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Port details
garlic Molecular viewer, editor, and visualization program
1.6_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
Maintainer: maho@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Jul 2003 06:41:18
License: not specified in port
Free, open source molecular viewer and editor for
protein structure, DNA structure, PDB, molecular rendering,
biological macromolecule.
Atoms may be drawn as spheres of different sizes.
Bonds may be drawn as cylindrical sticks, conical sticks or
as curved surfaces.
Five types of slab are available: planar, spherical,
semi-spherical, cylindrical and semi-cylindrical.
The slab position and thickness are visible in a small window.
Atomic bonds as well as atoms are treated as independent drawable objects.
and more.

WWW: http://www.zucic.org/garlic/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (302 items)
  1. bin/garlic
  2. share/garlic/.garlicrc
  3. share/garlic/residues.pdb
  4. share/doc/garlic/README
  5. share/doc/garlic/ascorbic_acid1.jpg
  6. share/doc/garlic/ascorbic_acid2.jpg
  7. share/doc/garlic/bold_statement.html
  8. share/doc/garlic/bugfixes/favicon.ico
  9. share/doc/garlic/bugfixes/garlic.gif
  10. share/doc/garlic/bugfixes/index.html
  11. share/doc/garlic/changes/favicon.ico
  12. share/doc/garlic/changes/garlic.gif
  13. share/doc/garlic/changes/index.html
  14. share/doc/garlic/commands/aacodes.gif
  15. share/doc/garlic/commands/add.html
  16. share/doc/garlic/commands/ang.html
  17. share/doc/garlic/commands/ato.html
  18. share/doc/garlic/commands/atoms.gif
  19. share/doc/garlic/commands/bac.html
  20. share/doc/garlic/commands/bal.html
  21. share/doc/garlic/commands/balls_and_sticks.gif
  22. share/doc/garlic/commands/bg.html
  23. share/doc/garlic/commands/blu.html
  24. share/doc/garlic/commands/blur1.gif
  25. share/doc/garlic/commands/blur2.gif
  26. share/doc/garlic/commands/blur3.gif
  27. share/doc/garlic/commands/blur4.gif
  28. share/doc/garlic/commands/blur5.gif
  29. share/doc/garlic/commands/blur6.gif
  30. share/doc/garlic/commands/blur7.gif
  31. share/doc/garlic/commands/blur8.gif
  32. share/doc/garlic/commands/bon.html
  33. share/doc/garlic/commands/bonds.gif
  34. share/doc/garlic/commands/cat.html
  35. share/doc/garlic/commands/cen.html
  36. share/doc/garlic/commands/chi_angles.gif
  37. share/doc/garlic/commands/col.html
  38. share/doc/garlic/commands/colors.png
  39. share/doc/garlic/commands/com.html
  40. share/doc/garlic/commands/cre.html
  41. share/doc/garlic/commands/dihedrals.html
  42. share/doc/garlic/commands/dis.html
  43. share/doc/garlic/commands/doc.html
  44. share/doc/garlic/commands/dock1.jpg
  45. share/doc/garlic/commands/dock2.jpg
  46. share/doc/garlic/commands/dum.html
  47. share/doc/garlic/commands/dummy_atoms.html
  48. share/doc/garlic/commands/edi.html
  49. share/doc/garlic/commands/eis_oct.gif
  50. share/doc/garlic/commands/exe.html
  51. share/doc/garlic/commands/exi.html
  52. share/doc/garlic/commands/fad.html
  53. share/doc/garlic/commands/favicon.ico
  54. share/doc/garlic/commands/fg.html
  55. share/doc/garlic/commands/fon.html
  56. share/doc/garlic/commands/garlic.gif
  57. share/doc/garlic/commands/generic_hint.gif
  58. share/doc/garlic/commands/gly_hint.gif
  59. share/doc/garlic/commands/gro.html
  60. share/doc/garlic/commands/hid.html
  61. share/doc/garlic/commands/hyb.html
  62. share/doc/garlic/commands/id.gif
  63. share/doc/garlic/commands/ign.html
  64. share/doc/garlic/commands/index.html
  65. share/doc/garlic/commands/insert
  66. share/doc/garlic/commands/kd_eis.gif
  67. share/doc/garlic/commands/kd_oct.gif
  68. share/doc/garlic/commands/lab.html
  69. share/doc/garlic/commands/large_probe.gif
  70. share/doc/garlic/commands/legend.gif
  71. share/doc/garlic/commands/loa.html
  72. share/doc/garlic/commands/log.html
  73. share/doc/garlic/commands/mem.html
  74. share/doc/garlic/commands/mon.html
  75. share/doc/garlic/commands/mov.html
  76. share/doc/garlic/commands/nei.html
  77. share/doc/garlic/commands/neighbor.gif
  78. share/doc/garlic/commands/omega_hint.gif
  79. share/doc/garlic/commands/papain1.jpg
  80. share/doc/garlic/commands/papain2.jpg
  81. share/doc/garlic/commands/pat.html
  82. share/doc/garlic/commands/patterns.gif
  83. share/doc/garlic/commands/pau.html
  84. share/doc/garlic/commands/phipsi.gif
  85. share/doc/garlic/commands/pla.html
  86. share/doc/garlic/commands/plane1.jpg
  87. share/doc/garlic/commands/plane2.jpg
  88. share/doc/garlic/commands/plane3.jpg
  89. share/doc/garlic/commands/plo.html
