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Port details
ncbi-vdb NCBI's virtualized back-end for accessing Sequence Read Archive
2.11.0_6 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 2.11.0_6Version of this port present on the latest quarterly branch.
Maintainer: mzaki@niid.go.jp search for ports maintained by this maintainer
Port Added: 2021-04-12 09:30:06
Last Update: 2023-04-23 09:09:58
Commit Hash: 8d3e020
License: PD
WWW:
https://github.com/ncbi/ncbi-vdb/wiki
Description:
NCBI-VDB is a virtualized back-end engine library for Sequencing Read Archives. The 'front-end' API are provided by biology/ngs-sdk port. Although the GitHub repository also contains Java and Python codes, this port currently builds only C- and C++-based libraries.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (39 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/ncbi-vdb-2.11.0_6/catalog.mk
  3. /usr/local/share/licenses/ncbi-vdb-2.11.0_6/LICENSE
  4. /usr/local/share/licenses/ncbi-vdb-2.11.0_6/PD
  5. include/ncbi-vdb/NGS.hpp
  6. lib/libkdf5-static.a
  7. lib/libkdf5.a
  8. lib/libkdf5.a.2
  9. lib/libkdf5.a.2.11.0
  10. lib/libkdf5.so
  11. lib/libkdf5.so.2
  12. lib/libkdf5.so.2.11.0
  13. lib/libncbi-ngs-c++-static.a
  14. lib/libncbi-ngs-c++.a
  15. lib/libncbi-ngs-c++.a.2
  16. lib/libncbi-ngs-c++.a.2.11.0
  17. lib/libncbi-ngs-static.a
  18. lib/libncbi-ngs.a
  19. lib/libncbi-ngs.a.2
  20. lib/libncbi-ngs.a.2.11.0
  21. lib/libncbi-vdb-static.a
  22. lib/libncbi-vdb.a
  23. lib/libncbi-vdb.a.2
  24. lib/libncbi-vdb.a.2.11.0
  25. lib/libncbi-vdb.so
  26. lib/libncbi-vdb.so.2
  27. lib/libncbi-vdb.so.2.11.0
  28. lib/libncbi-wvdb-static.a
  29. lib/libncbi-wvdb.a
  30. lib/libncbi-wvdb.a.2
  31. lib/libncbi-wvdb.a.2.11.0
  32. lib/libncbi-wvdb.so
  33. lib/libncbi-wvdb.so.2
  34. lib/libncbi-wvdb.so.2.11.0
  35. lib/ncbi/certs.kfg
  36. lib/ncbi/default.kfg
  37. @owner
  38. @group
  39. @mode
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Dependency lines:
  • ncbi-vdb>0:biology/ncbi-vdb
To install the port:
cd /usr/ports/biology/ncbi-vdb/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ncbi-vdb
  • pkg install ncbi-vdb
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ncbi-vdb
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: amd64 i386
distinfo:
TIMESTAMP = 1618218620 SHA256 (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 9a65e3885b9ae1ebecbec871f04ce3162ac3764fb556ecdc8c1e61993e2164aa SIZE (ncbi-ncbi-vdb-2.11.0_GH0.tar.gz) = 22277539

Expand this list (2 items)

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SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365

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Packages (timestamps in pop-ups are UTC):
ncbi-vdb
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-2.11.0_6--2.11.0_6---
FreeBSD:13:quarterly-2.11.0_6--2.11.0_6---
FreeBSD:14:latest-2.11.0_6--2.11.0_6---
FreeBSD:14:quarterly-2.11.0_6--2.11.0_6---
FreeBSD:15:latest-2.11.0_6n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. libepoll-shim>0 : devel/libepoll-shim
  3. gmake>=4.3 : devel/gmake
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Library dependencies:
  1. libxml2.so : textproc/libxml2
  2. libhdf5.so : science/hdf5
  3. libmbedtls.so : security/mbedtls
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_ncbi-vdb
USES:
compiler:c11 gmake localbase:ldflags perl5 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/ncbi/ncbi-vdb/tar.gz/2.11.0?dummy=/
Collapse this list.

