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Port details
ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
2012.06.20_1 biology on this many watch lists=2 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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Port Added: 29 Oct 2000 10:56:24
License: not specified in port
The NCBI (National Center for Biotechnology Information) development toolkit,
containing various libraries needed by NCBI applications, as well as a
software suite containing, amongst other things, NCBI BLAST 2.0.

From the README:

  The NCBI Software Development Toolkit was developed for the production and
  distribution of GenBank, Entrez, BLAST, and related services by NCBI. We
  make it freely available to the public without restriction to facilitate
  the use of NCBI by the scientific community. However, please understand
  that while we feel we have done a high quality job, this is not commercial
  software.

  The documentation lags considerably behind the software and we must make
  any changes required by our data production needs. Nontheless, many people
  have found it a useful and stable basis for a number of tools and
  applications.

WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (813 items)
  1. bin/Nentrez
  2. bin/Psequin
  3. bin/asn2ff
  4. bin/asn2gb
  5. bin/asn2idx
  6. bin/asn2xml
  7. bin/asndhuff
  8. bin/asntool
  9. bin/bl2seq
  10. bin/blastall
  11. bin/blastcl3
  12. bin/blastclust
  13. bin/blastpgp
  14. bin/cdscan
  15. bin/checksub
  16. bin/copymat
  17. bin/ddv
  18. bin/debruijn
  19. bin/demo_regexp
  20. bin/demo_regexp_grep
  21. bin/dosimple
  22. bin/entrcmd
  23. bin/entrez2
  24. bin/errhdr
  25. bin/fa2htgs
  26. bin/fastacmd
  27. bin/findspl
  28. bin/formatdb
  29. bin/formatrpsdb
  30. bin/gene2xml
  31. bin/getmesh
  32. bin/getpub
  33. bin/gil2bin
  34. bin/idfetch
  35. bin/impala
  36. bin/indexpub
  37. bin/makemat
  38. bin/makeset
  39. bin/megablast
  40. bin/ncbisort
  41. bin/rpsblast
  42. bin/sbtedit
  43. bin/seedtop
  44. bin/seqtest
  45. bin/taxblast
  46. bin/tbl2asn
  47. bin/udv
  48. bin/vecscreen
  49. include/ncbi/FSpCompat.h
  50. include/ncbi/FullPath.h
  51. include/ncbi/MoreCarbonAccessors.h
  52. include/ncbi/MoreFilesExtras.h
  53. include/ncbi/MoreFilesX.h
  54. include/ncbi/Optimization.h
  55. include/ncbi/OptimizationEnd.h
  56. include/ncbi/PubStructAsn.h
  57. include/ncbi/a2ferr.h
  58. include/ncbi/a2ferrdf.h
  59. include/ncbi/a2fstruc.h
  60. include/ncbi/aacomp.h
  61. include/ncbi/accentr.h
  62. include/ncbi/accid1.h
  63. include/ncbi/accutils.h
  64. include/ncbi/acerdapi.h
  65. include/ncbi/aceread.h
  66. include/ncbi/actutils.h
  67. include/ncbi/algorend.h
  68. include/ncbi/alignloc.h
  69. include/ncbi/alignmgr.h
  70. include/ncbi/alignmgr2.h
  71. include/ncbi/alignval.h
  72. include/ncbi/aliparse.h
  73. include/ncbi/aliread.h
  74. include/ncbi/all.h
  75. include/ncbi/allpub.h
  76. include/ncbi/apparam.h
  77. include/ncbi/asn.h
  78. include/ncbi/asn2ff.h
  79. include/ncbi/asn2ff6.h
  80. include/ncbi/asn2ffg.h
  81. include/ncbi/asn2ffp.h
  82. include/ncbi/asn2gnbi.h
  83. include/ncbi/asn2gnbk.h
  84. include/ncbi/asn2gnbp.h
  85. include/ncbi/asn2graphic.h
  86. include/ncbi/asn2graphicp.h
  87. include/ncbi/asnacces.h
  88. include/ncbi/asnalign.h
  89. include/ncbi/asnbibli.h
  90. include/ncbi/asnblock.h
  91. include/ncbi/asncode.h
  92. include/ncbi/asnent2.h
  93. include/ncbi/asnentgene.h
  94. include/ncbi/asnfdef.h
  95. include/ncbi/asnfeat.h
  96. include/ncbi/asngbseq.h
  97. include/ncbi/asngen.h
  98. include/ncbi/asnid0.h
  99. include/ncbi/asninsdseq.h
  100. include/ncbi/asnloc.h
  101. include/ncbi/asnmacro.h
  102. include/ncbi/asnmdrs.h
  103. include/ncbi/asnmedli.h
  104. include/ncbi/asnmim.h
  105. include/ncbi/asnmime.h
  106. include/ncbi/asnmla.h
  107. include/ncbi/asnmla2.h
  108. include/ncbi/asnneten.h
  109. include/ncbi/asnproj.h
  110. include/ncbi/asnprt.h
  111. include/ncbi/asnpub.h
  112. include/ncbi/asnpubme.h
  113. include/ncbi/asnres.h
  114. include/ncbi/asnseq.h
  115. include/ncbi/asnsset.h
  116. include/ncbi/asnsubmt.h
  117. include/ncbi/asntable.h
  118. include/ncbi/asntax1.h
  119. include/ncbi/asntax3.h
  120. include/ncbi/asntaxon.h
  121. include/ncbi/asntseq.h
  122. include/ncbi/asnvalid.h
