Package Details: nupack4 4.0.0.28-1

Git Clone URL: https://aur.archlinux.org/nupack4.git (read-only, click to copy)
Package Base: nupack4
Description: Software suite for the analysis and design of nucleic acid structures, devices, and systems.
Upstream URL: https://nupack.org
Licenses: custom
Submitter: cge
Maintainer: cge
Last Packager: cge
Votes: 1
Popularity: 0.000000
First Submitted: 2022-09-07 22:12 (UTC)
Last Updated: 2022-09-07 22:12 (UTC)

Pinned Comments

cge commented on 2022-09-07 22:14 (UTC)

Note: you probably want to install the binary version of NUPACK 4, not this source build. See below for more details.

NUPACK is available under a restricted license that is largely similar to the BSD 3-clause license, updated to address web applications, but with the notable exception that it allows for use and redistribution "non-commercial academic purposes only". Furthermore, access to the downloads requires requires a username and password that can be obtained through (free) registration, and sources and binary wheels are intentionally not in PyPI. While the license appears to allow for redistribution, in the interest of following the authors' wishes, this PKGBUILD does provide the source code automatically.

To use this PKGBUILD, if you can agree to the non-commercial academic license, register for a username and password at https://www.nupack.org/downloads, download the NUPACK 4 zip file there, and place the zip file in the same directory as this PKGBUILD.

Note that this PKGBUILD is for source installation, which may be significantly more complicated than simply installing a binary wheel, also available from the Nupack website. The intention of this PKGBUILD is to attempt to make source installation work smoothly in Arch Linux, using Arch and AUR packages as much as possible, and allowing installation in circumstances (for example, more recent Python versions) where binary wheels may not be suitable. The PKGBUILD makes certain changes to the build process:

  • The default build process uses a bundled vcpkg to build and install a number of external dependencies. This build process did not work on Arch the last time I tried it. The PKGBUILD removes vcpkg from the build process entirely, and instead uses Arch and AUR packages. In many cases, this means that newer versions of those dependencies are used than in the normal build process, which may cause breakages.
  • NUPACK 4 relies on an older version of TBB, and newer versions removed parts of the API it uses. This PKGBUILD thus requires an older version of TBB, which may cause problems for other packages on your system.
  • One error message in NUPACK 4 does not work well with newer versions of spdlog and fmt, and so is commented out.
  • SIMD support is currently disabled, as (a) libsimdpp is not currently in the AUR, and (b) when installed (I have a PKGBUILD for it locally), NUPACK 4 has build errors wwhen NUPACK_SIMD=ON that I don't currently understand.

Latest Comments

cge commented on 2022-09-07 22:14 (UTC)

Note: you probably want to install the binary version of NUPACK 4, not this source build. See below for more details.

NUPACK is available under a restricted license that is largely similar to the BSD 3-clause license, updated to address web applications, but with the notable exception that it allows for use and redistribution "non-commercial academic purposes only". Furthermore, access to the downloads requires requires a username and password that can be obtained through (free) registration, and sources and binary wheels are intentionally not in PyPI. While the license appears to allow for redistribution, in the interest of following the authors' wishes, this PKGBUILD does provide the source code automatically.

To use this PKGBUILD, if you can agree to the non-commercial academic license, register for a username and password at https://www.nupack.org/downloads, download the NUPACK 4 zip file there, and place the zip file in the same directory as this PKGBUILD.

Note that this PKGBUILD is for source installation, which may be significantly more complicated than simply installing a binary wheel, also available from the Nupack website. The intention of this PKGBUILD is to attempt to make source installation work smoothly in Arch Linux, using Arch and AUR packages as much as possible, and allowing installation in circumstances (for example, more recent Python versions) where binary wheels may not be suitable. The PKGBUILD makes certain changes to the build process:

  • The default build process uses a bundled vcpkg to build and install a number of external dependencies. This build process did not work on Arch the last time I tried it. The PKGBUILD removes vcpkg from the build process entirely, and instead uses Arch and AUR packages. In many cases, this means that newer versions of those dependencies are used than in the normal build process, which may cause breakages.
  • NUPACK 4 relies on an older version of TBB, and newer versions removed parts of the API it uses. This PKGBUILD thus requires an older version of TBB, which may cause problems for other packages on your system.
  • One error message in NUPACK 4 does not work well with newer versions of spdlog and fmt, and so is commented out.
  • SIMD support is currently disabled, as (a) libsimdpp is not currently in the AUR, and (b) when installed (I have a PKGBUILD for it locally), NUPACK 4 has build errors wwhen NUPACK_SIMD=ON that I don't currently understand.