  90. share/doc/garlic/commands/plot1.gif
  91. share/doc/garlic/commands/plot2.gif
  92. share/doc/garlic/commands/plot3.gif
  93. share/doc/garlic/commands/plot_eq1.gif
  94. share/doc/garlic/commands/plot_eq2.gif
  95. share/doc/garlic/commands/pos.html
  96. share/doc/garlic/commands/prepro_hint.gif
  97. share/doc/garlic/commands/pro.html
  98. share/doc/garlic/commands/pro_hint.gif
  99. share/doc/garlic/commands/probes.gif
  100. share/doc/garlic/commands/rad.html
  101. share/doc/garlic/commands/ram.html
  102. share/doc/garlic/commands/ramacont.gif
  103. share/doc/garlic/commands/ramaplot.gif
  104. share/doc/garlic/commands/ref.html
  105. share/doc/garlic/commands/ref_off.gif
  106. share/doc/garlic/commands/reg.html
  107. share/doc/garlic/commands/rep.html
  108. share/doc/garlic/commands/res.html
  109. share/doc/garlic/commands/residues.html
  110. share/doc/garlic/commands/rot.html
  111. share/doc/garlic/commands/sav.html
  112. share/doc/garlic/commands/sca.html
  113. share/doc/garlic/commands/schemes.jpg
  114. share/doc/garlic/commands/seahorse.gif
  115. share/doc/garlic/commands/sel.html
  116. share/doc/garlic/commands/seq.html
  117. share/doc/garlic/commands/set.html
  118. share/doc/garlic/commands/sho.html
  119. share/doc/garlic/commands/sla.html
  120. share/doc/garlic/commands/small_probe.gif
  121. share/doc/garlic/commands/squid.gif
  122. share/doc/garlic/commands/ssb.html
  123. share/doc/garlic/commands/ste.html
  124. share/doc/garlic/commands/stefin1.jpg
  125. share/doc/garlic/commands/stefin2.jpg
  126. share/doc/garlic/commands/sti.html
  127. share/doc/garlic/commands/str.gif
  128. share/doc/garlic/commands/str.html
  129. share/doc/garlic/commands/substmat.gif
  130. share/doc/garlic/commands/tag.html
  131. share/doc/garlic/commands/tbg.html
  132. share/doc/garlic/commands/tfg.html
  133. share/doc/garlic/commands/tit.html
  134. share/doc/garlic/commands/tra.html
  135. share/doc/garlic/commands/ven.html
  136. share/doc/garlic/commands/venn.gif
  137. share/doc/garlic/commands/whe.html
  138. share/doc/garlic/commands/wheel.gif
  139. share/doc/garlic/commands/win.html
  140. share/doc/garlic/competition/garlic.gif
  141. share/doc/garlic/competition/index.html
  142. share/doc/garlic/config/.garlicrc
  143. share/doc/garlic/config/favicon.ico
  144. share/doc/garlic/config/garlic.gif
  145. share/doc/garlic/config/important_files.html
  146. share/doc/garlic/config/index.html
  147. share/doc/garlic/controls/favicon.ico
  148. share/doc/garlic/controls/funkeys.jpg
  149. share/doc/garlic/controls/garlic.gif
  150. share/doc/garlic/controls/index.html
  151. share/doc/garlic/controls/modkeys.jpg
  152. share/doc/garlic/controls/numkeys.jpg
  153. share/doc/garlic/controls/pc.gif
  154. share/doc/garlic/controls/term.gif
  155. share/doc/garlic/cookbook/garlic.gif
  156. share/doc/garlic/cookbook/garlic_recipe1.html
  157. share/doc/garlic/cookbook/index.html
  158. share/doc/garlic/data/favicon.ico
  159. share/doc/garlic/data/garlic.gif
  160. share/doc/garlic/data/index.html
  161. share/doc/garlic/demo1.png
  162. share/doc/garlic/demo2.png
  163. share/doc/garlic/docs.html
  164. share/doc/garlic/download/favicon.ico
  165. share/doc/garlic/download/garlic.gif
  166. share/doc/garlic/download/index.html
  167. share/doc/garlic/favicon.ico
  168. share/doc/garlic/fdl.html
  169. share/doc/garlic/features/favicon.ico
  170. share/doc/garlic/features/garlic.gif
  171. share/doc/garlic/features/index.html
  172. share/doc/garlic/future-docs.html
  173. share/doc/garlic/gallery/favicon.ico
  174. share/doc/garlic/gallery/garlic.gif
  175. share/doc/garlic/gallery/index.html
  176. share/doc/garlic/gallery/small1.png
  177. share/doc/garlic/gallery/small10.png
  178. share/doc/garlic/gallery/small11.png
  179. share/doc/garlic/gallery/small12.png
  180. share/doc/garlic/gallery/small2.png
  181. share/doc/garlic/gallery/small3.png
  182. share/doc/garlic/gallery/small4.png
  183. share/doc/garlic/gallery/small5.png
  184. share/doc/garlic/gallery/small6.png
  185. share/doc/garlic/gallery/small7.png
  186. share/doc/garlic/gallery/small8.png
  187. share/doc/garlic/gallery/small9.png
  188. share/doc/garlic/garlic.gif
  189. share/doc/garlic/happy.gif
  190. share/doc/garlic/index.html
  191. share/doc/garlic/install/favicon.ico
  192. share/doc/garlic/install/garlic.gif
  193. share/doc/garlic/install/index.html
  194. share/doc/garlic/install/macosx.html
  195. share/doc/garlic/install/mol_path.html
  196. share/doc/garlic/install/octane.html
  197. share/doc/garlic/install/rs6000.html
