notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
This referral link gives you 10% off a Fastmail.com account and gives me a discount on my Fastmail account.

Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
vcflib C++ library and CLI tools for parsing and manipulating VCF files
1.0.7_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.7Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-17 03:11:48
Last Update: 2024-03-02 20:35:56
Commit Hash: 44f5f66
License: MIT
WWW:
https://github.com/vcflib/vcflib
Description:
The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of variation in individuals and populations of samples, and has become the defacto standard reporting format for a wide array of genomic variant detectors. vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both: an API for parsing and operating on records of genomic variation as it can be described by the VCF format and a collection of command-line utilities for executing complex manipulations on VCF files. The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (256 items)
Collapse this list.
  1. /usr/local/share/licenses/vcflib-1.0.7_1/catalog.mk
  2. /usr/local/share/licenses/vcflib-1.0.7_1/LICENSE
  3. /usr/local/share/licenses/vcflib-1.0.7_1/MIT
  4. bin/abba-baba
  5. bin/bFst
  6. bin/bed2region
  7. bin/bgziptabix
  8. bin/dumpContigsFromHeader
  9. bin/genotypeSummary
  10. bin/hapLrt
  11. bin/iHS
  12. bin/meltEHH
  13. bin/normalize-iHS
  14. bin/pFst
  15. bin/pVst
  16. bin/permuteGPAT++
  17. bin/permuteSmooth
  18. bin/plotHaps
  19. bin/popStats
  20. bin/segmentFst
  21. bin/segmentIhs
  22. bin/sequenceDiversity
  23. bin/smoother
  24. bin/vcf2bed.py
  25. bin/vcf2dag
  26. bin/vcf2fasta
  27. bin/vcf2sqlite.py
  28. bin/vcf2tsv
  29. bin/vcf_strip_extra_headers
  30. bin/vcfaddinfo
  31. bin/vcfafpath
  32. bin/vcfallelicprimitives
  33. bin/vcfaltcount
  34. bin/vcfannotate
  35. bin/vcfannotategenotypes
  36. bin/vcfbiallelic
  37. bin/vcfbreakmulti
  38. bin/vcfcat
  39. bin/vcfcheck
  40. bin/vcfclassify
  41. bin/vcfcleancomplex
  42. bin/vcfclearid
  43. bin/vcfclearinfo
  44. bin/vcfcombine
  45. bin/vcfcommonsamples
  46. bin/vcfcomplex
  47. bin/vcfcountalleles
  48. bin/vcfcreatemulti
  49. bin/vcfdistance
  50. bin/vcfecho
  51. bin/vcfentropy
  52. bin/vcfevenregions
  53. bin/vcffilter
  54. bin/vcffirstheader
  55. bin/vcffixup
  56. bin/vcfflatten
  57. bin/vcfgeno2alleles
  58. bin/vcfgeno2haplo
  59. bin/vcfgenosamplenames
  60. bin/vcfgenosummarize
  61. bin/vcfgenotypecompare
  62. bin/vcfgenotypes
  63. bin/vcfglbound
  64. bin/vcfglxgt
  65. bin/vcfgtcompare.sh
  66. bin/vcfhetcount
  67. bin/vcfhethomratio
  68. bin/vcfindelproximity
  69. bin/vcfindels
  70. bin/vcfindex
  71. bin/vcfinfo2qual
  72. bin/vcfinfosummarize
  73. bin/vcfintersect
  74. bin/vcfjoincalls
  75. bin/vcfkeepgeno
  76. bin/vcfkeepinfo
  77. bin/vcfkeepsamples
  78. bin/vcfld
  79. bin/vcfleftalign
  80. bin/vcflength
  81. bin/vcfmultiallelic
  82. bin/vcfmultiway
  83. bin/vcfmultiwayscripts
  84. bin/vcfnobiallelicsnps
  85. bin/vcfnoindels