  123. include/ncbi/bandalgn.h
  124. include/ncbi/binary.h
  125. include/ncbi/biosrc.h
  126. include/ncbi/blast.h
  127. include/ncbi/blast_dust.h
  128. include/ncbi/blastconcat.h
  129. include/ncbi/blastconcatdef.h
  130. include/ncbi/blastdef.h
  131. include/ncbi/blastkar.h
  132. include/ncbi/blastpat.h
  133. include/ncbi/blastpri.h
  134. include/ncbi/blfmtutl.h
  135. include/ncbi/blocks.h
  136. include/ncbi/blstspc.h
  137. include/ncbi/blstxml.h
  138. include/ncbi/bspview.h
  139. include/ncbi/bxmlobj.h
  140. include/ncbi/casn.h
  141. include/ncbi/cdconfig.h
  142. include/ncbi/cdd.h
  143. include/ncbi/cddapi.h
  144. include/ncbi/cddposutil.h
  145. include/ncbi/cddutil.h
  146. include/ncbi/cdentrez.h
  147. include/ncbi/cdnewlib.h
  148. include/ncbi/cdrgn.h
  149. include/ncbi/cdrom.h
  150. include/ncbi/cdromlib.h
  151. include/ncbi/cn3d.h
  152. include/ncbi/cn3dentr.h
  153. include/ncbi/cn3dmain.h
  154. include/ncbi/cn3dmesh.h
  155. include/ncbi/cn3dmodl.h
  156. include/ncbi/cn3dmsel.h
  157. include/ncbi/cn3dmsg.h
  158. include/ncbi/cn3dopen.h
  159. include/ncbi/cn3dsave.h
  160. include/ncbi/cn3dshim.h
  161. include/ncbi/cn3dstyl.h
  162. include/ncbi/cn3dxprt.h
  163. include/ncbi/codon.h
  164. include/ncbi/compo_heap.h
  165. include/ncbi/compo_mode_condition.h
  166. include/ncbi/composition_adjustment.h
  167. include/ncbi/composition_constants.h
  168. include/ncbi/connect/connect_export.h
  169. include/ncbi/connect/ncbi_ansi_ext.h
  170. include/ncbi/connect/ncbi_assert.h
  171. include/ncbi/connect/ncbi_base64.h
  172. include/ncbi/connect/ncbi_buffer.h
  173. include/ncbi/connect/ncbi_comm.h
  174. include/ncbi/connect/ncbi_config.h
  175. include/ncbi/connect/ncbi_connection.h
  176. include/ncbi/connect/ncbi_connector.h
  177. include/ncbi/connect/ncbi_connssl.h
  178. include/ncbi/connect/ncbi_connutil.h
  179. include/ncbi/connect/ncbi_core.h
  180. include/ncbi/connect/ncbi_core_c.h
  181. include/ncbi/connect/ncbi_dispd.h
  182. include/ncbi/connect/ncbi_file_connector.h
  183. include/ncbi/connect/ncbi_ftp_connector.h
  184. include/ncbi/connect/ncbi_gnutls.h
  185. include/ncbi/connect/ncbi_heapmgr.h
  186. include/ncbi/connect/ncbi_host_info.h
  187. include/ncbi/connect/ncbi_host_infop.h
  188. include/ncbi/connect/ncbi_http_connector.h
  189. include/ncbi/connect/ncbi_lb.h
  190. include/ncbi/connect/ncbi_lbsmd.h
  191. include/ncbi/connect/ncbi_local.h
  192. include/ncbi/connect/ncbi_memory_connector.h
  193. include/ncbi/connect/ncbi_priv.h
  194. include/ncbi/connect/ncbi_sendmail.h
  195. include/ncbi/connect/ncbi_server_info.h
  196. include/ncbi/connect/ncbi_server_infop.h
  197. include/ncbi/connect/ncbi_service.h
  198. include/ncbi/connect/ncbi_service_connector.h
  199. include/ncbi/connect/ncbi_servicep.h
  200. include/ncbi/connect/ncbi_socket.h
  201. include/ncbi/connect/ncbi_socket_connector.h
  202. include/ncbi/connect/ncbi_socket_unix.h
  203. include/ncbi/connect/ncbi_socketp.h
  204. include/ncbi/connect/ncbi_types.h
  205. include/ncbi/connect/ncbi_util.h
  206. include/ncbi/connect/ncbi_version.h
  207. include/ncbi/corematx.h
  208. include/ncbi/db_list.h
  209. include/ncbi/ddvclick.h
  210. include/ncbi/ddvcolor.h
  211. include/ncbi/ddvcreate.h
  212. include/ncbi/ddvgraph.h
  213. include/ncbi/ddvmain.h
  214. include/ncbi/ddvopen.h
  215. include/ncbi/ddvpanel.h
  216. include/ncbi/diagnost.h
  217. include/ncbi/dlogutil.h
  218. include/ncbi/document.h
  219. include/ncbi/dotmatrx.h
  220. include/ncbi/dotseq.h
  221. include/ncbi/dotviewer.h
  222. include/ncbi/drawingp.h
  223. include/ncbi/drawseq.h
  224. include/ncbi/dust.h
  225. include/ncbi/dvncode.h
  226. include/ncbi/edutil.h
  227. include/ncbi/egkludge.h
  228. include/ncbi/ent2api.h
  229. include/ncbi/entrez.h
  230. include/ncbi/entrez2.h
  231. include/ncbi/errdefn.h
  232. include/ncbi/explore.h
  233. include/ncbi/fastadl.h
  234. include/ncbi/fdlKludge.h
  235. include/ncbi/fdlobj.h
  236. include/ncbi/fea2seg.h
  237. include/ncbi/ffprint.h
  238. include/ncbi/findrepl.h
  239. include/ncbi/fstyle.h
  240. include/ncbi/fstylep.h
  241. include/ncbi/ftusrstr.h
  242. include/ncbi/gapxdrop.h
  243. include/ncbi/gather.h
  244. include/ncbi/gbfeat.h
  245. include/ncbi/gbftdef.h
  246. include/ncbi/gbparlex.h
  247. include/ncbi/gifgen.h