  198. share/doc/garlic/license/favicon.ico
  199. share/doc/garlic/license/garlic.gif
  200. share/doc/garlic/license/index.html
  201. share/doc/garlic/monster.gif
  202. share/doc/garlic/mouse/.xvpics/outcomp.gif
  203. share/doc/garlic/mouse/.xvpics/outplot.gif
  204. share/doc/garlic/mouse/.xvpics/outrama.gif
  205. share/doc/garlic/mouse/.xvpics/outstr.gif
  206. share/doc/garlic/mouse/favicon.ico
  207. share/doc/garlic/mouse/garlic.gif
  208. share/doc/garlic/mouse/index.html
  209. share/doc/garlic/mouse/neighbor.gif
  210. share/doc/garlic/mouse/outcomp.gif
  211. share/doc/garlic/mouse/outplot.gif
  212. share/doc/garlic/mouse/outrama.gif
  213. share/doc/garlic/mouse/outstr.gif
  214. share/doc/garlic/options/favicon.ico
  215. share/doc/garlic/options/garlic.gif
  216. share/doc/garlic/options/index.html
  217. share/doc/garlic/precompiled_packages/garlic.gif
  218. share/doc/garlic/precompiled_packages/index.html
  219. share/doc/garlic/refcard/favicon.ico
  220. share/doc/garlic/refcard/garlic.gif
  221. share/doc/garlic/refcard/index.html
  222. share/doc/garlic/refcard/refcard.html
  223. share/doc/garlic/scripts/atoms.script
  224. share/doc/garlic/scripts/bonds.script
  225. share/doc/garlic/scripts/colors.script
  226. share/doc/garlic/scripts/favicon.ico
  227. share/doc/garlic/scripts/garlic.gif
  228. share/doc/garlic/scripts/probes.script
  229. share/doc/garlic/support/favicon.ico
  230. share/doc/garlic/support/garlic.gif
  231. share/doc/garlic/support/index.html
  232. share/doc/garlic/techinfo/favicon.ico
  233. share/doc/garlic/techinfo/garlic.gif
  234. share/doc/garlic/techinfo/index.html
  235. share/doc/garlic/tolower.script
  236. share/doc/garlic/tutorial/favicon.ico
  237. share/doc/garlic/tutorial/garlic.gif
  238. share/doc/garlic/tutorial/index.html
  239. share/doc/garlic/tutorial/lesson1.html
  240. share/doc/garlic/tutorial/lesson10.html
  241. share/doc/garlic/tutorial/lesson11.html
  242. share/doc/garlic/tutorial/lesson12.html
  243. share/doc/garlic/tutorial/lesson2.html
  244. share/doc/garlic/tutorial/lesson3.html
  245. share/doc/garlic/tutorial/lesson4.html
  246. share/doc/garlic/tutorial/lesson5.html
  247. share/doc/garlic/tutorial/lesson6.html
  248. share/doc/garlic/tutorial/lesson7.html
  249. share/doc/garlic/tutorial/lesson8.html
  250. share/doc/garlic/tutorial/lesson9.html
  251. share/doc/garlic/tutorial/script1.html
  252. share/doc/garlic/tutorial/script2.html
  253. share/doc/garlic/tutorial/script3.html
  254. share/doc/garlic/tutorial/script4.html
  255. share/doc/garlic/tutorial/window.gif
  256. share/doc/garlic/versions.html
  257. share/doc/garlic/whatis/favicon.ico
  258. share/doc/garlic/whatis/garlic.gif
  259. share/doc/garlic/whatis/index.html
  260. share/examples/garlic/adrenaline.pdb
  261. share/examples/garlic/22porins.script
  262. share/examples/garlic/backup-hyd.script
  263. share/examples/garlic/patt.script
  264. share/examples/garlic/18-porins.script
  265. share/examples/garlic/18porins2.script
  266. share/examples/garlic/1mal.script
  267. share/examples/garlic/2fcp.script
  268. share/examples/garlic/2omf.script
  269. share/examples/garlic/2por.script
  270. share/examples/garlic/adrenalin.pdb
  271. share/examples/garlic/arrow.pdb
  272. share/examples/garlic/ascorbic-acid.pdb
  273. share/examples/garlic/atoms.script
  274. share/examples/garlic/barrel.script
  275. share/examples/garlic/bonds.script
  276. share/examples/garlic/borneol.pdb
  277. share/examples/garlic/box.pdb
  278. share/examples/garlic/ccacaa.script
  279. share/examples/garlic/colors.script
  280. share/examples/garlic/dance.script
  281. share/examples/garlic/gallery.script
  282. share/examples/garlic/geo.script
  283. share/examples/garlic/hyb.script
  284. share/examples/garlic/many-proteins.script
  285. share/examples/garlic/patterns.script
  286. share/examples/garlic/patterns2.script
  287. share/examples/garlic/patterns3.script
  288. share/examples/garlic/phe.pdb
  289. share/examples/garlic/porins.script
  290. share/examples/garlic/porins2.script
  291. share/examples/garlic/porins3.script
  292. share/examples/garlic/porins4.script
  293. share/examples/garlic/probes.script
  294. share/examples/garlic/rainbow.script
  295. share/examples/garlic/residues.pdb
  296. share/examples/garlic/sample.script
  297. share/examples/garlic/singleatom.pdb
  298. share/examples/garlic/singlebond.pdb
  299. share/examples/garlic/test.script
  300. share/examples/garlic/trp.pdb
  301. share/examples/garlic/two-positive.script
  302. share/examples/garlic/water.pdb
  303. Collapse this list.

