При обновлении до версии 15 обнаружилась ошибка установки dev-python/bsddb3, очевидно, в связи с лицензионным конфликтом в исходниках, вот вывод:

$ sudo emerge dev-python/bsddb3
Пароль: 

!!! Timed out while closing connection to binhost
Calculating dependencies... done!
>>> Verifying ebuild manifests
>>> Emerging (1 of 1) dev-python/bsddb3-6.0.1::gentoo
>>> Failed to emerge dev-python/bsddb3-6.0.1, Log file:
>>>  '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/temp/build.log'
>>> Jobs: 0 of 1 complete, 1 failed                 Load avg: 0.63, 0.29, 0.31
 * Package:    dev-python/bsddb3-6.0.1
 * Repository: gentoo
 * Maintainer: python@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 userland_GNU
 * FEATURES:   preserve-libs sandbox usersandbox
>>> Unpacking source...
>>> Unpacking bsddb3-6.0.1.tar.gz to /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work
>>> Source unpacked in /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work
>>> Preparing source in /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1 ...
 * Will copy sources from /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1
 * python2_7: copying to /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1-python2_7
>>> Source prepared.
>>> Configuring source in /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1 ...
include version 6.0
>>> Source configured.
>>> Compiling source in /var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1 ...
 * python2_7: running distutils-r1_run_phase python_compile
cp: ‘./build/bsddb3.egg-info’ and ‘/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1-python2_7/build/bsddb3.egg-info’ are the same file
/usr/bin/python2.7 setup.py build
Detected Berkeley DB version 6.0 from db.h

******* COMPILATION ABORTED *******

You are linking a Berkeley DB version licensed under AGPL3 or have a commercial license.

AGPL3 is a strong copyleft license and derivative works must be equivalently licensed.

You have two choices:

  1. If your code is AGPL3 or you have a commercial Berkeley DB license from Oracle, please, define the environment variable 'YES_I_HAVE_THE_RIGHT_TO_USE_THIS_BERKELEY_DB_VERSION' to any value, and try to install this python library again.

  2. In any other case, you have to link to a previous version of Berkeley DB. Remove Berlekey DB version 6.0 and let this python library try to locate an older version of the Berkeley DB library in your system. Alternatively, you can define the environment variable 'BERKELEYDB_DIR', or 'BERKELEYDB_INCDIR' and 'BERKELEYDB_LIBDIR', with the path of the Berkeley DB you want to use and try to install this python library again.

Sorry for the inconvenience. I am trying to protect you.

More details:

    https://forums.oracle.com/message/11184885
    http://lists.debian.org/debian-legal/2013/07/

******* COMPILATION ABORTED *******

 * ERROR: dev-python/bsddb3-6.0.1::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called src_compile
 *   environment, line 3844:  Called distutils-r1_src_compile
 *   environment, line 1021:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  333:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3355:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2423:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2421:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  599:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1014:  Called python_compile
 *   environment, line 2963:  Called distutils-r1_python_compile
 *   environment, line  893:  Called esetup.py 'build'
 *   environment, line 1503:  Called die
 * The specific snippet of code:
 *       "${@}" || die
 * 
 * If you need support, post the output of `emerge --info '=dev-python/bsddb3-6.0.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/bsddb3-6.0.1::gentoo'`.
 * The complete build log is located at '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/temp/build.log'.
 * The ebuild environment file is located at '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/temp/environment'.
 * Working directory: '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1-python2_7'
 * S: '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1'

 * Messages for package dev-python/bsddb3-6.0.1:

 * ERROR: dev-python/bsddb3-6.0.1::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called src_compile
 *   environment, line 3844:  Called distutils-r1_src_compile
 *   environment, line 1021:  Called _distutils-r1_run_foreach_impl 'python_compile'
 *   environment, line  333:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 3355:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2423:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile'
 *   environment, line 2421:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile'
 *   environment, line  599:  Called distutils-r1_run_phase 'python_compile'
 *   environment, line 1014:  Called python_compile
 *   environment, line 2963:  Called distutils-r1_python_compile
 *   environment, line  893:  Called esetup.py 'build'
 *   environment, line 1503:  Called die
 * The specific snippet of code:
 *       "${@}" || die
 * 
 * If you need support, post the output of `emerge --info '=dev-python/bsddb3-6.0.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/bsddb3-6.0.1::gentoo'`.
 * The complete build log is located at '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/temp/build.log'.
 * The ebuild environment file is located at '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/temp/environment'.
 * Working directory: '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1-python2_7'
 * S: '/var/calculate/tmp/portage/dev-python/bsddb3-6.0.1/work/bsddb3-6.0.1'

У меня этот пакет устанавливается как одна из зависимостей sci-biology/biopython. В тот момент обновление прервалось, и система осталась в полуобновлённом состоянии. Сейчас я переустановил её начисто, но при установке sci-biology/biopython ошибка воспроизвелась. Возможно, можно это как-то исправить, или другой пакет для этого слота поставить?

Вывод сборки прикрепляю.