  248. include/ncbi/glbpic.h
  249. include/ncbi/gphdraw.h
  250. include/ncbi/gtrdraw.h
  251. include/ncbi/gxydraw.h
  252. include/ncbi/id1.h
  253. include/ncbi/id1arch.h
  254. include/ncbi/id1gen.h
  255. include/ncbi/id1map.h
  256. include/ncbi/id2.h
  257. include/ncbi/id2gen.h
  258. include/ncbi/id2map.h
  259. include/ncbi/id2sgen.h
  260. include/ncbi/image.h
  261. include/ncbi/imagelst.h
  262. include/ncbi/import.h
  263. include/ncbi/ingenext.h
  264. include/ncbi/ingengraph.h
  265. include/ncbi/ingenwin.h
  266. include/ncbi/jsavlt.h
  267. include/ncbi/jzcoll.h
  268. include/ncbi/jzmisc.h
  269. include/ncbi/layout.h
  270. include/ncbi/legend.h
  271. include/ncbi/list.h
  272. include/ncbi/lnfac.h
  273. include/ncbi/lookup.h
  274. include/ncbi/lsqfetch.h
  275. include/ncbi/macroapi.h
  276. include/ncbi/macrodlg.h
  277. include/ncbi/mapcn3d.h
  278. include/ncbi/mapgene.h
  279. include/ncbi/mapmime.h
  280. include/ncbi/mapmla.h
  281. include/ncbi/mappingp.h
  282. include/ncbi/mapproj.h
  283. include/ncbi/mappubme.h
  284. include/ncbi/maputil.h
  285. include/ncbi/matrix.h
  286. include/ncbi/matrix_frequency_data.h
  287. include/ncbi/mbalign.h
  288. include/ncbi/mblast.h
  289. include/ncbi/mconsist.h
  290. include/ncbi/mdrcherr.h
  291. include/ncbi/medarch.h
  292. include/ncbi/medutil.h
  293. include/ncbi/medview.h
  294. include/ncbi/mimapi.h
  295. include/ncbi/mkbioseq.h
  296. include/ncbi/mla2api.h
  297. include/ncbi/mlkludge.h
  298. include/ncbi/mmdb1.h
  299. include/ncbi/mmdb2.h
  300. include/ncbi/mmdb3.h
  301. include/ncbi/mmdbapi.h
  302. include/ncbi/mmdbapi1.h
  303. include/ncbi/mmdbapi2.h
  304. include/ncbi/mmdbapi3.h
  305. include/ncbi/mmdbapi4.h
  306. include/ncbi/mmdbdata.h
  307. include/ncbi/mmdblocl.h
  308. include/ncbi/motif.h
  309. include/ncbi/ncbi.h
  310. include/ncbi/ncbi_skew_guard.h
  311. include/ncbi/ncbibs.h
  312. include/ncbi/ncbidraw.h
  313. include/ncbi/ncbienv.h
  314. include/ncbi/ncbierr.h
  315. include/ncbi/ncbifile.h
  316. include/ncbi/ncbigif.h
  317. include/ncbi/ncbilang.h
  318. include/ncbi/ncbilcl.h
  319. include/ncbi/ncbimain.h
  320. include/ncbi/ncbimath.h
  321. include/ncbi/ncbimem.h
  322. include/ncbi/ncbimisc.h
  323. include/ncbi/ncbimsg.h
  324. include/ncbi/ncbinet.h
  325. include/ncbi/ncbiopt.h
  326. include/ncbi/ncbiport.h
  327. include/ncbi/ncbiprop.h
  328. include/ncbi/ncbisam.h
  329. include/ncbi/ncbisami.h
  330. include/ncbi/ncbisgml.h
  331. include/ncbi/ncbisort.h
  332. include/ncbi/ncbisrti.h
  333. include/ncbi/ncbistd.h
  334. include/ncbi/ncbistr.h
  335. include/ncbi/ncbithr.h
  336. include/ncbi/ncbitime.h
  337. include/ncbi/ncbiwin.h
  338. include/ncbi/ncbiwww.h
  339. include/ncbi/needleman.h
  340. include/ncbi/netblap3.h
  341. include/ncbi/netcnfg.h
  342. include/ncbi/netentr.h
  343. include/ncbi/netlib.h
  344. include/ncbi/netpriv.h
  345. include/ncbi/netscape.h
  346. include/ncbi/ni_error.h
  347. include/ncbi/ni_lib_.h
  348. include/ncbi/ni_types.h
  349. include/ncbi/nlm_linear_algebra.h
  350. include/ncbi/objacces.h
  351. include/ncbi/objalign.h
  352. include/ncbi/objalignloc.h
  353. include/ncbi/objall.h
  354. include/ncbi/objbibli.h
  355. include/ncbi/objblock.h
  356. include/ncbi/objblst3.h
  357. include/ncbi/objcdd.h
  358. include/ncbi/objcn3d.h
  359. include/ncbi/objcode.h
  360. include/ncbi/objegkludge.h
  361. include/ncbi/objent2.h
  362. include/ncbi/objentgene.h
  363. include/ncbi/objentr.h
  364. include/ncbi/objfdef.h
  365. include/ncbi/objfeat.h
  366. include/ncbi/objgbseq.h
  367. include/ncbi/objgen.h
  368. include/ncbi/objinsdseq.h
  369. include/ncbi/objloc.h
  370. include/ncbi/objmacro.h
  371. include/ncbi/objmdrs.h
  372. include/ncbi/objmedli.h
  373. include/ncbi/objmgr.h
  374. include/ncbi/objmim.h
  375. include/ncbi/objmime.h
  376. include/ncbi/objmla.h
  377. include/ncbi/objmla2.h
  378. include/ncbi/objmmdb1.h
  379. include/ncbi/objmmdb2.h
  380. include/ncbi/objmmdb3.h
  381. include/ncbi/objneten.h
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  387. include/ncbi/objres.h
  388. include/ncbi/objscoremat.h
  389. include/ncbi/objseq.h
  390. include/ncbi/objspell.h
  391. include/ncbi/objsset.h
  392. include/ncbi/objsub.h
  393. include/ncbi/objtable.h
  394. include/ncbi/objtax1.h
