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)
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
in the migration path, lmdb, the lmdb 0.x is supposed to get removed at
some point.
Approved by: mat (portmgr)
Reviewed by: mat
Differential Revision: https://reviews.freebsd.org/D60741
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
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biology/ncbi-cxx-toolkit: only for aarch64, amd64
This port uses SIMD intrincis to compute CRC checksums.
It's probably easy to add a generic code path if desired.
Approved by: portmgr (build fix blanket)
MFH: 2026Q1
Sponsored by: Raptor Computing Systems, LLC
graphics/proj: Update to 9.1.0
Release notes:
https://proj.org/news.html#id37
Also remove proj-data dependency.
You can use proj to retrieve data or install graphics/proj-data
manually.
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)
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.
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Update CONFLICTS definitions in categories a* to c*
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit)
Fix CONFLICTS entries of multiple ports
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.
This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.
Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above )
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590
