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Port details
p5-Bio-MAGETAB Data model and utility API for the MAGE-TAB format
1.31_2 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. 1.31_2Version of this port present on the latest quarterly branch.
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-07-01 09:03:56
Last Update: 2019-04-23 15:11:51
SVN Revision: 499759
Also Listed In: perl5
License: GPLv2
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (121 items)
  1. /usr/local/share/licenses/p5-Bio-MAGETAB-1.31_2/catalog.mk
  2. /usr/local/share/licenses/p5-Bio-MAGETAB-1.31_2/LICENSE
  3. /usr/local/share/licenses/p5-Bio-MAGETAB-1.31_2/GPLv2
  4. bin/deploy_magetab_db.pl
  5. bin/fix_ae_magetab.pl
  6. bin/read_magetab.pl
  7. bin/unload_magetab_namespace.pl
  8. lib/perl5/site_perl/Bio/MAGETAB.pm
  9. lib/perl5/site_perl/Bio/MAGETAB/ArrayDesign.pm
  10. lib/perl5/site_perl/Bio/MAGETAB/Assay.pm
  11. lib/perl5/site_perl/Bio/MAGETAB/BaseClass.pm
  12. lib/perl5/site_perl/Bio/MAGETAB/Comment.pm
  13. lib/perl5/site_perl/Bio/MAGETAB/CompositeElement.pm
  14. lib/perl5/site_perl/Bio/MAGETAB/Contact.pm
  15. lib/perl5/site_perl/Bio/MAGETAB/ControlledTerm.pm
  16. lib/perl5/site_perl/Bio/MAGETAB/Data.pm
  17. lib/perl5/site_perl/Bio/MAGETAB/DataAcquisition.pm
  18. lib/perl5/site_perl/Bio/MAGETAB/DataFile.pm
  19. lib/perl5/site_perl/Bio/MAGETAB/DataMatrix.pm
  20. lib/perl5/site_perl/Bio/MAGETAB/DatabaseEntry.pm
  21. lib/perl5/site_perl/Bio/MAGETAB/DesignElement.pm
  22. lib/perl5/site_perl/Bio/MAGETAB/Edge.pm
  23. lib/perl5/site_perl/Bio/MAGETAB/Event.pm
  24. lib/perl5/site_perl/Bio/MAGETAB/Extract.pm
  25. lib/perl5/site_perl/Bio/MAGETAB/Factor.pm
  26. lib/perl5/site_perl/Bio/MAGETAB/FactorValue.pm
  27. lib/perl5/site_perl/Bio/MAGETAB/Feature.pm
  28. lib/perl5/site_perl/Bio/MAGETAB/Investigation.pm
  29. lib/perl5/site_perl/Bio/MAGETAB/LabeledExtract.pm
  30. lib/perl5/site_perl/Bio/MAGETAB/Material.pm
  31. lib/perl5/site_perl/Bio/MAGETAB/MatrixColumn.pm
  32. lib/perl5/site_perl/Bio/MAGETAB/MatrixRow.pm
  33. lib/perl5/site_perl/Bio/MAGETAB/Measurement.pm
  34. lib/perl5/site_perl/Bio/MAGETAB/Node.pm
  35. lib/perl5/site_perl/Bio/MAGETAB/Normalization.pm
  36. lib/perl5/site_perl/Bio/MAGETAB/ParameterValue.pm
  37. lib/perl5/site_perl/Bio/MAGETAB/Protocol.pm
  38. lib/perl5/site_perl/Bio/MAGETAB/ProtocolApplication.pm
  39. lib/perl5/site_perl/Bio/MAGETAB/ProtocolParameter.pm
  40. lib/perl5/site_perl/Bio/MAGETAB/Publication.pm
  41. lib/perl5/site_perl/Bio/MAGETAB/Reporter.pm
  42. lib/perl5/site_perl/Bio/MAGETAB/SDRF.pm
  43. lib/perl5/site_perl/Bio/MAGETAB/SDRFRow.pm
  44. lib/perl5/site_perl/Bio/MAGETAB/Sample.pm
  45. lib/perl5/site_perl/Bio/MAGETAB/Source.pm
  46. lib/perl5/site_perl/Bio/MAGETAB/TermSource.pm
  47. lib/perl5/site_perl/Bio/MAGETAB/Types.pm
  48. lib/perl5/site_perl/Bio/MAGETAB/Util/Builder.pm
  49. lib/perl5/site_perl/Bio/MAGETAB/Util/DBLoader.pm
  50. lib/perl5/site_perl/Bio/MAGETAB/Util/Persistence.pm
  51. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader.pm
  52. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader/ADF.pm
  53. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader/DataMatrix.pm
  54. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader/IDF.pm
  55. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader/SDRF.pm
  56. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader/Tabfile.pm
  57. lib/perl5/site_perl/Bio/MAGETAB/Util/Reader/TagValueFile.pm
  58. lib/perl5/site_perl/Bio/MAGETAB/Util/RewriteAE.pm
  59. lib/perl5/site_perl/Bio/MAGETAB/Util/Writer.pm
  60. lib/perl5/site_perl/Bio/MAGETAB/Util/Writer/ADF.pm