  395. include/ncbi/objtax3.h
  396. include/ncbi/objtseq.h
  397. include/ncbi/objvalid.h
  398. include/ncbi/odlbox.h
  399. include/ncbi/optimize_target_freq.h
  400. include/ncbi/panels.h
  401. include/ncbi/parsegb.h
  402. include/ncbi/pcre.h
  403. include/ncbi/pcre_config.h
  404. include/ncbi/pcre_internal.h
  405. include/ncbi/pcreposix.h
  406. include/ncbi/pdiagnos.h
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  408. include/ncbi/pictur3d.h
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  412. include/ncbi/pobutil.h
  413. include/ncbi/posit.h
  414. include/ncbi/ppict3d.h
  415. include/ncbi/profiles.h
  416. include/ncbi/prtgene.h
  417. include/ncbi/prtutil.h
  418. include/ncbi/prunebsc.h
  419. include/ncbi/pubdesc.h
  420. include/ncbi/puberr.h
  421. include/ncbi/qblastapi.h
  422. include/ncbi/readdb.h
  423. include/ncbi/redo_alignment.h
  424. include/ncbi/regex.h
  425. include/ncbi/rpsutil.h
  426. include/ncbi/saldist.h
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  428. include/ncbi/saledit.h
  429. include/ncbi/salfiles.h
  430. include/ncbi/salign.h
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  432. include/ncbi/salogif.h
  433. include/ncbi/salpacc.h
  434. include/ncbi/salpanel.h
  435. include/ncbi/salparam.h
  436. include/ncbi/salpedit.h
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  439. include/ncbi/salptool.h
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  442. include/ncbi/salstruc.h
  443. include/ncbi/salutil.h
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  445. include/ncbi/satutil.h
  446. include/ncbi/scoremat.h
  447. include/ncbi/sdisplay.h
  448. include/ncbi/sec.h
  449. include/ncbi/seed.h
  450. include/ncbi/seg.h
  451. include/ncbi/seqanal.h
  452. include/ncbi/seqcons.h
  453. include/ncbi/seqfltr.h
  454. include/ncbi/seqgraph.h
  455. include/ncbi/seqgrphx.h
  456. include/ncbi/seqmgr.h
  457. include/ncbi/seqmtrx.h
  458. include/ncbi/seqpanel.h
  459. include/ncbi/seqpcc.h
  460. include/ncbi/seqport.h
  461. include/ncbi/seqscrl.h
  462. include/ncbi/seqsplit.h
  463. include/ncbi/seqsub.h
  464. include/ncbi/sequtil.h
  465. include/ncbi/shim3d.h
  466. include/ncbi/showalignwrap.h
  467. include/ncbi/simple.h
  468. include/ncbi/simutil.h
  469. include/ncbi/smith_waterman.h
  470. include/ncbi/spell.h
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  473. include/ncbi/splutil.h
  474. include/ncbi/sqnutils.h
  475. include/ncbi/strimprt.h
  476. include/ncbi/strucapi.h
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  478. include/ncbi/subutil.h
  479. include/ncbi/suggapi.h
  480. include/ncbi/suggen.h
  481. include/ncbi/suggest.h
  482. include/ncbi/suggslp.h
  483. include/ncbi/sugmap.h
  484. include/ncbi/sugprefx.h
  485. include/ncbi/tax1map.h
  486. include/ncbi/tax3api.h
  487. include/ncbi/taxblast.h
  488. include/ncbi/taxext.h
  489. include/ncbi/taxinc.h
  490. include/ncbi/taxon1.h
  491. include/ncbi/taxuerr.h
  492. include/ncbi/taxutil.h
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  506. include/ncbi/tsprintf.h
  507. include/ncbi/txalign.h
  508. include/ncbi/txclient.h
  509. include/ncbi/txcommon.h
  510. include/ncbi/udvdef.h
  511. include/ncbi/udviewer.h
  512. include/ncbi/udvseq.h
  513. include/ncbi/undefwin.h
  514. include/ncbi/unified_pvalues.h
  515. include/ncbi/urkbias.h
  516. include/ncbi/urkcnsrt.h
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  525. include/ncbi/urkutil.h
  526. include/ncbi/urlquery.h
  527. include/ncbi/utilpars.h
  528. include/ncbi/utilpub.h
  529. include/ncbi/valapi.h
  530. include/ncbi/valdlg.h
  531. include/ncbi/valid.h
  532. include/ncbi/validatr.h
  533. include/ncbi/validerr.h
  534. include/ncbi/vast2cn3d.h
  535. include/ncbi/vast2mage.h
  536. include/ncbi/vast2pdb.h
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  539. include/ncbi/vecscnapi.h
  540. include/ncbi/vecscrn.h
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  548. include/ncbi/vibpcc.h
  549. include/ncbi/vibprocs.h
  550. include/ncbi/vibrant.h
  551. include/ncbi/vibrgb.h
  552. include/ncbi/vibtree.h
  553. include/ncbi/vibtypes.h
  554. include/ncbi/viewer.h
  555. include/ncbi/viewer3d.h
  556. include/ncbi/viewerp.h
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  558. include/ncbi/vsm.h