  86. bin/vcfnosnps
  87. bin/vcfnulldotslashdot
  88. bin/vcfnullgenofields
  89. bin/vcfnumalt
  90. bin/vcfoverlay
  91. bin/vcfparsealts
  92. bin/vcfplotaltdiscrepancy.r
  93. bin/vcfplotaltdiscrepancy.sh
  94. bin/vcfplotsitediscrepancy.r
  95. bin/vcfplottstv.sh
  96. bin/vcfprimers
  97. bin/vcfprintaltdiscrepancy.r
  98. bin/vcfprintaltdiscrepancy.sh
  99. bin/vcfqual2info
  100. bin/vcfqualfilter
  101. bin/vcfrandom
  102. bin/vcfrandomsample
  103. bin/vcfregionreduce
  104. bin/vcfregionreduce_and_cut
  105. bin/vcfregionreduce_pipe
  106. bin/vcfregionreduce_uncompressed
  107. bin/vcfremap
  108. bin/vcfremoveaberrantgenotypes
  109. bin/vcfremovenonATGC
  110. bin/vcfremovesamples
  111. bin/vcfroc
  112. bin/vcfsample2info
  113. bin/vcfsamplediff
  114. bin/vcfsamplenames
  115. bin/vcfsitesummarize
  116. bin/vcfsnps
  117. bin/vcfsort
  118. bin/vcfstats
  119. bin/vcfstreamsort
  120. bin/vcfuniq
  121. bin/vcfuniqalleles
  122. bin/vcfvarstats
  123. bin/vcfwave
  124. bin/wcFst
  125. include/BandedSmithWaterman.h
  126. include/BedReader.h
  127. include/Fasta.h
  128. include/IndelAllele.h
  129. include/IntervalTree.h
  130. include/LargeFileSupport.h
  131. include/LeftAlign.h
  132. include/LeftAlign.hpp
  133. include/Mosaik.h
  134. include/Region.h
  135. include/Repeats.h
  136. include/SmithWatermanGotoh.h
  137. include/Variant.h
  138. include/allele.hpp
  139. include/catch.hpp
  140. include/cdflib.hpp
  141. include/cigar.hpp
  142. include/convert.h
  143. include/disorder.h
  144. include/filevercmp.h
  145. include/gpatInfo.hpp
  146. include/join.h
  147. include/makeUnique.h
  148. include/mt19937ar.h
  149. include/multichoose.h
  150. include/multipermute.h
  151. include/murmur3.hpp
  152. include/pdflib.hpp
  153. include/rkmh.hpp
  154. include/rnglib.hpp
  155. include/split.h
  156. include/ssw.hpp
  157. include/ssw_cpp.hpp
  158. include/var.hpp
  159. include/vcf-c-api.h
  160. include/vec128int.h
  161. include/veclib_types.h
  162. lib/libvcflib.a
  163. @comment lib/libzig.a
  164. lib/pyvcflib.cpython-39.so
  165. share/man/man1/abba-baba.1.gz
  166. share/man/man1/bFst.1.gz
  167. share/man/man1/dumpContigsFromHeader.1.gz
  168. share/man/man1/genotypeSummary.1.gz
  169. share/man/man1/hapLrt.1.gz
  170. share/man/man1/iHS.1.gz
  171. share/man/man1/meltEHH.1.gz
  172. share/man/man1/normalize-iHS.1.gz
  173. share/man/man1/pFst.1.gz
  174. share/man/man1/pVst.1.gz
  175. share/man/man1/permuteGPAT++.1.gz
  176. share/man/man1/permuteSmooth.1.gz
  177. share/man/man1/plotHaps.1.gz
  178. share/man/man1/popStats.1.gz
  179. share/man/man1/pyvcflib.1.gz
  180. share/man/man1/segmentFst.1.gz
  181. share/man/man1/segmentIhs.1.gz
  182. share/man/man1/sequenceDiversity.1.gz
  183. share/man/man1/smoother.1.gz
  184. share/man/man1/vcf2dag.1.gz
  185. share/man/man1/vcf2fasta.1.gz
  186. share/man/man1/vcf2tsv.1.gz
  187. share/man/man1/vcfaddinfo.1.gz
  188. share/man/man1/vcfafpath.1.gz
  189. share/man/man1/vcfallelicprimitives.1.gz
  190. share/man/man1/vcfaltcount.1.gz
  191. share/man/man1/vcfannotate.1.gz