  61. lib/perl5/site_perl/Bio/MAGETAB/Util/Writer/GraphViz.pm
  62. lib/perl5/site_perl/Bio/MAGETAB/Util/Writer/IDF.pm
  63. lib/perl5/site_perl/Bio/MAGETAB/Util/Writer/SDRF.pm
  64. lib/perl5/site_perl/Bio/MAGETAB/Util/Writer/Tabfile.pm
  65. lib/perl5/site_perl/man/man3/Bio::MAGETAB.3.gz
  66. lib/perl5/site_perl/man/man3/Bio::MAGETAB::ArrayDesign.3.gz
  67. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Assay.3.gz
  68. lib/perl5/site_perl/man/man3/Bio::MAGETAB::BaseClass.3.gz
  69. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Comment.3.gz
  70. lib/perl5/site_perl/man/man3/Bio::MAGETAB::CompositeElement.3.gz
  71. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Contact.3.gz
  72. lib/perl5/site_perl/man/man3/Bio::MAGETAB::ControlledTerm.3.gz
  73. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Data.3.gz
  74. lib/perl5/site_perl/man/man3/Bio::MAGETAB::DataAcquisition.3.gz
  75. lib/perl5/site_perl/man/man3/Bio::MAGETAB::DataFile.3.gz
  76. lib/perl5/site_perl/man/man3/Bio::MAGETAB::DataMatrix.3.gz
  77. lib/perl5/site_perl/man/man3/Bio::MAGETAB::DatabaseEntry.3.gz
  78. lib/perl5/site_perl/man/man3/Bio::MAGETAB::DesignElement.3.gz
  79. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Edge.3.gz
  80. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Event.3.gz
  81. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Extract.3.gz
  82. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Factor.3.gz
  83. lib/perl5/site_perl/man/man3/Bio::MAGETAB::FactorValue.3.gz
  84. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Feature.3.gz
  85. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Investigation.3.gz
  86. lib/perl5/site_perl/man/man3/Bio::MAGETAB::LabeledExtract.3.gz
  87. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Material.3.gz
  88. lib/perl5/site_perl/man/man3/Bio::MAGETAB::MatrixColumn.3.gz
  89. lib/perl5/site_perl/man/man3/Bio::MAGETAB::MatrixRow.3.gz
  90. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Measurement.3.gz
  91. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Node.3.gz
  92. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Normalization.3.gz
  93. lib/perl5/site_perl/man/man3/Bio::MAGETAB::ParameterValue.3.gz
  94. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Protocol.3.gz
  95. lib/perl5/site_perl/man/man3/Bio::MAGETAB::ProtocolApplication.3.gz
  96. lib/perl5/site_perl/man/man3/Bio::MAGETAB::ProtocolParameter.3.gz
  97. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Publication.3.gz
  98. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Reporter.3.gz
  99. lib/perl5/site_perl/man/man3/Bio::MAGETAB::SDRF.3.gz
  100. lib/perl5/site_perl/man/man3/Bio::MAGETAB::SDRFRow.3.gz
  101. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Sample.3.gz
  102. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Source.3.gz
  103. lib/perl5/site_perl/man/man3/Bio::MAGETAB::TermSource.3.gz
  104. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Types.3.gz
  105. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Builder.3.gz
  106. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::DBLoader.3.gz
  107. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Persistence.3.gz
  108. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader.3.gz
  109. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader::ADF.3.gz
  110. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader::DataMatrix.3.gz
  111. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader::IDF.3.gz
  112. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader::SDRF.3.gz
  113. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader::Tabfile.3.gz