  559. include/ncbi/vsmfile.h
  560. include/ncbi/vsmpriv.h
  561. include/ncbi/vsmutil.h
  562. include/ncbi/wwwblast.h
  563. include/ncbi/xmlblast.h
  564. lib/ncbi/libblast.a
  565. lib/ncbi/libblastapi.a
  566. lib/ncbi/libblastcompadj.a
  567. lib/ncbi/libddvlib.a
  568. lib/ncbi/libncbi.a
  569. lib/ncbi/libncbiCacc.a
  570. lib/ncbi/libncbiNacc.a
  571. lib/ncbi/libncbiacc.a
  572. lib/ncbi/libncbicdr.a
  573. lib/ncbi/libncbicn3d.a
  574. lib/ncbi/libncbidesk.a
  575. lib/ncbi/libncbiid1.a
  576. lib/ncbi/libncbimla.a
  577. lib/ncbi/libncbimmdb.a
  578. lib/ncbi/libncbiobj.a
  579. lib/ncbi/libncbitool.a
  580. lib/ncbi/libncbitxc2.a
  581. lib/ncbi/libnetblast.a
  582. lib/ncbi/libnetcli.a
  583. lib/ncbi/libnetentr.a
  584. lib/ncbi/libregexp.a
  585. lib/ncbi/libvibgif.a
  586. lib/ncbi/libvibnet.a
  587. lib/ncbi/libvibrant.a
  588. man/man1/Psequin.1.gz
  589. man/man1/asn2ff.1.gz
  590. man/man1/asn2idx.1.gz
  591. man/man1/asn2xml.1.gz
  592. man/man1/asndhuff.1.gz
  593. man/man1/asntool.1.gz
  594. man/man1/bl2seq.1.gz
  595. man/man1/blast.1.gz
  596. man/man1/blastall.1.gz
  597. man/man1/blastcl3.1.gz
  598. man/man1/blastclust.1.gz
  599. man/man1/blastpgp.1.gz
  600. man/man1/cdscan.1.gz
  601. man/man1/checksub.1.gz
  602. man/man1/copymat.1.gz
  603. man/man1/ddv.1.gz
  604. man/man1/debruijn.1.gz
  605. man/man1/entrez2.1.gz
  606. man/man1/errhdr.1.gz
  607. man/man1/fa2htgs.1.gz
  608. man/man1/fastacmd.1.gz
  609. man/man1/findspl.1.gz
  610. man/man1/formatdb.1.gz
  611. man/man1/formatrpsdb.1.gz
  612. man/man1/getmesh.1.gz
  613. man/man1/getpub.1.gz
  614. man/man1/gil2bin.1.gz
  615. man/man1/idfetch.1.gz
  616. man/man1/impala.1.gz
  617. man/man1/indexpub.1.gz
  618. man/man1/makemat.1.gz
  619. man/man1/megablast.1.gz
  620. man/man1/rpsblast.1.gz
  621. man/man1/seedtop.1.gz
  622. man/man1/taxblast.1.gz
  623. man/man1/tbl2asn.1.gz
  624. man/man1/udv.1.gz
  625. man/man1/vecscreen.1.gz
  626. share/doc/ncbi-toolkit/FAQ.txt
  627. share/doc/ncbi-toolkit/README.asn2xml
  628. share/doc/ncbi-toolkit/README.sdk
  629. share/doc/ncbi-toolkit/access.txt
  630. share/doc/ncbi-toolkit/asn2gb.txt
  631. share/doc/ncbi-toolkit/asn2gph.txt
  632. share/doc/ncbi-toolkit/blast/bl2seq.html
  633. share/doc/ncbi-toolkit/blast/blast.html
  634. share/doc/ncbi-toolkit/blast/blastall.html
  635. share/doc/ncbi-toolkit/blast/blastclust.html
  636. share/doc/ncbi-toolkit/blast/blastdb.html
  637. share/doc/ncbi-toolkit/blast/blastftp.html
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  641. share/doc/ncbi-toolkit/blast/formatdb.html
  642. share/doc/ncbi-toolkit/blast/formatrpsdb.html
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  647. share/doc/ncbi-toolkit/blast/netblast.html
  648. share/doc/ncbi-toolkit/blast/rpsblast.html
  649. share/doc/ncbi-toolkit/blast/scoring.pdf
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  653. share/doc/ncbi-toolkit/fa2htgs/README
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  657. share/doc/ncbi-toolkit/fwd_check.sh
  658. share/doc/ncbi-toolkit/gene2xml.txt
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  667. share/doc/ncbi-toolkit/images/graphic.png
  668. share/doc/ncbi-toolkit/images/loc_page.png
  669. share/doc/ncbi-toolkit/images/logo.png
  670. share/doc/ncbi-toolkit/images/ncbi_sequin.css
  671. share/doc/ncbi-toolkit/images/net_cfg.png
  672. share/doc/ncbi-toolkit/images/nucaln.png
  673. share/doc/ncbi-toolkit/images/nucset.png
  674. share/doc/ncbi-toolkit/images/nucsing1.png
  675. share/doc/ncbi-toolkit/images/nucsing2.png
  676. share/doc/ncbi-toolkit/images/organism.png
  677. share/doc/ncbi-toolkit/images/props_pg.png
  678. share/doc/ncbi-toolkit/images/protein1.png
  679. share/doc/ncbi-toolkit/images/protein2.png
  680. share/doc/ncbi-toolkit/images/sequence.png
  681. share/doc/ncbi-toolkit/images/submit.png
  682. share/doc/ncbi-toolkit/images/update.png
  683. share/doc/ncbi-toolkit/images/validate.png
  684. share/doc/ncbi-toolkit/images/welcome.png
  685. share/doc/ncbi-toolkit/ncbixml.txt
  686. share/doc/ncbi-toolkit/sdk.doc
  687. share/doc/ncbi-toolkit/seq_install/Makefile
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  689. share/doc/ncbi-toolkit/seq_install/ftp_example.css
  690. share/doc/ncbi-toolkit/seq_install/ftp_example.xml
  691. share/doc/ncbi-toolkit/seq_install/left.GIF
