biology/ncbi-cxx-toolkit 30.8.0_1 FreeBSD

NCBI C++ Toolkit

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-20
Commit: 85ba298b7e
License: PD
Categories: biology, science, devel
Package size: 32991.7 KiB, 192649.6 KiB installed

Description

NCBI C++ Toolkit provides free, portable, public domain libraries with no restrictions use. It has been written in the National Center for Biotechnology Information in Bethesda, MD.

It is vaguely a successor, or a new generation of biology/ncbi-toolkit.

It contains: * Networking and Interprocess Communication (IPC) library * MultiThreading Library * CGI and Fast-CGI Library, HTML Generation Library * SQL Database Access Library, C++ wrapper library for BerkeleyDB * C++ IOSTREAM Adaptor/Wrapper Library * GZIP and BZ2 C++ Wrapper Library with IOSTREAM adaptors * ASN.1 and XML Serialization Library with C++ Code Generator Tool (datatool) * Date and Time Library * File System Function Library * Command-Line Argument, Configuration and Environment Processing Library * Sequence Alignment Algorithms Library * BLAST Engine Library * Biological Sequences Retrieval and Processing Library * Portable FLTK and OpenGL based GUI and graphic libraries * XmlWrapp (XML parsing and handling, XSLT, XPath)

In the other systems

The newest version among them is 30.8.0, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/ncbi-cxx-toolkit

30.8.0_1 newest

none known

[email protected]

2026-10-20

HardenedBSD

biology/ncbi-cxx-toolkit

30.7.0 behind since 2026-10-09

no data

[email protected]

GhostBSD

biology/ncbi-cxx-toolkit

30.7.0 behind since 2026-10-09

no data

[email protected]

Version history 2

30.8.0 2026-10-09 d137080db4
30.7.0 2026-08-05 e65645d3e5

Upstream's version as each commit to the port's Makefile set it, or as this site first saw it in the system's packages; the tree's own revisions are not versions here.

Install

Binary package:

pkg install ncbi-cxx-toolkit

From the ports tree:

cd /usr/ports/biology/ncbi-cxx-toolkit/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	ncbi-cxx-toolkit>0:biology/ncbi-cxx-toolkit

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

30.8.0

30.8.0_1

FreeBSD:14:quarterly

30.7.0

n/a

FreeBSD:15:latest

30.8.0

30.8.0_1

n/a

FreeBSD:15:quarterly

30.7.0

n/a

FreeBSD:16:latest

30.8.0

30.8.0_1

n/a

FreeBSD:16:quarterly

n/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/ncbi-cxx-toolkit"]
  me --> d0["archivers/liblz4"]
  me --> d1["archivers/zstd"]
  me --> d2["converters/libiconv"]
  me --> d3["databases/lmdb0"]
  me --> d4["databases/mysql84-client"]
  me --> d5["databases/openldap26-client"]
  me --> d6["devel/gettext-runtime"]
  me --> d7["devel/libcbor"]
  me -.-> dmore(["29 more"])
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

As this port's Makefile names them.

Library 5

libcdd.so : math/cddlib
liblmdb0.so : databases/lmdb0
libpcre.so : devel/pcre
libunwind.so : devel/libunwind
libzstd.so : archivers/zstd

Runtime 1

bash : shells/bash

The full lists below include those, and their dependencies in turn.

Build dependencies 37

Run dependencies 37

No port depends on this one.

Configuration

No options to configure.

USES: compiler:c++17-lang gmake mysql perl5 python shebangfix ssl xorg
Service scripts: none
Conflicts with: dakota libxdiff ncbi-blast+ ncbi-toolkit proj py*-speedtest-cli

Files

distinfo 1

File

Size

SHA256

ncbi-ncbi-cxx-toolkit-public-release-30.8.0_GH0.tar.gz

6.2317516e+07

0df68f90abe6a48ad8927cf8dca5888a11a520bf8855f1621a4a5d27839a2769

Commit history 4

Date Commit Credits Log message

2026-10-20

85ba298b7e

Baptiste Daroussin

databases/lmdb: allow to install both 0.x and 1.x together

LMDB 1.0 and the legacy 0.9 ABI cannot be mixed, the datanase format are incompatibles as well. Rename or relocate everything databases/lmdb0 installs so that it no longer overlaps with databases/lmdb: - the utilities are now mdb_copy0, mdb_dump0, mdb_load0 and mdb_stat0 - the header is include/lmdb0/lmdb.h - the linker name is liblmdb0.so, the shared object keeps its ABI name liblmdb.so.0 so already linked programs are unaffected - the pkg-config file is lmdb0.pc A compatibility prefix holding the previous layout is also installed under ${PREFIX}/lmdb0/ (include/, lib/ and libdata/pkgconfig/) so that build systems which expect to find lmdb.h and -llmdb relative to a single directory only need a path change. Now all ports should migrate to lmdb 1.X and use the lmdb 0.9 port to ease …

2026-10-09 d137080db4 Yuri Victorovich biology/ncbi-cxx-toolkit: update 30.7.0 → 30.8.0

2026-08-05 e65645d3e5 Yuri Victorovich biology/ncbi-cxx-toolkit: update 30.4.0 → 30.7.0

2026-07-06

5f9d389f29

Xin LI

databases/lmdb0: Add port for LMDB 0.9.x legacy ABI

LMDB 1.0 introduced an incompatible on-disk format change and subtle API breakage: applications that compiled cleanly against 1.0 headers could fail silently at run time. Known affected ports include dns/knot3, mail/bogofilter, and mail/postfix; the postfix issue has been confirmed upstream. Linux distributions such as Arch Linux have observed the same breakage. Samba can also be affected in certain configurations. Because the regression is not detectable in an -exp build run -- the postfix failure only manifests at run time, and bogofilter was caught only because post-build self-tests happen to exercise this path -- we cannot rely on package builds to validate the 1.0 upgrade. This commit introduces databases/lmdb0 as a holding port for the 0.9.35 …