  192. share/man/man1/vcfannotategenotypes.1.gz
  193. share/man/man1/vcfbreakmulti.1.gz
  194. share/man/man1/vcfcat.1.gz
  195. share/man/man1/vcfcheck.1.gz
  196. share/man/man1/vcfclassify.1.gz
  197. share/man/man1/vcfcleancomplex.1.gz
  198. share/man/man1/vcfcombine.1.gz
  199. share/man/man1/vcfcommonsamples.1.gz
  200. share/man/man1/vcfcountalleles.1.gz
  201. share/man/man1/vcfcreatemulti.1.gz
  202. share/man/man1/vcfdistance.1.gz
  203. share/man/man1/vcfecho.1.gz
  204. share/man/man1/vcfentropy.1.gz
  205. share/man/man1/vcfevenregions.1.gz
  206. share/man/man1/vcffilter.1.gz
  207. share/man/man1/vcffixup.1.gz
  208. share/man/man1/vcfflatten.1.gz
  209. share/man/man1/vcfgeno2alleles.1.gz
  210. share/man/man1/vcfgeno2haplo.1.gz
  211. share/man/man1/vcfgenosamplenames.1.gz
  212. share/man/man1/vcfgenosummarize.1.gz
  213. share/man/man1/vcfgenotypecompare.1.gz
  214. share/man/man1/vcfgenotypes.1.gz
  215. share/man/man1/vcfglbound.1.gz
  216. share/man/man1/vcfglxgt.1.gz
  217. share/man/man1/vcfhetcount.1.gz
  218. share/man/man1/vcfhethomratio.1.gz
  219. share/man/man1/vcfindex.1.gz
  220. share/man/man1/vcfinfo2qual.1.gz
  221. share/man/man1/vcfinfosummarize.1.gz
  222. share/man/man1/vcfintersect.1.gz
  223. share/man/man1/vcfkeepgeno.1.gz
  224. share/man/man1/vcfkeepinfo.1.gz
  225. share/man/man1/vcfkeepsamples.1.gz
  226. share/man/man1/vcfld.1.gz
  227. share/man/man1/vcfleftalign.1.gz
  228. share/man/man1/vcflength.1.gz
  229. share/man/man1/vcflib-api.1.gz
  230. share/man/man1/vcflib.1.gz
  231. share/man/man1/vcfnulldotslashdot.1.gz
  232. share/man/man1/vcfnullgenofields.1.gz
  233. share/man/man1/vcfnumalt.1.gz
  234. share/man/man1/vcfoverlay.1.gz
  235. share/man/man1/vcfparsealts.1.gz
  236. share/man/man1/vcfprimers.1.gz
  237. share/man/man1/vcfqual2info.1.gz
  238. share/man/man1/vcfrandom.1.gz
  239. share/man/man1/vcfrandomsample.1.gz
  240. share/man/man1/vcfremap.1.gz
  241. share/man/man1/vcfremoveaberrantgenotypes.1.gz
  242. share/man/man1/vcfremovesamples.1.gz
  243. share/man/man1/vcfroc.1.gz
  244. share/man/man1/vcfsample2info.1.gz
  245. share/man/man1/vcfsamplediff.1.gz
  246. share/man/man1/vcfsamplenames.1.gz
  247. share/man/man1/vcfsitesummarize.1.gz
  248. share/man/man1/vcfstats.1.gz
  249. share/man/man1/vcfstreamsort.1.gz
  250. share/man/man1/vcfuniq.1.gz
  251. share/man/man1/vcfuniqalleles.1.gz
  252. share/man/man1/vcfwave.1.gz
  253. share/man/man1/wcFst.1.gz
  254. @owner
  255. @group
  256. @mode
Collapse this list.
Dependency lines:
  • vcflib>0:biology/vcflib
Conflicts:
CONFLICTS_INSTALL:
  • filevercmp
  • libdisorder
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/vcflib/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/vcflib
  • pkg install vcflib
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: vcflib
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: armv6 armv7
distinfo:
TIMESTAMP = 1675907454 SHA256 (ekg-vcflib-v1.0.7_GH0.tar.gz) = 37ddf471c5fec2c7fa5d1c2c2e80b3e9d30e401ee3b82156f6ae994652950a38 SIZE (ekg-vcflib-v1.0.7_GH0.tar.gz) = 23546536