  114. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Reader::TagValueFile.3.gz
  115. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::RewriteAE.3.gz
  116. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Writer.3.gz
  117. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Writer::ADF.3.gz
  118. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Writer::GraphViz.3.gz
  119. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Writer::IDF.3.gz
  120. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Writer::SDRF.3.gz
  121. lib/perl5/site_perl/man/man3/Bio::MAGETAB::Util::Writer::Tabfile.3.gz
Collapse this list.
Dependency lines:
  • p5-Bio-MAGETAB>0:biology/p5-Bio-MAGETAB
To install the port: cd /usr/ports/biology/p5-Bio-MAGETAB/ && make install clean
To add the package: pkg install p5-Bio-MAGETAB
PKGNAME: p5-Bio-MAGETAB
Flavors: there is no flavor information for this port.
distinfo:
Packages:
p5-Bio-MAGETAB
ABIlatestquarterly
FreeBSD:11:aarch641.31_11.31_2
FreeBSD:11:amd641.31_21.31_2
FreeBSD:11:armv61.31_11.31_2
FreeBSD:11:i3861.31_21.31_2
FreeBSD:11:mips1.31_11.31_2
FreeBSD:11:mips641.31_11.31_2
FreeBSD:12:aarch641.31_11.31_2
FreeBSD:12:amd641.31_21.31_2
FreeBSD:12:armv61.31_11.31_2
FreeBSD:12:armv71.31_11.31_2
FreeBSD:12:i3861.31_21.31_2
FreeBSD:12:mips1.31_11.31_2
FreeBSD:12:mips641.31_11.31_2
FreeBSD:12:powerpc64-1.31_2
FreeBSD:13:aarch641.31_2-
FreeBSD:13:amd641.31_2-
FreeBSD:13:armv61.31_2-
FreeBSD:13:armv71.31_2-
FreeBSD:13:i3861.31_2-
FreeBSD:13:mips1.31_2-
FreeBSD:13:mips641.31_2-
FreeBSD:13:powerpc641.31_2-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-Date-Manip>=5.44 : devel/p5-Date-Manip
  2. p5-DateTime>=0.43.02 : devel/p5-DateTime
  3. p5-DateTime-Format-DateManip>=0.04 : devel/p5-DateTime-Format-DateManip
  4. p5-Email-Valid>=0.179 : mail/p5-Email-Valid
  5. p5-Moose>=0.43 : devel/p5-Moose
  6. p5-MooseX-FollowPBP>=0.04 : devel/p5-MooseX-FollowPBP
  7. p5-MooseX-Types>=0.10 : devel/p5-MooseX-Types
  8. p5-Params-Coerce>=0.14 : devel/p5-Params-Coerce
  9. p5-Parse-RecDescent>=1.965001 : devel/p5-Parse-RecDescent
  10. p5-Text-CSV_XS>=0.32 : textproc/p5-Text-CSV_XS
  11. p5-URI>=1.35 : net/p5-URI
  12. perl5>=5.28.r1<5.29 : lang/perl5.28
  13. perl5>=5.28.r1<5.29 : lang/perl5.28
Runtime dependencies:
  1. p5-Date-Manip>=5.44 : devel/p5-Date-Manip
  2. p5-DateTime>=0.43.02 : devel/p5-DateTime
  3. p5-DateTime-Format-DateManip>=0.04 : devel/p5-DateTime-Format-DateManip
  4. p5-Email-Valid>=0.179 : mail/p5-Email-Valid
  5. p5-Moose>=0.43 : devel/p5-Moose
  6. p5-MooseX-FollowPBP>=0.04 : devel/p5-MooseX-FollowPBP
  7. p5-MooseX-Types>=0.10 : devel/p5-MooseX-Types
  8. p5-Params-Coerce>=0.14 : devel/p5-Params-Coerce
  9. p5-Parse-RecDescent>=1.965001 : devel/p5-Parse-RecDescent
  10. p5-Text-CSV_XS>=0.32 : textproc/p5-Text-CSV_XS
  11. p5-URI>=1.35 : net/p5-URI
  12. perl5>=5.28.r1<5.29 : lang/perl5.28
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/Bio/
  2. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/
  3. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Bio/
  4. ftp://ftp.funet.fi/pub/languages/perl/CPAN/modules/by-module/Bio/
  5. ftp://ftp.kddlabs.co.jp/lang/perl/CPAN/modules/by-module/Bio/
  6. ftp://ftp.mirrorservice.org/sites/cpan.perl.org/CPAN/modules/by-module/Bio/
  7. http://backpan.perl.org/modules/by-module/Bio/
  8. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/Bio/
  9. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/Bio/
  10. https://cpan.metacpan.org/modules/by-module/
  11. https://cpan.metacpan.org/modules/by-module/Bio/
  12. https://www.cpan.org/modules/by-module/Bio/