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

PKGNAME: garlic

distinfo:

SHA256 (garlic-1.6.tar.gz) = c99da419cb022d7120074baeaf922b3c66223fb7e78ef932e5a254fd6e0a0c8b
SIZE (garlic-1.6.tar.gz) = 559663
SHA256 (garlic-1.6-doc.tar.gz) = 747dcea06f3f771941a4d506c744212bfdc6f89053faa5bd1f14bc9274f3f2aa
SIZE (garlic-1.6-doc.tar.gz) = 1210063


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

Build dependencies:
  1. gmake : devel/gmake
  2. x11.pc : x11/libX11
Runtime dependencies:
  1. x11.pc : x11/libX11
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for garlic-1.6_1:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
     OPTIMIZED_CFLAGS=off: Use extra compiler optimizations
===> Use 'make config' to modify these settings

USES:
gmake

Master Sites:
  1. http://www.zucic.org/sources/garlic-1.6/

Number of commits found: 26

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
20 Oct 2014 07:10:48
Original commit files touched by this commit  1.6_1
Revision:371237
bapt search for other commits by this committer
Cleanup plist
17 Jul 2014 10:13:06
Original commit files touched by this commit  1.6_1
Revision:362131
marino search for other commits by this committer
biology/garlic: Stage properly to unbreak

The main problem was the WRKDIR is not within STAGEDIR.  Fix this while
moving all the directory creation steps into one.  While here
set TAR to use switches as outlined in its man page.