  692. share/doc/ncbi-toolkit/seq_install/mac-ie.css
  693. share/doc/ncbi-toolkit/seq_install/mac-netscape.css
  694. share/doc/ncbi-toolkit/seq_install/main.xslt
  695. share/doc/ncbi-toolkit/seq_install/ncbi_sequin.css
  696. share/doc/ncbi-toolkit/seq_install/seq_download.css
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  709. share/doc/ncbi-toolkit/seq_install/seq_unix_download.css
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  711. share/doc/ncbi-toolkit/seq_install/seq_unix_download.xml
  712. share/doc/ncbi-toolkit/seq_install/seq_win_download.css
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  716. share/doc/ncbi-toolkit/seq_install/sniff.js
  717. share/doc/ncbi-toolkit/seq_install/spacer10.GIF
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  721. share/doc/ncbi-toolkit/seq_install/win-netscape.css
  722. share/doc/ncbi-toolkit/sequin.htm
  723. share/doc/ncbi-toolkit/tbl2asn.txt
  724. share/ncbi-toolkit/16SCore.nhr
  725. share/ncbi-toolkit/16SCore.nin
  726. share/ncbi-toolkit/16SCore.nsq
  727. share/ncbi-toolkit/64-matK-FINAL-aligned-DNA.fas.nhr
  728. share/ncbi-toolkit/64-matK-FINAL-aligned-DNA.fas.nin
  729. share/ncbi-toolkit/64-matK-FINAL-aligned-DNA.fas.nsq
  730. share/ncbi-toolkit/64-rbcL-FINAL-aligned-DNA.fas.nhr
  731. share/ncbi-toolkit/64-rbcL-FINAL-aligned-DNA.fas.nin
  732. share/ncbi-toolkit/64-rbcL-FINAL-aligned-DNA.fas.nsq
  733. share/ncbi-toolkit/BLOSUM45
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  736. share/ncbi-toolkit/BLOSUM80
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  738. share/ncbi-toolkit/Combined16SrRNA.nhr
  739. share/ncbi-toolkit/Combined16SrRNA.nin
  740. share/ncbi-toolkit/Combined16SrRNA.nsq
  741. share/ncbi-toolkit/Combined16SrRNA_2-12-2008.nhr
  742. share/ncbi-toolkit/Combined16SrRNA_2-12-2008.nin
  743. share/ncbi-toolkit/Combined16SrRNA_2-12-2008.nsq
  744. share/ncbi-toolkit/ContactPotential
  745. share/ncbi-toolkit/KSat.flt
  746. share/ncbi-toolkit/KSchoth.flt
  747. share/ncbi-toolkit/KSesigc.mat
  748. share/ncbi-toolkit/KSesigl.mat
  749. share/ncbi-toolkit/KSgc.flt
  750. share/ncbi-toolkit/KShopp.flt
  751. share/ncbi-toolkit/KSkyte.flt
  752. share/ncbi-toolkit/KSmtidk.mat
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  760. share/ncbi-toolkit/KSpyr.flt
  761. share/ncbi-toolkit/LSURef_93.fasta.nhr
  762. share/ncbi-toolkit/LSURef_93.fasta.nin
  763. share/ncbi-toolkit/LSURef_93.fasta.nsq
  764. share/ncbi-toolkit/PAM250
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  767. share/ncbi-toolkit/SSURef_93.fasta.nhr
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  769. share/ncbi-toolkit/SSURef_93.fasta.nsq
  770. share/ncbi-toolkit/UniVec.nhr
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  773. share/ncbi-toolkit/UniVec_Core.nhr
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  775. share/ncbi-toolkit/UniVec_Core.nsq
  776. share/ncbi-toolkit/asn2ff.prt
  777. share/ncbi-toolkit/autofix.prt
  778. share/ncbi-toolkit/blast.prt
  779. share/ncbi-toolkit/bstdt.prt
  780. share/ncbi-toolkit/bstdt.val
  781. share/ncbi-toolkit/country_lat_lon.txt
  782. share/ncbi-toolkit/ecnum_ambiguous.txt
  783. share/ncbi-toolkit/ecnum_deleted.txt
  784. share/ncbi-toolkit/ecnum_replaced.txt
  785. share/ncbi-toolkit/ecnum_specific.txt
  786. share/ncbi-toolkit/featdef.prt
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  788. share/ncbi-toolkit/gc.prt
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  791. share/ncbi-toolkit/institution_codes.txt
  792. share/ncbi-toolkit/lat_lon_country.txt
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  795. share/ncbi-toolkit/lineages.txt
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  797. share/ncbi-toolkit/ncbiendo.dat
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  799. share/ncbi-toolkit/ncbipros.dat
  800. share/ncbi-toolkit/ncbiren.dat
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  803. share/ncbi-toolkit/organelle_products.prt
  804. share/ncbi-toolkit/product_rules.prt
  805. share/ncbi-toolkit/pubkey.enc
  806. share/ncbi-toolkit/rRNA_blast.nal
  807. share/ncbi-toolkit/rRNAstrand.nal
  808. share/ncbi-toolkit/seqcode.prt
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  812. share/ncbi-toolkit/taxlist.txt
  813. share/ncbi-toolkit/validrules.prt
  814. Collapse this list.