Number of commits found: 29

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Apr 2019 14:11:51
Original commit files touched by this commit  1.31_2
Revision:499759
sunpoet search for other commits by this committer
Fix typo

- Bump PORTREVISION for dependency change

Notified by:	mat
22 Apr 2019 20:42:09
Original commit files touched by this commit  1.31_1
Revision:499678
sunpoet search for other commits by this committer
Sort PLIST
06 Apr 2019 14:43:15
Original commit files touched by this commit  1.31_1
Revision:498107
sunpoet search for other commits by this committer
Use real PORTVERSION of devel/p5-Parse-RecDescent
06 Oct 2018 13:06:45
Original commit files touched by this commit  1.31_1
Revision:481365
des search for other commits by this committer
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
for where it resulted in a change in output from build-depends-list or
run-depends-list.

Approved by:	portmgr (adamw)
27 May 2018 20:15:20
Original commit files touched by this commit  1.31_1
Revision:470993
sunpoet search for other commits by this committer
Update WWW

search.cpan.org is shutting down.
It will redirect to metacpan.org after June 25, 2018.

With hat:	perl
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.31_1
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
12 Mar 2015 23:00:03
Original commit files touched by this commit  1.31_1
Revision:381151
adamw search for other commits by this committer
Some OCD cleanups on some of the perl@ ports.

- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
  the plist was randomized before committing

A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.
26 Nov 2014 13:08:38
Original commit files touched by this commit  1.31_1
Revision:373448
mat search for other commits by this committer
Change the way Perl modules are installed, update the default Perl to 5.18.

Before, we had:

  site_perl :           lib/perl5/site_perl/5.18
  site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
  perl_man3 :           lib/perl5/5.18/man/man3

Now we have:

  site_perl : lib/perl5/site_perl
  site_arch : lib/perl5/site_perl/mach/5.18
  perl_man3 : lib/perl5/site_perl/man/man3

Modules without any .so will be installed at the same place regardless of the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
20 Oct 2014 07:10:48
Original commit files touched by this commit  1.31
Revision:371237
bapt search for other commits by this committer
Cleanup plist
16 May 2014 13:33:03
Original commit files touched by this commit  1.31
Revision:354223
jadawin search for other commits by this committer
- update to 1.31
28 Nov 2013 15:05:08
Original commit files touched by this commit  1.28
Revision:335098
jadawin search for other commits by this committer
- Update to 1.28