Also, the permission setting in stagedir is not necessary, so it's simply
been removed.
05 Jul 2014 00:15:40
Original commit files touched by this commit  1.6
Revision:360705
adamw search for other commits by this committer
Missed a NOPORTDOCS.
04 Jul 2014 23:46:53
Original commit files touched by this commit  1.6
Revision:360690
adamw search for other commits by this committer
Remove NOPORTDOCS and NOPORTEXAMPLES from unstaged ports. Stage a couple while
we're here. Remove any other references to NOPORT*.

Approved by:	portmgr (blanket for modernization)
13 Mar 2014 07:41:34
Original commit files touched by this commit  1.6
Revision:348042
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.6
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)
25 Jul 2012 06:32:08
Original commit files touched by this commit  1.6
cs search for other commits by this committer
Fix typos in COMMENT
11 May 2011 05:55:27
Original commit files touched by this commit  1.6
maho search for other commits by this committer
Update to 1.6. Web site has been moved.
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.5_2
miwi search for other commits by this committer
- Get Rid MD5 support
19 Apr 2008 17:56:05
Original commit files touched by this commit  1.5_2
  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)
24 Mar 2008 13:03:55
Original commit files touched by this commit  1.5_2
miwi search for other commits by this committer
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)
19 May 2007 20:32:57
Original commit files touched by this commit  1.5_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}.
03 May 2006 23:26:35
Original commit files touched by this commit  1.5
edwin search for other commits by this committer
Remove USE_REINPLACE from all categories starting with B
15 Mar 2006 08:10:49
Original commit files touched by this commit  1.5
maho search for other commits by this committer
Update to 1.5

Submitted by:   distfile survey by kris, fenner
22 Jan 2006 08:20:34
Original commit files touched by this commit  1.4_2
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
12 Apr 2005 03:26:57
Original commit files touched by this commit  1.4_2
obrien search for other commits by this committer
At Kris's request, back out the MACHINE_ARCH spelling correction until
after 5.4-RELEASE.
11 Apr 2005 08:04:41
Original commit files touched by this commit  1.4_2
obrien search for other commits by this committer
Assist getting more ports working on AMD64 by obeying the
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.
06 May 2004 19:49:54
Original commit files touched by this commit  1.4_2
maho search for other commits by this committer
Make portlint happy by replacing space to tab

PR:             65409
Submitted by:   trevor
18 Mar 2004 04:57:07
Original commit files touched by this commit  1.4_2
maho search for other commits by this committer
1) Silent version up without changing the version number
   very minor change in README
2) change WWW: section at pkg-descr
3) SIZEify

Submitted by:   kris via bento
22 Feb 2004 00:42:32
Original commit files touched by this commit  1.4_2
kris search for other commits by this committer
BROKEN: Checksum mismatch
04 Feb 2004 05:21:48
Original commit files touched by this commit  1.4_2
marcus search for other commits by this committer
Bump PORTREVISION on all ports that depend on gettext to aid with upgrading.

(Part 2)
28 Dec 2003 08:02:14
Original commit files touched by this commit  1.4_1
maho search for other commits by this committer
silent updates of archives:
a) program: Draw the hydrophobicity function F5
b) documentation: add very minor description not
   related FreeBSD.

1) bump portrevision
2) several clean ups for Makefile
22 Oct 2003 09:29:55
Original commit files touched by this commit  1.4
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
01 Sep 2003 22:00:01
Original commit files touched by this commit  1.4
maho search for other commits by this committer
Silent changes to the port distfile which *not* have significant
functional differences.
just changing very minor change of documatation, adding very minor
functionality and some cleanup for coding

Submitted by:   bento's log
31 Jul 2003 08:06:09
Original commit files touched by this commit  1.4
maho search for other commits by this committer
Add USE_XLIB=yes to compile

Submitted by:   kris via bento
28 Jul 2003 06:38:37
Original commit files touched by this commit  1.4
maho search for other commits by this committer
A new port garlic, free molecular viewer and editor, free molecular
visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.

Number of commits found: 26

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Latest Vulnerabilities
gitlabDec 14
torDec 14
asterisk13Dec 13
asterisk13*Dec 13
asterisk13*Dec 13
asterisk13*Dec 13
libxml2Dec 13
curl*Dec 11
linux-c7-curl*Dec 11
wiresharkDec 10
procmail*Dec 08
opensslDec 07
firefoxDec 05
firefox-esrDec 05
linux-firefoxDec 05

16 vulnerabilities affecting 82 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2017-12-14 11:01:19


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Calculated hourly:
Port count 32125
Broken 123
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Restricted 173
No CDROM 77
Vulnerable 43
Expired 10
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new 24 hours 4
new 48 hours11
new 7 days78
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