependent ports. Bump PORTREVISIONS of all dependent ports. PR: 183141 Approved by: portmgr (bdrewery) Notes: svn path=/head/; revision=331644
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-5/+2
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.Gerald Pfeifer2013-08-171-1/+1
| | | | | | | | | | | | | | | | | Right now this is a noop in the former case and a noop in the latter case unless lang/gcc44 has been installed explicitly. This puts a bit more emphasis on standardizing on a canonical version "current" GCC and makes it easier to update that canonical version by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port. That is, USE_GCC=yes means "use a decent/modern version of GCC" without having to worry about details. Approved by: portmgr (bdrewery) Notes: svn path=/head/; revision=324851
* - convert USE_CMAKE to USESMax Brazhnikov2013-03-221-2/+1
| | | | | | | | | | - while here clean up some ports from CMAKE_VERBOSE, which is intended for users Approved by: portmgr (miwi) Notes: svn path=/head/; revision=314960
* Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out.Gerald Pfeifer2012-07-211-1/+1
| | | | | | | Approved by: maintainer Notes: svn path=/head/; revision=301291
* - Fix maintainer emailDmitry Marakasov2012-06-071-1/+1
| | | | | | | Submitted by: maintainer via private email Notes: svn path=/head/; revision=298690
* SeqAn is an open source C++ library of efficient algorithmsDmitry Marakasov2012-06-067-0/+2229
and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. WWW: http://www.seqan.de/ PR: 167571 Submitted by: Hannes <h2+fbsdports@fsfe.org> Notes: svn path=/head/; revision=298619
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