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Release Notes (Version 25.2, September 2021)

The previous Release Notes can be seen here.

These notes give a somewhat superficial and incomplete (albeit still useful) description of the latest NCBI C++ Toolkit changes, fixes and additions. Some important topics (especially numerous bug fixes and feature improvements, but possibly a bigger fish) are out of scope of these notes. Feel free to write to the mailing group https://www.ncbi.nlm.nih.gov/mailman/listinfo/cpp with any questions or reports.

Download

Download the source code archives at: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Sep_30_2021/

The sources correspond to the NCBI production tree sources, which are originally based on the development tree source snapshot from November, 2020; and also include many hundreds of important and safe code updates made since then and through September, 2021.

Third Party Packages

Some parts of the C++ Toolkit cannot be built without 3rd party libraries, and other parts of the Toolkit will work more efficiently or provide more functionality if some 3rd-party packages (such as BerkeleyDB which is used for local data cache and for local data storage) are available.

Table 1. Currently Supported/Tested Versions of Third Party Packages

Package Versions expected to work (obtained by build-environment inspection in some cases) Versions known to work (used in-house on any platform)
BerkeleyDB 4.3.0 or newer 4.5.20, 4.6.21.NC, 4.6.21.1, 5.3.21
Boost Test 1.35.0 or newer 1.62.0, 1.65.1, 1.66.0, 1.71.0
FastCGI All versions 2.4.0, 2.4.1
libbzip2 All versions 1.0.6, 1.0.8
libjpeg(-turbo) All versions 8c, 9b, 9c (libjpeg),
1.2.90, 2.0.5 (libjpeg-turbo)
libpng All versions 1.5.13, 1.6.26, 1.6.34, 1.6.37
libtiff All versions 3.6.1, 4.0.3, 4.0.6, 4.1.0
libungif All versions 4.1.3 (libungif),
4.1.6, 5.1.4 (giflib)
libxml2 All versions 2.7.8, 2.9.1, 2.9.4, 2.9.10
libxslt 1.1.14 or newer 1.1.26, 1.1.28, 1.1.29, 1.1.34
LZO 2.x 2.05, 2.08, 2.09, 2.10
PCRE All versions 8.32, 8.39, 8.42, 8.43
SQLite3 3.6.6 or newer 3.7.17, 3.22.0, 3.26.0, 3.31.1, 3.34.1
Sybase All versions 16.0
zlib All versions 1.2.7, 1.2.11

The user is expected to download and build the 3rd party packages themselves. The release’s package list includes links to download sites. However, the user still needs a list of the 3rd party packages and which versions of them are compatible with the release.

Build

For guidelines to configure, build and install the Toolkit see here.

New Developments

HIGHLIGHTS

There have been significant additions and improvements in all parts of the Toolkit since the last public release of the NCBI C++ Toolkit. Here, only very few are listed, mostly related to major formal changes:

  • Adjusted code to work with GI identifiers whose values exceed 31 bit. Please use type ‘TGi’ for the GI values. The 31-bit boundary is currently expected to be crossed around January 2022… but it can happen earlier.
  • Started using C++14 specific features, so you will now need a C++14 compliant compiler to build the Toolkit.
  • Dropped support of 32-bit platforms for good.
  • Added “CMake” based build system (experimental). It currently co-exists with the “legacy” configure/PTB based build system.
  • Ported to work on ARM processors (doesn’t yet work with the VDB Toolkit though, need to use –without-vdb flag).

Documentation

Location

The documentation is available online as a searchable book “The NCBI C++ Toolkit”: https://ncbi.github.io/cxx-toolkit/.

Content

A C/C++ Symbol Search query appears on each page of the online Toolkit documentation. You can use this to perform a symbol search on the up-to-date public or in-house versions using source browsers LXR, Doxygen and Library - or do an overall search.

Public access to our SVN trunk:

Supported Platforms (OS’s and Compilers)

This release was successfully tested on at least the following platforms (but may also work on other platforms). Since the previous release, some platforms were dropped from this list and some were added. Also, it can happen that some projects would not work (or even compile) in the absence of 3rd-party packages, or with older or newer versions of such packages. In these cases, just skipping such projects (e.g. using flag “-k” for make on Unix), can get you through.

In cases where multiple compilers or versions are supported, the mainstream one is shown in bold. Other versions might also work, but must support C++14; minimum versions are GCC 5.x, Clang 3.4.x, ICC 17.x, and MS VS 2017.

Unix

Operating System Architecture Compilers  
CentOS 7.x (LIBC 2.17) x86-64 GCC 7.3, 8.3, 9.1, 10.2; Clang 7.0; ICC (20)17, (20)19, (20)21  
Ubuntu 18.04 (LIBC 2.27) x86-64 GCC 7.5  
FreeBSD 12.2 x86-64 Clang 10.0  
Ubuntu 20.04 (LIBC 2.31) Graviton 2 (ARM) Clang 10.0; GCC 9.3 experimental

MS Windows

Operating System Architecture Compilers
MS Windows x86-64 MS Visual C++ 2017 (MSVC 14.1)
MS Windows x86-64 MS Visual C++ 2019 (MSVC 16.9.5) experimental
Cygwin 6.3 x86-64 GCC 7.4- nominal support only.

macOS

Operating System Architecture Compilers
macOS 10.13 (Darwin 17.x) x86-64 Apple Clang 10, Xcode; nominal support only at this point.
macOS 10.14 (Darwin 18.x) x86-64 Apple Clang 11, Xcode
macOS 10.15 (Darwin 19.x) x86-64 Apple Clang 12, Xcode

Added Platforms

Official support for macOS 10.14, 10.15; for Ubuntu 18.04 and 20.04; for ICC (20)19 and (20)21 on CentOS; for FreeBSD 12.2 is new in this release. Also added experimental ARM support.

Discontinued Platforms

Compiler Operating System Architecture
All 32-bit compilers All 32-bit OS’s All 32-bit processors
MS Visual C++ 2015 (MSVC 14) MS Windows x86-64
Apple Clang 8 macOS 10.11.x (Darwin 15) x86-64
Apple Clang 9 macOS 10.12.x (Darwin 16) x86-64
  Ubuntu 14.04 x86-64
  Ubuntu 16.04 x86-64
  FreeBSD 11.2 x86-64
  CentOS 6.x x86-64

Last Updated

This document was last updated on September 30, 2021.