Sponsored by:	OBS
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.27
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)
02 Aug 2013 18:52:11
Original commit files touched by this commit  1.27
Revision:324174
mat search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
- Remove MAKE_JOBS_SAFE=yes, it's the default.
29 Mar 2013 00:44:54
Original commit files touched by this commit  1.27
Revision:315509
eadler search for other commits by this committer
For perl@ owned ports:

- Fix COMMENT
- Trim header
05 Feb 2013 14:45:15
Original commit files touched by this commit  1.27
Revision:311717
jadawin search for other commits by this committer
- Update to 1.27
- Changelog: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.27/Changes
25 Oct 2012 00:18:33
Original commit files touched by this commit  1.26
Revision:306360
wen search for other commits by this committer
- Update to 1.26
Changes: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.26/Changes

Feature safe:	yes
19 Jul 2012 16:42:55
Original commit files touched by this commit  1.23

sunpoet search for other commits by this committer
- Update to 1.23
- Add LICENSE
- Remove WRKSRC

Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes
09 Feb 2012 03:28:51
Original commit files touched by this commit  1.22

sunpoet search for other commits by this committer
- Update to 1.22

Changes:        http://search.cpan.org/dist/Bio-MAGETAB/Changes
23 Nov 2011 17:40:48
Original commit files touched by this commit  1.21

sunpoet search for other commits by this committer
- Update to 1.21

Changes:        http://search.cpan.org/dist/Bio-MAGETAB/Changes
Feature safe:   yes
25 Sep 2011 00:07:08
Original commit files touched by this commit  1.20

swills search for other commits by this committer
- Add build depends to silence build warnings
13 Jul 2011 06:48:25
Original commit files touched by this commit  1.20

sunpoet search for other commits by this committer
- Update to 1.20
- Sort RUN_DEPENDS and MAN3

Changes:        http://search.cpan.org/dist/Bio-MAGETAB/Changes
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.13

miwi search for other commits by this committer
- Get Rid MD5 support
07 Sep 2010 07:00:17
Original commit files touched by this commit  1.13

wen search for other commits by this committer
- Update to 1.13

PR:             ports/150317
Submitted by:   Frederic Culot <frederic@culot.org>
18 Aug 2010 12:05:38
Original commit files touched by this commit  1.12

az search for other commits by this committer
Update to 1.12:
- dependency on MooseX::FollowPBP added
- dependency on Moose::Policy removed

PR:             ports/149612
Submitted by:   Frederic Culot <frederic@culot.org>
10 Jun 2010 16:56:04
Original commit files touched by this commit  1.10

tobez search for other commits by this committer
Update to 1.10.

Changes:        http://search.cpan.org/dist/Bio-MAGETAB/Changes
08 May 2010 08:35:32
Original commit files touched by this commit  1.00

wen search for other commits by this committer
- Update to 1.00
- Set maintainer to perl@
03 Feb 2010 08:25:35
Original commit files touched by this commit  0.99

wen search for other commits by this committer
- Update to 0.99
- Update my mail address to FreeBSD
30 Jul 2009 23:04:49
Original commit files touched by this commit  0.98

pgollucci search for other commits by this committer
Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plists

PR:             ports/136771
Exp Run by:     pav
Approved by:    portmgr (pav)
01 Jul 2009 09:03:28
Original commit files touched by this commit  0.98

miwi search for other commits by this committer
p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This
is a beta release. All functions have now been implemented and most
have test suites; the exceptions include the modules involved in
export of MAGE-TAB documents, which are still a little experimental in
nature. The API is mostly finalised (and fully documented), but some
details may yet change where necessary to improve usability.

WWW: http://search.cpan.org/dist/Bio-MAGETAB/

PR:             ports/136021
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 29

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new fortnight55
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