To install the port: cd /usr/ports/biology/ncbi-toolkit/ && make install clean
To add the package: pkg install ncbi-toolkit

PKGNAME: ncbi-toolkit

distinfo:

SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c
SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. xpm.pc : x11/libXpm
Runtime dependencies:
  1. xpm.pc : x11/libXpm
Library dependencies:
  1. libpng.so : graphics/png
  2. libiconv.so : converters/libiconv
  3. libXm.so.4 : x11-toolkits/open-motif

This port is required by:

for Build * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
===> The following configuration options are available for ncbi-toolkit-2012.06.20_1:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

USES:
iconv motif

Master Sites:
  1. ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/20120620/

Number of commits found: 44

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
08 Dec 2016 16:39:11
Original commit files touched by this commit  2012.06.20_1
Revision:428135
tijl search for other commits by this committer
Remove libjpeg.so.11 compatibility link that was added in r374303 to
prevent massive PORTREVISION bumps.  Bump dependent ports that have not
been bumped since.
02 Nov 2016 22:45:14
Original commit files touched by this commit  2012.06.20
Revision:425174
mat search for other commits by this committer
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
24 Jun 2016 09:04:45
Original commit files touched by this commit  2012.06.20
Revision:417414
amdmi3 search for other commits by this committer
- Add missing dependency, fixing build
- Switch to options helpers
20 Oct 2014 07:10:48
Original commit files touched by this commit  2012.06.20
Revision:371237
bapt search for other commits by this committer
Cleanup plist
23 Mar 2014 20:50:54
Original commit files touched by this commit  2012.06.20
Revision:348888
pawel search for other commits by this committer
Add staging support
20 Sep 2013 15:55:44
Original commit files touched by this commit  2012.06.20
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
04 Sep 2013 18:06:08
Original commit files touched by this commit  2012.06.20
Revision:326307
madpilot search for other commits by this committer
- Make ports use the libc provided iconv implementation on 10-CURRENT
  after r254273
- Fix a bunch of ports to properly work after this
- Mark converters/libiconv as IGNORE for systems with iconv in libc

Reviewed by:	bapt
Approved by:	portmgr (bapt)
Discussed with:	bapt, bsam (who both contributed ideas and code)
09 Jul 2013 21:49:36
Original commit files touched by this commit  2012.06.20
Revision:322587
bapt search for other commits by this committer
Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake
14 Mar 2013 05:27:58
Original commit files touched by this commit  2012.06.20
Revision:314129
miwi search for other commits by this committer
- Update to 2012.06.20

PR:		176544
Submitted by:	Ports Fury
01 Oct 2012 14:45:17
Original commit files touched by this commit  2009.03.01_1
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
22 Oct 2011 23:50:23
Original commit files touched by this commit  2009.03.01_1
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
02 May 2011 12:41:44
Original commit files touched by this commit  2009.03.01_1
makc search for other commits by this committer
Fix build with open-motif-2.3.3

PR:             ports/154044
Submitted by:   Mikhail Tsatsenko <m.tsatsenko at gmail.com>
Exp-runs by:    pav
19 Mar 2011 12:38:54
Original commit files touched by this commit  2009.03.01
miwi search for other commits by this committer
- Get Rid MD5 support
31 Jan 2010 03:42:20
Original commit files touched by this commit  2009.03.01
pgollucci search for other commits by this committer
- use $SUB_FILES to dynamically adjust pkg-message

PR:             ports/142408
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>
Approved by:    fernan@iib.unsam.edu.ar (maintainer)
28 Mar 2009 16:59:39
Original commit files touched by this commit  2009.03.01
miwi search for other commits by this committer
- Update to 2009.03.01