Number of commits found: 11

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.11.0_6
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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)
2.11.0_5
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)
2.11.0_5
20 Jul 2022 14:35:24
commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35commit hash: 5564b3b420db29745d2d4981d1963200ddf53e35 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>
2.11.0_4
18 Jul 2022 12:50:17
commit hash: 7e7034a7fa7d3aa61b31394702d0f88ad504bb6ccommit hash: 7e7034a7fa7d3aa61b31394702d0f88ad504bb6ccommit hash: 7e7034a7fa7d3aa61b31394702d0f88ad504bb6ccommit hash: 7e7034a7fa7d3aa61b31394702d0f88ad504bb6c files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
biology/ncbi-vdb: Fix build with HDF5 1.12.0+
2.11.0_4
10 Apr 2022 19:11:41
commit hash: d63665f7cd9c99880704a3c5bc221829cb009744commit hash: d63665f7cd9c99880704a3c5bc221829cb009744commit hash: d63665f7cd9c99880704a3c5bc221829cb009744commit hash: d63665f7cd9c99880704a3c5bc221829cb009744 files touched by this commit
Charlie Li (vishwin) search for other commits by this committer
textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)
2.11.0_3
26 Mar 2022 08:27:27
commit hash: 247c7db7513f1264922428278678da641c5a3f52commit hash: 247c7db7513f1264922428278678da641c5a3f52commit hash: 247c7db7513f1264922428278678da641c5a3f52commit hash: 247c7db7513f1264922428278678da641c5a3f52 files touched by this commit
Matthias Fechner (mfechner) search for other commits by this committer
textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246
2.11.0_2
28 Jan 2022 12:14:09
commit hash: b93e64d3c3240d1e4a8fc510b14aa2175e5be012commit hash: b93e64d3c3240d1e4a8fc510b14aa2175e5be012commit hash: b93e64d3c3240d1e4a8fc510b14aa2175e5be012commit hash: b93e64d3c3240d1e4a8fc510b14aa2175e5be012 files touched by this commit
Tijl Coosemans (tijl) search for other commits by this committer
security/mbedtls: Update to 2.28.0 and fix make test

Also bump dependent ports for library version change.

PR:		255084
2.11.0_1
26 Apr 2021 14:17:32
commit hash: bc9e901a170f2015b41f1a0c4b23c17436d0e432commit hash: bc9e901a170f2015b41f1a0c4b23c17436d0e432commit hash: bc9e901a170f2015b41f1a0c4b23c17436d0e432commit hash: bc9e901a170f2015b41f1a0c4b23c17436d0e432 files touched by this commit
Jan Beich (jbeich) search for other commits by this committer
devel/libepoll-shim: update to 0.0.20210418

Changes:	https://github.com/jiixyj/epoll-shim/compare/v0.0.20210322...v0.0.20210418
Reported by:	portscout
Approved by:	manu
Differential Revision:	https://reviews.freebsd.org/D29822
2.11.0_1
12 Apr 2021 18:03:14
commit hash: 353678f54b5fcc1821077ab3f84fe389a1ef2b9bcommit hash: 353678f54b5fcc1821077ab3f84fe389a1ef2b9bcommit hash: 353678f54b5fcc1821077ab3f84fe389a1ef2b9bcommit hash: 353678f54b5fcc1821077ab3f84fe389a1ef2b9b files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/ncbi-vdb: Restore static libs installed with symlinks as shared libs are
usually installed

Symlinks like this libxx.a->libxx.a.N.N.N first looked broken but it turned out
that this is intentional.

PR:		223273
2.11.0
12 Apr 2021 09:29:42
commit hash: d55fba431adf6bc61c3553dd91625a4b16115cf6commit hash: d55fba431adf6bc61c3553dd91625a4b16115cf6commit hash: d55fba431adf6bc61c3553dd91625a4b16115cf6commit hash: d55fba431adf6bc61c3553dd91625a4b16115cf6 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequence
Read Archive

PR:		223273
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (original version)

Number of commits found: 11