Expand this list (18 items)

Collapse this list.

SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059 SIZE (ekg-filevercmp-df20dcc_GH0.tar.gz) = 3113 SHA256 (ekg-fsom-56695e1_GH0.tar.gz) = d1cc62bf72a75b74149336799fcbe237eaa662161fb0cfdac5ba6d5825248180 SIZE (ekg-fsom-56695e1_GH0.tar.gz) = 9767 SHA256 (ekg-intervaltree-aa59377_GH0.tar.gz) = 8d42eee645bcb196da03077c6f567f61529add3a581bb98d85f5c9cfe4b50774 SIZE (ekg-intervaltree-aa59377_GH0.tar.gz) = 72545 SHA256 (edawson-libVCFH-44b6580_GH0.tar.gz) = 3c90a6c5f1fbe88bedb4a0dcdc1e55dfa51c58f2acd9b31bceead226ab84785c SIZE (edawson-libVCFH-44b6580_GH0.tar.gz) = 2956 SHA256 (ekg-multichoose-e1f94ae_GH0.tar.gz) = 78ffaa36b6f82685230a3d263c9b556ab55a97196036764473f2b1ee66997ca8 SIZE (ekg-multichoose-e1f94ae_GH0.tar.gz) = 6585 SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867 SHA256 (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962

Collapse this list.


Packages (timestamps in pop-ups are UTC):
vcflib
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.0.7_11.0.7_1--1.0.7_1---
FreeBSD:13:quarterly1.0.71.0.7--1.0.7-1.0.71.0.7
FreeBSD:14:latest1.0.7_11.0.7_11.0.3_1-1.0.7_1--1.0.7
FreeBSD:14:quarterly1.0.71.0.7--1.0.7-1.0.71.0.7
FreeBSD:15:latest1.0.7_11.0.7_1n/a-n/a-1.0.71.0.7
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. pybind11>0 : devel/pybind11
  2. cmake : devel/cmake-core
  3. gmake>=4.3 : devel/gmake
  4. pkgconf>=1.3.0_1 : devel/pkgconf
  5. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
Library dependencies:
  1. libhts.so : biology/htslib
  2. libcurl.so : ftp/curl
  3. libwfa2.so : biology/wfa2-lib
This port is required by:
for Run
  1. biology/ddocent

Configuration Options:
===> The following configuration options are available for vcflib-1.0.7_1: ZIG=off: Include Zig language support ===> Use 'make config' to modify these settings
Options name:
biology_vcflib
USES:
cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.7?dummy=/
Collapse this list.

Number of commits found: 24

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.0.7_1
02 Mar 2024 20:35:56
commit hash: 44f5f66effbcd759bce03421231713a9b7c0e170commit hash: 44f5f66effbcd759bce03421231713a9b7c0e170commit hash: 44f5f66effbcd759bce03421231713a9b7c0e170commit hash: 44f5f66effbcd759bce03421231713a9b7c0e170 files touched by this commit
Nuno Teixeira (eduardo) search for other commits by this committer
biology/vcflib: Move man pages to share/man

Approved by:	portmgr (blanket)
1.0.7
01 Jan 2024 05:37:19
commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3 files touched by this commit
Jan Beich (jbeich) search for other commits by this committer
Author: Nathan Fisher
lang/zig: update to 0.11.0

Changes:	https://ziglang.org/download/0.11.0/release-notes.html
PR:		273124
Approved by:	dch (maintainer)
1.0.7
30 Jul 2023 22:59:09
commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3 files touched by this commit
Robert Clausecker (fuz) search for other commits by this committer
biology/vcflib: not for armv6/7

Requires OpenMP which is not supported on armv6/armv7.