PR:             133099
Submitted by:   Fernan Aguero <fernan.aguero@gmail.com>
Approved by:    maintainer
19 Apr 2008 17:56:05
Original commit files touched by this commit  2006.05.07_1
  Sanity Test Failure
miwi search for other commits by this committer
- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+

Thanks to all Helpers:
        Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
        ehaupt, nox, itetcu, flz, pav

PR:             116263
Tested on:      pointyhat
Approved by:    portmgr (pav)
19 May 2007 20:32:57
Original commit files touched by this commit  2006.05.07_1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
09 Dec 2006 07:48:18
Original commit files touched by this commit  2006.05.07
rafan search for other commits by this committer
- Respect X11BASE

Approved by:    portmgr (linimon)
06 Jun 2006 12:05:19
Original commit files touched by this commit  2006.05.07
itetcu search for other commits by this committer
Update biology/ncbi-toolkit to the latest release.
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
 blastall now uses the new engine by default, resulting
 in significant performance improvements and enabling
 query concatenation for all program types.

PR:             ports/98570
Submitted by:   maintainer
Approved by:    lawrance (mentor, implict)
22 Jan 2006 01:25:24
Original commit files touched by this commit  2005.12.06
edwin search for other commits by this committer
Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)
14 Jan 2006 19:34:43
Original commit files touched by this commit  2005.12.06
pav search for other commits by this committer
- Update to 2005.12.06

PR:             ports/91714
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
11 Oct 2005 22:33:35
Original commit files touched by this commit  2005.06.05
sem search for other commits by this committer
- Update to 20050605

PR:             ports/87266
Submitted by:   maintainer
14 Sep 2005 09:24:04
Original commit files touched by this commit  2004.10.20_1
vs search for other commits by this committer
Don't strip static libraries on installation ;)
(Unbreaks e.g. biology/nclever)
20 Mar 2005 11:47:59
Original commit files touched by this commit  2004.10.20
pav search for other commits by this committer
- Fix man page damage I did last night

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
19 Mar 2005 21:32:13
Original commit files touched by this commit  2004.10.20
pav search for other commits by this committer
- Update to 2.2.10 from 20041020
- Transfer maintainership

PR:             ports/67735
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    old maintainer indirectly in
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html
01 Nov 2004 22:21:02
Original commit files touched by this commit  2004.06.16
pav search for other commits by this committer
- Update to 2004.06.16

Inspired by:    ports/72726
Approved by:    maintainer timeout (2 weeks)
13 Nov 2003 14:45:08
Original commit files touched by this commit  2003.04.21
trevor search for other commits by this committer
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
22 Oct 2003 09:29:55
Original commit files touched by this commit  2003.04.21
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
05 May 2003 12:24:08
Original commit files touched by this commit  2003.04.21
arved search for other commits by this committer
Update to 2003.04.21

PR:             51709
Submitted by:   Tony Maher <tonymaher@optushome.com.au>
21 Feb 2003 11:01:38
Original commit files touched by this commit  2002.04.26
knu search for other commits by this committer
De-pkg-comment.
21 Sep 2002 14:56:18
Original commit files touched by this commit  2002.04.26
ijliao search for other commits by this committer
add forgotten "USE_REINPLACE=yes"

Submitted by:   maintainer
21 Sep 2002 06:59:28
Original commit files touched by this commit  2002.04.26
ijliao search for other commits by this committer
upgrade to 20020426

PR:             39357
Submitted by:   maintainer
08 Jun 2002 00:40:10
Original commit files touched by this commit  2001.12.20
petef search for other commits by this committer
Correct MASTER_SITES.

PR:             39016
Submitted by:   maintainer
22 Feb 2002 07:57:07
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pat search for other commits by this committer
Update to 2001.12.20    
19 Sep 2001 14:03:18
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wjv search for other commits by this committer
- Add installation of include files   - Bump PORTREVISION    
06 Aug 2001 11:50:02
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wjv search for other commits by this committer
Update maintainer's email address.    
10 Jul 2001 17:35:08
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fenner search for other commits by this committer
Update Tony Maher's email address.    
20 Jun 2001 15:25:55
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wjv search for other commits by this committer
Update to version 2001.04.03; add installation of some documentation.    
18 Dec 2000 20:32:56
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demon search for other commits by this committer
Remove trailing period and package name from the pkg-comment.    
15 Nov 2000 00:54:09
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jeh search for other commits by this committer
They made changes to the "blast" program.    
07 Nov 2000 23:28:20
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asami search for other commits by this committer
Change motif to a normal dependency.  REQUIRES_MOTIF is now called   USE_MOTIF
and generates a LIB_DEPENDS to x11-toolkits/open-motif.  As   before, it implies
USE_XPM (and therefore USE_XLIB).  Motif-dummy is   removed from
PKG_IGNORE_DEPENDS, whose sole resident is now XFree86-3.    
03 Nov 2000 13:23:15
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jeh search for other commits by this committer
Yes.  They did re-roll this version, it is legit.   They donot version the dist,
but store them in versioned dir.  Update    Makefile to handle that.   Update
CHECKSUM    
02 Nov 2000 11:25:50
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jeh search for other commits by this committer
Updated to new version.  That is the pits, the day after it becomes   a port
they release a new version.  This is a new version, w/o a number.    
29 Oct 2000 13:56:24
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jeh search for other commits by this committer
New Port: biology/ncbi-toolkit   National Center for Biotechnology Information
(NCBI) Development Toolkit.    

Number of commits found: 44

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