Approved by:	portmgr (build fix blanket)
MFH:		2023Q3
1.0.7
09 Feb 2023 15:35:32
commit hash: 5fee60fc3c922a534c2200372385de54590122a9commit hash: 5fee60fc3c922a534c2200372385de54590122a9commit hash: 5fee60fc3c922a534c2200372385de54590122a9commit hash: 5fee60fc3c922a534c2200372385de54590122a9 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.7

Fixes regression in 1.0.6

Made Zig language support a default off option
Zig is experimental and problematic

Reported by:    portscout
1.0.6_1
31 Jan 2023 16:25:33
commit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1fcommit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1fcommit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1fcommit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1f files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Unbreak build on aarch64, probably others

Patch out hard-coded -march=native, not supported by clang aarch64
1.0.6
30 Jan 2023 22:05:19
commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.6

A few minor upstream fixes
Unbundle WFA2-lib, which may be useful outside vcflib
Update some submodules to latest commit (no recent releases available)
1.0.5_2
26 Jan 2023 14:14:07
commit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534ccommit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534ccommit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534ccommit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534c files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Patch in time.h for struct timespec

Forgot to add patch file to repo during upgrade
Needed on 12.3-RELEASE
1.0.5_1
23 Jan 2023 23:51:41
commit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55dcommit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55dcommit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55dcommit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55d files touched by this commit
Jan Beich (jbeich) search for other commits by this committer
lang/zig: rebuild consumers after 91552559ae79

Propagate standard library and miscompilation fixes into binary packages.
1.0.5
22 Jan 2023 17:13:14
commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.5

Numerous new features and enhancements

Changes:    https://github.com/vcflib/vcflib/tags

Reported by:    portscout
1.0.3_1
06 Jan 2023 01:29:53
commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Bump PORTREVISION for biology/htslib update
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.0.3
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.0.3
29 Jun 2022 14:53:54
commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS_INSTALL in benchmarks and biology

Approved by:	portmgr (implicit)
1.0.3
06 Feb 2022 18:36:07
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
1.0.3
28 Jan 2022 00:09:13
commit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3bcommit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3bcommit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3bcommit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3b files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.3

Several new commands
A few bug fixes and enhancements

Changes:        https://github.com/vcflib/vcflib/tags

Reported by:    portscout
1.0.2
16 Dec 2021 21:49:25
commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/vcflib: unbreak on riscv64
1.0.2
04 Nov 2021 14:23:17
commit hash: e02229c22ccbe188c405dcb5d81d14e5c809411ecommit hash: e02229c22ccbe188c405dcb5d81d14e5c809411ecommit hash: e02229c22ccbe188c405dcb5d81d14e5c809411ecommit hash: e02229c22ccbe188c405dcb5d81d14e5c809411e files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.2

Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others

Changes:        https://github.com/vcflib/vcflib/tags

PR:             259622
Reported by:    pkubaj
1.0.0.r1.130_1
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
1.0.0.r1.130_1
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.0.0.r1.130_1
28 Mar 2021 16:39:24
Revision:569399Original commit files touched by this commit
pkubaj search for other commits by this committer
biology/vcflib: fix build on powerpc64le

Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared
identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
    __builtin_ia32_emms();
1.0.0.r1.130_1
02 Jan 2021 01:46:09
Revision:559904Original commit files touched by this commit
linimon search for other commits by this committer
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
1.0.0.r1.130_1
03 Aug 2020 17:40:04
Revision:544090Original commit files touched by this commit
jwb search for other commits by this committer
biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
1.0.0.r1.130
22 Jun 2018 00:03:08
Revision:473010Original commit files touched by this commit
linimon search for other commits by this committer
Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
1.0.0.r1.130
17 Apr 2018 03:11:39
Revision:467553Original commit files touched by this commit
jwb search for other commits by this committer
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15109

Number of commits found: 24